Drop "CCP4: Software for Macromolecular Crystallography"

obsoletes: Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=160190 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=324059 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=332485 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=367771 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=367773 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=383227 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=448756 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=460502 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=460504 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=466936 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=467040 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=467048 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=476580 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478580 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478586 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478588 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478594 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478604 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=521646 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=528512 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=530878 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=540760 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=555614 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=556498 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=557038 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=561196 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=562780 Signed-off-by: Justin Lecher <jlec@gentoo.org>
author: Justin Lecher <jlec@gentoo.org> 2015-10-26 08:29:56 +0100
committer: Justin Lecher <jlec@gentoo.org> 2015-10-26 08:32:25 +0100
commit: 7d62034735e700ca67e977470d79f5571b15b221 (patch)
tree: 78d45bafd1284caf0c06b4b98131677301303cbb /sci-chemistry
parent: add co-maintainer Coacher to metadata (diff)
download: gentoo-7d62034735e700ca67e977470d79f5571b15b221.tar.gz
gentoo-7d62034735e700ca67e977470d79f5571b15b221.tar.bz2
gentoo-7d62034735e700ca67e977470d79f5571b15b221.zip
153 files changed, 0 insertions, 7838 deletions
diff --git a/sci-chemistry/arp-warp-bin/Manifest b/sci-chemistry/arp-warp-bin/Manifest
deleted file mode 100644
index 739b86dac839..000000000000
--- a/sci-chemistry/arp-warp-bin/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST arp_warp_7.5.tar.gz 198643246 SHA256 d16fc6775905e56e5159f4a658f654b98d94f78143a2537ba67bffaed7ef1ad8 SHA512 351ed4bad863bac63005d128c693b7dde60c03ca5e8bd449ea602646f7f856c022070e542bcacae2793fbde88d67e7b5639bedeec55eeb191017a2ec19d03768 WHIRLPOOL d4ea42179a8a406508c82320567dc39ce419a2cba8b9e6ed05739dbbf0c9aba072b720c56987c4c94806ba2772f9c8787bde898f7c76543cc4702f00b7f16532
diff --git a/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild b/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild
deleted file mode 100644
index ef10d0ab3d5d..000000000000
--- a/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils prefix
-
-MY_P="arp_warp_${PV}"
-
-DESCRIPTION="Improvement and interpretation of crystallographic electron density maps"
-SRC_URI="${MY_P}.tar.gz"
-HOMEPAGE="http://www.embl-hamburg.de/ARP/"
-
-LICENSE="ArpWarp"
-SLOT="0"
-KEYWORDS="-* amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="cpu_flags_x86_sse2"
-
-REQUIRED_USE="cpu_flags_x86_sse2"
-
-RDEPEND="
-	app-shells/tcsh
-	sci-chemistry/refmac
-	virtual/awk
-	virtual/jre
-	virtual/opengl
-	x11-libs/libX11"
-DEPEND=""
-
-RESTRICT="fetch"
-
-S="${WORKDIR}/${MY_P}"
-
-QA_PREBUILT="opt/arp-warp-bin/bin/*"
-
-pkg_nofetch(){
-	elog "Fill out the form at http://www.embl-hamburg.de/ARP/"
-	elog "and place ${A} in ${DISTDIR}"
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/7.3-setup.patch
-	eprefixify "${S}"/share/arpwarp_setup_base.*
-
-	sed -e '/exit/d' -i "${S}"/share/arpwarp_setup_base.* || die
-}
-
-src_install(){
-	m_type=$(uname -m)
-	os_type=$(uname)
-
-	exeinto /opt/${PN}/bin/bin-${m_type}-${os_type}
-	doexe "${S}"/bin/bin-${m_type}-${os_type}/* "${S}"/share/*{pl,sh}
-
-	insinto /opt/${PN}/bin/bin-${m_type}-${os_type}
-	doins "${S}"/share/*{gif,bmp,XYZ,bash,csh,dat,lib,tbl,llh,prm}
-
-	insinto /etc/profile.d/
-	newins "${S}"/share/arpwarp_setup_base.csh 90arpwarp_setup.csh
-	newins "${S}"/share/arpwarp_setup_base.bash 90arpwarp_setup.sh
-
-	dodoc "${S}"/README manual/UserGuide${PV}.pdf
-	dohtml -r "${S}"/manual/html/*
-}
-
-pkg_postinst(){
-	testcommand=$(echo 3 2 | awk '{printf"%3.1f",$1/$2}')
-	if [ $testcommand == "1,5" ];then
-	  ewarn "*** ERROR ***"
-	  ewarn "   3/2=" $testcommand
-	  ewarn "Invalid decimal separator (must be ".")"
-	  ewarn "You need to set this correctly!!!"
-	  echo
-	  ewarn "One way of setting the decimal separator is:"
-	  ewarn "setenv LC_NUMERIC C' in your .cshrc file"
-	  ewarn "\tor"
-	  ewarn "export LC_NUMERIC=C' in your .bashrc file"
-	  ewarn "Otherwise please consult your system manager"
-	fi
-}
diff --git a/sci-chemistry/arp-warp-bin/files/7.3-setup.patch b/sci-chemistry/arp-warp-bin/files/7.3-setup.patch
deleted file mode 100644
index faed9c1102fd..000000000000
--- a/sci-chemistry/arp-warp-bin/files/7.3-setup.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff --git a/share/arpwarp_setup_base.bash b/share/arpwarp_setup_base.bash
-index 29e769c..0b8a51e 100644
---- a/share/arpwarp_setup_base.bash
-+++ b/share/arpwarp_setup_base.bash
-@@ -13,10 +13,10 @@ else
-     identifier=${nameprocessor}'-'${namesystem}
- fi
- #
--arpwarphome="$1X"
-+arpwarphome="@GENTOO_PORTAGE_EPREFIX@/opt/arp-warp-bin"
- #
- export warpbin=${arpwarphome}/bin/bin-${identifier}
--export warpdoc=${arpwarphome}/manual
-+export warpdoc=@GENTOO_PORTAGE_EPREFIX@/usr/share/doc/arp-warp-bin-7.1/html/
- export PATH=${warpbin}:${PATH}
- #
- # Checks for existence of $warpbin directory
-diff --git a/share/arpwarp_setup_base.csh b/share/arpwarp_setup_base.csh
-index 41b11e9..a4edcff 100644
---- a/share/arpwarp_setup_base.csh
-+++ b/share/arpwarp_setup_base.csh
-@@ -13,7 +13,7 @@ else
-     set identifier = ${nameprocessor}'-'${namesystem}
- endif
- #
--set arpwarphome = '$1X'
-+set arpwarphome = '@GENTOO_PORTAGE_EPREFIX@/opt/arp-warp-bin'
- #
- setenv warpbin ${arpwarphome}/bin/bin-${identifier}
- #
diff --git a/sci-chemistry/arp-warp-bin/metadata.xml b/sci-chemistry/arp-warp-bin/metadata.xml
deleted file mode 100644
index 51fdedab1b38..000000000000
--- a/sci-chemistry/arp-warp-bin/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-</pkgmetadata>
diff --git a/sci-chemistry/balbes/Manifest b/sci-chemistry/balbes/Manifest
deleted file mode 100644
index c5f8b2747027..000000000000
--- a/sci-chemistry/balbes/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST balbes-1.0.0_p100317.tar.gz 506464 SHA256 c5bf6c2086e1a3d7d380e5501c0cffdb91cbf77c74d2951dd345273f21921d0c SHA512 0029e459877113de212574daec8532f0d225e96772c6a777d34af94e5f11c1253ca941266e68da79e0a5c5a96416a824f76c6f1d8652d9a60a34756989cae41e WHIRLPOOL 9024490eea43ef526f00aff9f2045e2689dd6d9e7575c9fd3de2a23fc4af3ad784660df4c78c9aa6380df1dac9fbf46c8b6be105a3094761ebdd43c5cb541beb
-DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c
diff --git a/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild b/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild
deleted file mode 100644
index 5334207c0229..000000000000
--- a/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild
+++ /dev/null
@@ -1,79 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-CCP4VER="6.1.3"
-PYTHON_DEPEND="2"
-
-inherit eutils fortran-2 python toolchain-funcs
-
-DESCRIPTION="Automated molecular replacement (MR) pipeline"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~fei/balbes/index.html"
-SRC_URI="
-	mirror://gentoo/${P}.tar.gz
-	ftp://ftp.ccp4.ac.uk/ccp4/${CCP4VER}/ccp4-${CCP4VER}-core-src.tar.gz"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-# bundled PyXML is modified and cannot be replaced
-
-COMMON_DEPEND="sci-libs/ccp4-libs"
-RDEPEND="${COMMON_DEPEND}
-	~sci-libs/balbes-db-${CCP4VER}
-	!<=sci-chemistry/ccp4-apps-6.1.3-r1"
-DEPEND="${COMMON_DEPEND}"
-
-S="${WORKDIR}"/src
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python_set_active_version 2
-}
-
-src_unpack() {
-	unpack ${P}.tar.gz
-	tar xvzf "${DISTDIR}"/ccp4-${CCP4VER}-core-src.tar.gz \
-		ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py \
-		ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4
-	python_convert_shebangs 2 "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes
-}
-
-src_prepare() {
-	mkdir "${WORKDIR}"/bin || die
-	epatch "${FILESDIR}"/${PV}-makefile.patch
-	cd "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/
-	epatch "${FILESDIR}"/pyxml-0.8.4-python-2.6.patch
-}
-
-src_compile() {
-	emake \
-		BLANC_FORT="$(tc-getFC) ${FFLAGS}" || die
-	cd "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4
-	find build -delete
-	$(PYTHON) setup.py build
-	find xml/xslt test -delete
-}
-
-src_install() {
-	insinto /usr/share/balbes/BALBES_0.0.1/
-	doins -r \
-		 "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py \
-		 "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4 || die
-	dobin \
-		"${WORKDIR}"/bin/* \
-		"${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes \
-		|| die
-}
-
-pkg_postinst() {
-	python_mod_optimize /usr/share/balbes/BALBES_0.0.1/{bin_py,PyXML-0.8.4}
-}
-
-pkg_postrm() {
-	python_mod_cleanup /usr/share/balbes/BALBES_0.0.1/{bin_py,PyXML-0.8.4}
-}
diff --git a/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch b/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch
deleted file mode 100644
index da17240642d7..000000000000
--- a/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch
+++ /dev/null
@@ -1,107 +0,0 @@
-diff --git a/makefile b/makefile
-index baaceb5..85a7baf 100755
---- a/makefile
-+++ b/makefile
-@@ -70,6 +70,15 @@ OBJDB_G =  get_pdb_list.o
- 
- #OBJDB_Z =  blanc2mtz.o libutils.o
- 
-+# incomplete targets:
-+# dimer_search_db domain_search_db domain align3
-+all: search_db get_structure_db manage_db search_dm dom2ch \
-+            save_si get_pdb_list_db update_db \
-+            update_dom_db bl2mtz check_file_db fobs2cif sol_check \
-+            get_trns p2s check_cell alt_sg \
-+            align cell_list create_bins \
-+            get_pdb_list_db get_ch get_nm get_mod
-+
- search_db: sdb_l
- 
- get_structure_db: tdb_l
-@@ -201,58 +210,58 @@ save_seg_id.o: save_seg_id.f
- 	$(BLANC_FORT) -c save_seg_id.f 
- 
- sdb_l: $(OBJDB_S)
--	$(BLANC_FORT) -o ../bin/search_DB $(OBJDB_S)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/search_DB $(OBJDB_S)
- tdb_l: $(OBJDB_T)
--	$(BLANC_FORT) -o ../bin/get_structure_DB $(OBJDB_T)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/get_structure_DB $(OBJDB_T)
- mdb_l: $(OBJDB_M)
--	$(BLANC_FORT) -o ../bin/manage_DB $(OBJDB_M)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/manage_DB $(OBJDB_M)
- mdm_l: $(OBJDB_MD)
--	$(BLANC_FORT) -o ../bin/search_DOM $(OBJDB_MD)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/search_DOM $(OBJDB_MD)
- d2c_l: $(OBJDB_A)
--	$(BLANC_FORT) -o ../bin/domain2chain $(OBJDB_A)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/domain2chain $(OBJDB_A)
- upd_l: $(OBJDB_U)
--	$(BLANC_FORT) -o ../bin/update_DB $(OBJDB_U)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/update_DB $(OBJDB_U)
- dom_l: $(OBJDB_V)
--	$(BLANC_FORT) -o ../bin/update_domain_DB $(OBJDB_V)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/update_domain_DB $(OBJDB_V)
- ddb_l: $(OBJDB_D)
--	$(BLANC_FORT) -o ../bin/dimer_search $(OBJDB_D)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/dimer_search $(OBJDB_D)
- dmdb_l: $(OBJDB_N)
--	$(BLANC_FORT) -o ../bin/domain_search $(OBJDB_N)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/domain_search $(OBJDB_N)
- gdb_l: $(OBJDB_G)
--	$(BLANC_FORT) -o ../bin/get_pdb_list $(OBJDB_G)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/get_pdb_list $(OBJDB_G)
- b2m_l: blanc2mtz.o libutils.o
--	$(BLANC_FORT) -o ../bin/blanc2mtz  blanc2mtz.o libutils.o $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/blanc2mtz  blanc2mtz.o libutils.o -lccp4f -lccp4c
- f2c_l: f2cif.o libutils.o
--	$(BLANC_FORT) -o ../bin/f2cif  f2cif.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/f2cif  f2cif.o libutils.o
- chf_l: check_file_DB.o libutils.o
--	$(BLANC_FORT) -o ../bin/check_file_DB check_file_DB.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/check_file_DB check_file_DB.o libutils.o
- chc_l: check_cell_sg.o libutils.o
--	$(BLANC_FORT) -o ../bin/check_cell_sg check_cell_sg.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/check_cell_sg check_cell_sg.o libutils.o
- asl_l: alt_sg_list.o libutils.o
--	$(BLANC_FORT) -o ../bin/alt_sg_list alt_sg_list.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/alt_sg_list alt_sg_list.o libutils.o
- sc_l: $(OBJDB_C)
--	$(BLANC_FORT) -o ../bin/solution_check $(OBJDB_C)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/solution_check $(OBJDB_C)
- gt_l: $(OBJDB_R)
--	$(BLANC_FORT) -o ../bin/get_trans $(OBJDB_R)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/get_trans $(OBJDB_R)
- dmn_l: domain.o libutils.o
--	$(BLANC_FORT) -o ../bin/domain domain.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/domain domain.o libutils.o
- pack: pdb_pack.o libutils.o
--	$(BLANC_FORT) -o ../bin/pdb_pack pdb_pack.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/pdb_pack pdb_pack.o libutils.o
- p2s_l: $(OBJDB_P)
--	$(BLANC_FORT) -o ../bin/pdb2s $(OBJDB_P)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/pdb2s $(OBJDB_P)
- aln_l: align_DB.o  DB_subr.o libutils.o
--	$(BLANC_FORT) -o ../bin/align_DB align_DB.o DB_subr.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/align_DB align_DB.o DB_subr.o libutils.o
- aln3_l: align_DB_new.o  DB_subr.o libutils.o
--	$(BLANC_FORT) -o ../bin/align_DB_new align_DB_new.o DB_subr.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/align_DB_new align_DB_new.o DB_subr.o libutils.o
- cell_l: create_cell_list.o  DB_subr.o libutils.o
--	$(BLANC_FORT) -o ../bin/create_cell_list create_cell_list.o DB_subr.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/create_cell_list create_cell_list.o DB_subr.o libutils.o
- getch_l: get_chain.o  DB_subr.o libutils.o
--	$(BLANC_FORT) -o ../bin/get_chain get_chain.o DB_subr.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/get_chain get_chain.o DB_subr.o libutils.o
- getnmr_l: get_nmr.o  DB_subr.o libutils.o
--	$(BLANC_FORT) -o ../bin/get_nmr get_nmr.o DB_subr.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/get_nmr get_nmr.o DB_subr.o libutils.o
- getmod_l: get_model.o libutils.o
--	$(BLANC_FORT) -o ../bin/get_model get_model.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/get_model get_model.o libutils.o
- crb_l: create_binaries.o  DB_subr.o libutils.o
--	$(BLANC_FORT) -o ../bin/create_binaries create_binaries.o DB_subr.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/create_binaries create_binaries.o DB_subr.o libutils.o
- save_si_l: save_seg_id.o  DB_subr.o libutils.o
--	$(BLANC_FORT) -o ../bin/save_seg_id save_seg_id.o DB_subr.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/save_seg_id save_seg_id.o DB_subr.o libutils.o
diff --git a/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch b/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch
deleted file mode 100644
index d29b0b6a9eb2..000000000000
--- a/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-diff -rupN PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py PyXML-0.8.4/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py
---- PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py	2008-12-15 16:54:36.000000000 +0900
-+++ PyXML-0.8.4/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py	2008-12-15 16:57:02.000000000 +0900
-@@ -24,8 +24,8 @@ class ParsedAbbreviatedAbsoluteLocationP
-         self._rel = rel
-         nt = ParsedNodeTest.ParsedNodeTest('node', '')
-         ppl = ParsedPredicateList.ParsedPredicateList([])
--        as = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self')
--        self._step = ParsedStep.ParsedStep(as, nt, ppl)
-+        as_ = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self')
-+        self._step = ParsedStep.ParsedStep(as_, nt, ppl)
-         return
- 
-     def evaluate(self, context):
-diff -rupN PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py
---- PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py	2008-12-15 16:54:36.000000000 +0900
-+++ PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py	2008-12-15 16:58:58.000000000 +0900
-@@ -28,8 +28,8 @@ class ParsedAbbreviatedRelativeLocationP
-         self._right = right
-         nt = ParsedNodeTest.ParsedNodeTest('node','')
-         ppl = ParsedPredicateList.ParsedPredicateList([])
--        as = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self')
--        self._middle = ParsedStep.ParsedStep(as, nt, ppl)
-+        as_ = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self')
-+        self._middle = ParsedStep.ParsedStep(as_, nt, ppl)
- 
-     def evaluate(self, context):
-         res = []
diff --git a/sci-chemistry/balbes/metadata.xml b/sci-chemistry/balbes/metadata.xml
deleted file mode 100644
index 4bb6be5e5d0c..000000000000
--- a/sci-chemistry/balbes/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>sci-chemistry</herd>
-	<maintainer>
-		<email>jlec@gentoo.org</email>
-	</maintainer>
-	<longdescription>
-	BALBES is a system for solving protein structures using x-ray 
-	crystalographic data. Molecular Replacement(MR) is its core 
-	scientific method. BALBES aims to integrate all components, 
-	necessary for finding a solution structure by MR, into one system. 
-	It consists of a database, scientific programs and a python 
-	pipeline. The system is automated so that it needs no user's 
-	intervention when running complicated combination of jobs such 
-	as model searching, molecular replacement and refinement.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/ccp4-apps/Manifest b/sci-chemistry/ccp4-apps/Manifest
deleted file mode 100644
index e56aec5512a2..000000000000
--- a/sci-chemistry/ccp4-apps/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST 6.1.3-oasis4.0.patch.bz2 946 SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b SHA512 7c7bf4ef90550708bf41b1831dbe71c38418b46455adb3d42ec609d287894ac9260d9671f1759f71c713ced72fa004b9808391ea6874007ac8b7d7637f349d32 WHIRLPOOL a2bc27e1e054e1717c387f3800533fa490c03d1d18d3fe3cff4676f0ec47799a1681a206e01013c1b8f8e41162303446a824b86effeef2ed73f059feb07fb820
-DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c
diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild
deleted file mode 100644
index 5e1032133922..000000000000
--- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild
+++ /dev/null
@@ -1,395 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools eutils fortran-2 flag-o-matic gnuconfig python-single-r1 toolchain-funcs
-
-MY_P="${PN/-apps}-${PV}"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-PATCH_TOT="0"
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-SRC_URI="
-	${SRC}/${PV}/${MY_P}-core-src.tar.gz
-	https://dev.gentoo.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2"
-# patch tarball from upstream
-	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
-# patches created by us
-	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} https://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
-
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE="examples X"
-
-X11DEPS="
-	x11-libs/libX11
-	x11-libs/libXaw
-	x11-libs/libXt
-	x11-libs/libxdl_view"
-
-TKDEPS="
-	>=dev-lang/tk-8.3:0=
-	>=dev-tcltk/blt-2.4
-	dev-tcltk/iwidgets
-	dev-tcltk/itcl
-	dev-tcltk/itk
-	>=dev-tcltk/tdom-0.8
-	dev-tcltk/tktreectrl"
-
-SCILIBS="
-	~sci-libs/ccp4-libs-${PV}
-	>=sci-libs/ccp4-libs-${PV}-r7
-	sci-libs/clipper
-	sci-libs/fftw:2.1
-	sci-libs/mmdb:0
-	sci-libs/ssm
-	virtual/blas
-	virtual/lapack"
-
-SCIAPPS="
-	sci-chemistry/pdb-extract
-	sci-chemistry/pymol
-	sci-chemistry/rasmol
-	>=sci-chemistry/oasis-4.0-r1"
-
-RDEPEND="
-	${TKDEPS}
-	${SCILIBS}
-	app-shells/tcsh
-	dev-python/pyxml
-	dev-libs/libxml2:2
-	dev-libs/libjwc_c
-	dev-libs/libjwc_f
-	dev-libs/boehm-gc
-	!app-office/sc
-	!<sci-chemistry/ccp4-6.1.3
-	X? ( ${X11DEPS} )"
-DEPEND="${RDEPEND}
-	X? (
-		x11-misc/imake
-		x11-proto/inputproto
-		x11-proto/xextproto
-	)"
-PDEPEND="${SCIAPPS}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	tc-export PKG_CONFIG
-	einfo "Applying upstream patches ..."
-	for patch in $(seq $PATCH_TOT); do
-		base="PATCH${patch}"
-		dir=$(eval echo \${${base}[0]})
-		p=$(eval echo \${${base}[1]})
-		pushd "${dir}" >& /dev/null
-		ccp_patch "${DISTDIR}/${p}"
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-	[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	einfo "Applying Gentoo patches ..."
-
-	# it tries to create libdir, bindir etc on live system in configure
-	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
-	# We already have sci-chemistry/rasmol
-	# Also remember to create the bindir.
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch
-
-	# libraries come from sci-libs/ccp4-libs
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch
-
-	# We have seperate ebuilds for those
-	for bin in molref xia scala imosflm balbes; do
-		ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch
-	done
-
-	# don't configure what is not build
-	ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch
-
-	# Set python paths correctly
-	ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch
-
-	# Set python paths correctly
-	ccp_patch "${FILESDIR}"/${PV}-pisa.patch
-
-	# Set python paths correctly
-	ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch
-
-	# Fix upstreams code
-	ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
-
-	# Not renaming, but unbundling libs
-	ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch
-
-	# Use pkg-config to detect BLAS/LAPCK
-	ccp_patch "${FILESDIR}"/${PV}-lapack.patch
-
-	# unbundle libs
-	ccp_patch "${FILESDIR}"/${PV}-unbundle.patch
-
-	# tcl-8.6
-	ccp_patch "${FILESDIR}"/${P}-tcl8.6.patch
-
-	# Update things for oasis 4 usage
-	epatch "${WORKDIR}"/${PV}-oasis4.0.patch
-	sed 's: oasis : :g' -i src/Makefile.in || die
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete
-
-	sed \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		-e 's:-Wl,-rpath,$CLIB::g' \
-		-e 's: -rpath $CLIB::g' \
-		-e 's: -I${srcdir}/include/cpp_c_headers::g' \
-		-e 's:sleep 1:sleep .2:g' \
-		-e 's:\\$(XCIF_LIB):-L$srcdir/lib/ccif -lccif:g' \
-		-e 's:\\$(XLAPACK_LIB):${XLAPACK_LIB}:g' \
-		-e 's:\\$(CXX_LIBS):\${CXX_LIBS}:g' \
-		-e 's:\\$(XLDFLAGS):\${XLDFLAGS}:g' \
-		-i configure || die
-
-	sed \
-		-e '/o crunch2/s:$: ${XLAPACK_LIB}:g' \
-		-i src/Makefile* || die
-
-	find "${S}" -name "Makefile.*" \
-		-exec sed -e 's|_FLAGS-|_FLAGS:-|g' -e "s:\(eval \$([[:alnum:]]*)\):\1 \$(GENTOOLDFLAGS):g" -i '{}' \;
-
-	# Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version
-	sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure || die
-
-	# Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
-	pushd src/rapper 2>/dev/null
-		eautoreconf
-	popd 2>/dev/null
-
-	gnuconfig_update
-
-	python_fix_shebang -f .
-}
-
-src_configure() {
-	# Build system is broken if we set LDFLAGS
-	export GENTOOLDFLAGS="${LDFLAGS}"
-	unset LDFLAGS
-
-	# These are broken with ./src/procheck/ps.f
-	filter-flags "-floop-*"
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "$(tc-getFC)" = "ifort" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${S}"/include/ccp4.setup
-
-	# We agree to the license by emerging this, set in LICENSE
-	sed -i \
-		-e "s~^\(^agreed=\).*~\1yes~g" \
-		"${S}"/configure || die
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	export CC=$(tc-getCC)
-	export CXX=$(tc-getCXX)
-	export COPTIM=${CFLAGS}
-	export CXXOPTIM=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=$(tc-getFC)
-	export FOPTIM=${FFLAGS:- -O2}
-	export BINSORT_SCR="${T}"
-	export CCP4_MASTER="${WORKDIR}"
-	export CCP4I_TCLTK="${EPREFIX}/usr/bin"
-	export MAKE="make ${MAKEOPTS} ${EXTRA_EMAKE}"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		$(use_enable X x) \
-		--with-shared-libs \
-		--with-fftw="${EPREFIX}/usr" \
-		--with-warnings \
-		--disable-pdb_extract \
-		--disable-cctbx \
-		--disable-phaser \
-		--disable-diffractionImg \
-		--disable-clipper \
-		--disable-ssm \
-		--disable-mosflm \
-		--disable-mrbump \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "configure failed"
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd src/clipper_progs 2>/dev/null
-	econf \
-		--prefix="${S}" \
-		--bindir="${ED}"/usr/libexec/ccp4/bin \
-		--with-ccp4="${S}" \
-		--with-clipper="${EPREFIX}/usr" \
-		--with-fftw="${EPREFIX}/usr" \
-		--with-mmdb="${EPREFIX}/usr" \
-		CXX=$(tc-getCXX)
-	popd 2>/dev/null
-}
-
-src_compile() {
-	# fsplit is required for the programs
-	pushd lib/src 2>/dev/null
-		emake fsplit -j1 || die
-	popd 2>/dev/null
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd src/clipper_progs 2>/dev/null
-		emake || die
-	popd 2>/dev/null
-
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	# if we don't make this, a ton of programs fail to install
-	mkdir "${S}"/bin || die
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd "${S}"/src/clipper_progs 2>/dev/null
-		emake install || die
-	popd 2>/dev/null
-
-	einstall || die "install failed"
-
-	# Collision with sci-chemistry/mrbump
-	rm -f "${S}"/bin/{mrbump,pydbviewer} || die
-
-	# Bins
-	exeinto /usr/libexec/ccp4/bin/
-	doexe "${S}"/bin/* || die
-
-	# Libs
-	for file in "${S}"/lib/*; do
-		if [[ -d ${file} ]]; then
-			continue
-		elif [[ -x ${file} ]]; then
-			dolib.so ${file} || die
-		else
-			insinto /usr/$(get_libdir)
-			doins ${file} || die
-		fi
-	done
-
-	rm -f "${S}"/include/ccp4.setup*
-
-	# smartie -- log parsing
-	insinto /usr/share/ccp4
-	doins -r "${S}"/share/smartie || die
-
-	# Install docs and examples
-	local _man
-	pushd "${S}"/man/cat1 > /dev/null
-	for _man in *; do
-		newman ${_man} ${_man%??}-ccp4${_man:${#_man}-2:2}
-	done
-	popd > /dev/null
-
-	mv "${S}"/manual/README "${S}"/manual/README-manual
-	dodoc manual/* README CHANGES doc/* examples/README || die
-
-	rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.*
-	rm "${ED}"/usr/share/doc/${PF}/COPYING.*
-
-	dohtml -r "${S}"/html/*
-
-	if use examples; then
-		for i in data rnase toxd; do
-			docinto examples/${i}
-			dodoc "${S}"/examples/${i}/*
-		done
-
-		docinto examples/tutorial
-		dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css
-		for i in data results; do
-			docinto examples/tutorial/${i}
-			dodoc "${S}"/examples/tutorial/${i}/*
-		done
-
-		for i in non-runnable runnable; do
-			docinto examples/unix/${i}
-			dodoc "${S}"/examples/unix/${i}/*
-		done
-	fi
-	# Needed for ccp4i docs to work
-	dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die
-
-	cat >> "${T}"/baubles <<- EOF
-	#!${EPREFIX}/bin/bash
-	exec "${EPYTHON}" "\${CCP4}/share/ccp4/smartie/baubles.py"
-	EOF
-
-	exeinto /usr/libexec/ccp4/bin/
-	doexe "${T}"/baubles || die
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch
deleted file mode 100644
index 433a78dbd23b..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch
+++ /dev/null
@@ -1,70 +0,0 @@
---- src/clipper_progs/src/intensity_target.h.orig	2010-01-21 11:27:13.236795886 -0600
-+++ src/clipper_progs/src/intensity_target.h	2010-01-21 11:31:33.450686927 -0600
-@@ -70,9 +70,31 @@
-   {
-   public:
-     //! constructor: takes the datalist against which to calc target
--    TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ );
-+    TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ )
-+    {
-+      hkl_data1 = &hkl_data1_;
-+      hkl_data2 = &hkl_data2_;
-+    }
-     //! return the value and derivatives of the target function
--    Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const;
-+    Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const
-+    {
-+      Rderiv result;
-+      result.r = result.dr = result.dr2 = 0.0;
-+      const T1& it1 = (*hkl_data1)[ih];
-+      const T2& it2 = (*hkl_data2)[ih];
-+      if ( !it1.missing() && !it2.missing() )
-+        if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) {
-+          const ftype eps = ih.hkl_class().epsilon();
-+          const ftype i1 = it1.I() / eps;
-+          const ftype i2 = it2.I() / eps;
-+          const ftype w = sqrt( i1 * i2 );    
-+          const ftype d = intensityh + log(i1) - log(i2);
-+          result.r   =       w * d * d;
-+          result.dr  = 2.0 * w * d;
-+          result.dr2 = 2.0 * w;
-+      }
-+      return result;
-+    }
-     //! the type of the function: optionally used to improve convergence
-     FNtype type() const { return QUADRATIC; }
-   private:
-@@ -109,33 +131,4 @@
-     return result;
-   }
- 
--  // Log I1-I2 scaling
--
--  template<class T1, class T2> TargetFn_scaleLogI1I2<T1,T2>::TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ )
--  {
--    hkl_data1 = &hkl_data1_;
--    hkl_data2 = &hkl_data2_;
--  }
--
--  template<class T1, class T2> TargetFn_base::Rderiv TargetFn_scaleLogI1I2<T1,T2>::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const
--  {
--    Rderiv result;
--    result.r = result.dr = result.dr2 = 0.0;
--    const T1& it1 = (*hkl_data1)[ih];
--    const T2& it2 = (*hkl_data2)[ih];
--    if ( !it1.missing() && !it2.missing() )
--      if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) {
--	const ftype eps = ih.hkl_class().epsilon();
--	const ftype i1 = it1.I() / eps;
--	const ftype i2 = it2.I() / eps;
--	const ftype w = sqrt( i1 * i2 );    
--	const ftype d = intensityh + log(i1) - log(i2);
--	result.r   =       w * d * d;
--	result.dr  = 2.0 * w * d;
--	result.dr2 = 2.0 * w;
--    }
--    return result;
--  }
--
--
- #endif
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch
deleted file mode 100644
index f1df3e5e19f9..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-diff --git a/share/Makefile.in b/share/Makefile.in
-index 2d4f20b..4500993 100755
---- a/share/Makefile.in
-+++ b/share/Makefile.in
-@@ -18,9 +18,6 @@ install :
- 	for i in $(MRBUMP_TARGETS); do \
- 	   test -s $(MRBUMP_BINDIR)/$$i  &&  $(INSTALL_PROGRAM) $(MRBUMP_BINDIR)/$$i $(bindir)/$$i || true ;\
- 	done
--	for i in $(BALBES_TARGETS); do \
--	  test -s $(BALBES_BINDIR)/$$i  &&  $(INSTALL_PROGRAM) $(BALBES_BINDIR)/$$i $(bindir)/$$i || true ;\
--	done
- 
- clean : ; -rm -f core *.o *~ a.out 
- 
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch
deleted file mode 100644
index e62ae12adfbe..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch
+++ /dev/null
@@ -1,24 +0,0 @@
---- ccp4-6.1.1/x-windows/Makefile.in	2008-08-11 19:20:01.000000000 +0200
-+++ ccp4-6.1.1/x-windows/Makefile.in.new	2009-02-27 14:32:25.000000000 +0100
-@@ -35,7 +35,7 @@
- #
- # all
- #
--all : xdlview libjwc_c libjwc_f rotgen_ hklview xjiffy rasmol2 ipmosflm
-+all : rotgen_ hklview xjiffy
- #
- # xdl_view
- #
-@@ -157,11 +157,10 @@
- #
- install_obj = hklview rotgen ipmosflm
- install: all
-+	mkdir -p $(bindir)
- 	$(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir)
- 	cd $(srcdir)/XCCPJIFFY ; $(MAKE) bindir=$(bindir) libdir=$(libdir) install
--	$(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir)
- 	cd $(rotgen_dir); $(MAKE) install
--	$(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir)
- #
- # clean
- #
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch
deleted file mode 100644
index f645643e1c67..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4i/Makefile.in	2009-06-19 15:08:53.000000000 +0200
-+++ ccp4i/Makefile.in.new	2009-08-04 21:10:14.000000000 +0200
-@@ -9,7 +9,7 @@
- SHELL = /bin/sh
- DESTDIR = $(prefix)
- CCP4I_BINDIR = $(top_srcdir)/ccp4i/bin
--CCP4I_TARGETS = ccp4i imosflm loggraph crank mapslicer
-+CCP4I_TARGETS = ccp4i loggraph crank mapslicer
- 
- install :
- 	for i in $(CCP4I_TARGETS); do \
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch
deleted file mode 100644
index 1d1323005540..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch
+++ /dev/null
@@ -1,35 +0,0 @@
---- Makefile.in	2009-06-19 15:13:29.000000000 +0200
-+++ Makefile.in.new	2009-08-02 23:06:41.000000000 +0200
-@@ -2,7 +2,7 @@
- # $Id$
- 
- SHELL = /bin/sh
--DIRS = $(fftwdir) $(clipperdir) $(diffimdir) $(lapackdir) $(ccifdir) lib/src $(ssmdir) src lib/data unsupported/src x-windows share ccp4i $(prereleasedir)
-+DIRS = src lib/data unsupported/src x-windows share ccp4i $(prereleasedir)
- # this is for the benefit of makes that don't pass variable values in
- # recursive invocations, so that you can override these values on the
- # command line at the top level
-@@ -69,19 +69,19 @@
- 	$(MAKE) -i $(MFLAGS) $(MVARS) install; else true; fi ; \
- 	$(MAKE) install
- 
--srcdir :  FORCE libdir
-+srcdir :  FORCE 
- 	if test -d src; then cd src; $(MAKE) $(MFLAGS) $(MVARS); else true; fi
- 
- supported : srcdir
- 
--unsupported :  FORCE libdir
-+unsupported :  FORCE
- 	if test -d unsupported/src; then cd unsupported/src;  \
- 	   $(MAKE) $(MFLAGS) $(MVARS); else true; fi
- 
--datadir : FORCE libdir
-+datadir : FORCE
- 	cd lib/data; $(MAKE) $(MFLAGS) $(MVARS)
- 
--xwindir : FORCE libdir
-+xwindir : FORCE
- 	if test -f x-windows/Makefile; then cd x-windows; \
- 	   $(MAKE) -i $(MFLAGS) ; else true; fi
- 
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch
deleted file mode 100644
index f16b0ecb938c..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- src/pisa/Makefile.am	2007-07-10 10:56:05.000000000 +0200
-+++ src/pisa/Makefile.am.new	2009-06-11 21:16:51.000000000 +0200
-@@ -1,4 +1,4 @@
--SUBDIRS = molref pisastore sbase
-+SUBDIRS = pisastore sbase
- 
- pkgdatadir = $(datadir)/pisa
- 
---- src/pisa/Makefile.in	2009-06-12 21:12:08.000000000 +0200
-+++ src/pisa/Makefile.in.new	2009-06-12 21:41:52.000000000 +0200
-@@ -82,7 +82,7 @@
- am__quote = @am__quote@
- install_sh = @install_sh@
- pisa_LDFLAGS = @pisa_LDFLAGS@
--SUBDIRS = molref pisastore sbase
-+SUBDIRS = pisastore sbase
- 
- dist_pkgdata_DATA = pisa.cfg
- 
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch
deleted file mode 100644
index af4fd8219c4f..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch
+++ /dev/null
@@ -1,42 +0,0 @@
---- ./src/Makefile.in	2009-03-20 15:06:41.000000000 +0100
-+++ ./src/Makefile.in.new	2009-07-31 23:46:13.000000000 +0200
-@@ -50,7 +50,7 @@
- 
- # these live in subdirectories and have more than one dependency:
- OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \
--         scala dm dmmulti stereo mapmask maprot ncsmask \
-+         dm dmmulti stereo mapmask maprot ncsmask \
-          sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \
-          anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat 
- 
-@@ -637,7 +637,7 @@
- 
- ### scala, mapmask, maprot, ncsmask, combat
- 
--scala mapmask maprot ncsmask combat sc dyndom: # dependencies below
-+mapmask maprot ncsmask combat sc dyndom: # dependencies below
- 	@$(SETFLAGS) pwd=`pwd` ; rm -f $@; \
- 	  cd $(srcdir)/$@_; \
- 	  echo $(FC) $${$@_FLAGS-"$(FFLAGS)"} -c -o $$pwd/$@.o `pwd`/$@.f ;\
-@@ -1002,21 +1002,6 @@
- proclean:	$(srcdir)/procheck/clean.f $(srcdir)/procheck/brkcln.par
- rmsdev:		$(srcdir)/procheck/rmsdev.f $(srcdir)/procheck/rmsdev.inc
- 
--scaladir = $(srcdir)/scala_
--scala : $(scaladir)/scala.f $(scaladir)/column.fh $(scaladir)/orient.fh \
--	$(scaladir)/params.fh $(scaladir)/rfile.fh $(scaladir)/scales.fh \
--	$(scaladir)/nbtchc.fh $(scaladir)/parameter.fh $(scaladir)/refcon.fh \
--	$(scaladir)/rundef.fh $(scaladir)/sdfacc.fh $(scaladir)/flags.fh \
--	$(scaladir)/inout.fh $(scaladir)/dump.fh $(scaladir)/tie.fh \
--	$(scaladir)/outcon.fh $(scaladir)/version.fh $(scaladir)/anomtc.fh \
--        $(scaladir)/axes.fh $(scaladir)/bigarg.fh \
--        $(scaladir)/errors.fh $(scaladir)/flow.fh $(scaladir)/glocon.fh \
--        $(scaladir)/means.fh $(scaladir)/refflg.fh $(scaladir)/stats.fh \
--        $(scaladir)/symmty.fh $(scaladir)/sharvest.fh $(scaladir)/chtml.fh \
--        $(scaladir)/htmbuf.fh $(scaladir)/sphhrm.fh $(scaladir)/crlncf.fh \
--        $(scaladir)/datasets.fh $(scaladir)/dts_storage.fh \
--        $(scaladir)/sclinimeans.fh $(scaladir)/timecor.fh
--
- freemask.o:	$(dmdir)/freemask.f $(dmdir)/crystal.fh $(dmdir)/cycl.fh \
- 		$(dmdir)/dmheader.fh $(dmdir)/io.fh $(dmdir)/output.fh \
- 		$(dmdir)/params.fh $(dmdir)/uvwdata.fh
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch
deleted file mode 100644
index 3af4af503fa6..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- src/Makefile.in	2009-07-05 16:50:25.000000000 +0200
-+++ src/Makefile.in.new	2009-07-05 19:38:06.000000000 +0200
-@@ -50,9 +50,9 @@
- 
- # these live in subdirectories and have more than one dependency:
- OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \
--         scala dm dmmulti stereo mapmask maprot ncsmask chef \
-+         scala dm dmmulti stereo mapmask maprot ncsmask \
-          sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \
--         anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat 
-+         anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf 
- 
- # targets built from .c sources:
- CSIMPLE = pltdev binsort
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch
deleted file mode 100644
index 1e59578473ff..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch
+++ /dev/null
@@ -1,111 +0,0 @@
---- configure	2009-08-07 12:11:28.000000000 +0200
-+++ configure.new.nolib	2009-08-17 22:30:39.000000000 +0200
-@@ -3113,41 +3113,6 @@
-     RX_L="$configdir/lib/rxdispencer/rx"
-     export RX_H RX_L
-   fi
--  echo 
--  echo "Running separate configure for CCIF library."
--  echo
--  cd lib/ccif
--  echo "Updating modification times for configuration files"
--  echo "Please wait..."
--  for i in configure.in aclocal.m4 configure Makefile.in; do
--    touch $i && sleep 1   
--  done
--  echo "...done."      
--
--  if [ "X$LIBFOPTIM" != "X" ]; then
--    FOPTIM_save=$FOPTIM
--    FOPTIM=$LIBFOPTIM
--    FFLAGS="${FOPTIM} ${XFFLAGS}"
--  fi
--  if [ "X$LIBCOPTIM" != "X" ]; then
--    COPTIM_save=$COPTIM
--    COPTIM=$LIBCOPTIM
--    CFLAGS="${COPTIM} ${XCFLAGS}"
--  fi
--  ( touch /tmp/$$.cache_file 2>/dev/null && \
--    cat /dev/null > /tmp/$$.cache_file && \
--    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file ) || \
--    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif
--  rm -f /tmp/$$.cache_file
--  if [ "X$LIBFOPTIM" != "X" ]; then
--    FOPTIM=$FOPTIM_save
--    FFLAGS="${FOPTIM} ${XFFLAGS}"
--  fi
--  if [ "X$LIBCOPTIM" != "X" ]; then
--    COPTIM=$COPTIM_save
--    CFLAGS="${COPTIM} ${XCFLAGS}"
--  fi
--  cd ../..
-   echo
-   echo "Returning to main configure."
-   echo
-@@ -5094,53 +5059,6 @@
-   echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}"
-   ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} 
-   echo
--  echo "CCP4 configure: Running separate configure for libjwc_c library."
--  echo
--  cd ${srcdir}/${xwindir}/libjwc/libjwc_c
--  echo "Updating modification times for configuration files in libjwc_c"
--  echo "Please wait..."
--  for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do
--    touch $i && sleep 1
--  done
--  echo "...done."
--  echo
--  echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}"
--  ( touch /tmp/$$.cache_file 2>/dev/null && \
--    cat /dev/null > /tmp/$$.cache_file && \
--    ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \
--    ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}
--  rm -f /tmp/$$.cache_file
--  echo
--  echo "CCP4 configure: Running separate configure for libjwc_f library."
--  echo
--  cd ${srcdir}/${xwindir}/libjwc/libjwc_f
--  # for g77 3.1 some builds do not have no-common for system libs,
--  # so disable for now
--  echo "Updating modification times for configuration files in libjwc_f"
--  echo "Please wait..."
--  for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do
--    touch $i && sleep 1
--  done
--  echo "...done."
--  echo
--  # for g77 3.1 some builds do not have no-common for system libs,
--  # so disable for now
--  case $system in
--  Darwin* )
--    echo "configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}"
--    ( touch /tmp/$$.cache_file 2>/dev/null && \
--      cat /dev/null > /tmp/$$.cache_file && \
--      ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \
--      ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}
--    ;;
--  * )
--    echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}"
--    ( touch /tmp/$$.cache_file 2>/dev/null && \
--      cat /dev/null > /tmp/$$.cache_file && \
--      ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \
--      ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}
--  esac
--  rm -f /tmp/$$.cache_file
- 
-   if test "$non_shared" = yes; then
- #this is a bit of a cheat/fudge but that's life!
-@@ -5210,12 +5128,6 @@
-   fi
- 
-   echo
--  echo "CCP4 configure: Running separate configure for Mosflm"
--  echo
--  cd ${srcdir}/${mosflmdir}
--  echo "configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}"
--  ./configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}
--  echo
-   cd ../..
-   echo "Returning to main configure."
-   echo
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch
deleted file mode 100644
index 583697cea0a1..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch
+++ /dev/null
@@ -1,87 +0,0 @@
---- ccp4-6.0.99e.orig/configure	2008-07-31 10:37:22.000000000 -0700
-+++ ccp4-6.0.99e/configure	2008-07-31 10:39:18.000000000 -0700
-@@ -643,45 +643,45 @@
- #     echo "! Beware -- the $system installation isn't properly tested." ; }
- syswarn='echo; echo "! Beware -- the $system installation is not properly tested."'
- 
--if test -z "$onlylibs" ; then 
--   for i in CCP4_SCR BINSORT_SCR; do
--     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
--     else
--       eval echo "! No directory \$$i and can\'t create it."
--       echo "  Check the value of $i."
--       badvar=1
--     fi
--   done
--
--   for i in libdir bindir includedir; do
--     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
--     else
--       eval echo "! No directory \$$i and can\'t create it."
--       echo "  Check the argument of --$i."
--       badvar=1
--     fi
--   done
--
--   for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
--     if test -d $i || mkdir $i; then :
--     else
--       eval echo "! No directory $i and can\'t create it."
--       badvar=1
--     fi
--   done
--else
--   # Kludge to fool the "Makefile" target in the top-level CCP4
--   # Makefile into not trying to remake src/Makefile.in
--   for i in $srcdir/src $srcdir/lib/src ; do
--     if test -d $i || mkdir $i; then
--       if ! test -f $i/Makefile.in ; then
--         echo
--         echo "onlylibs: making dummy file $i/Makefile.in"
--	 touch $i/Makefile.in
--       fi
--     fi
--   done
--fi
-+#if test -z "$onlylibs" ; then 
-+#   for i in CCP4_SCR BINSORT_SCR; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the value of $i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in libdir bindir includedir; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the argument of --$i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
-+#     if test -d $i || mkdir $i; then :
-+#     else
-+#       eval echo "! No directory $i and can\'t create it."
-+#       badvar=1
-+#     fi
-+#   done
-+#else
-+#   # Kludge to fool the "Makefile" target in the top-level CCP4
-+#   # Makefile into not trying to remake src/Makefile.in
-+#   for i in $srcdir/src $srcdir/lib/src ; do
-+#     if test -d $i || mkdir $i; then
-+#       if ! test -f $i/Makefile.in ; then
-+#         echo
-+#         echo "onlylibs: making dummy file $i/Makefile.in"
-+#	 touch $i/Makefile.in
-+#       fi
-+#     fi
-+#   done
-+#fi
- 
- ### sanity checks
- 
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch b/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch
deleted file mode 100644
index db8236063043..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch
+++ /dev/null
@@ -1,152 +0,0 @@
-diff --git a/lib/DiffractionImage/Bruker/FRM_LIB.c b/lib/DiffractionImage/Bruker/FRM_LIB.c
-index bfda882..f821e04 100755
---- a/lib/DiffractionImage/Bruker/FRM_LIB.c
-+++ b/lib/DiffractionImage/Bruker/FRM_LIB.c
-@@ -38,6 +38,8 @@ FRM_LIB: Routines for reading, writing, and handling frame files.
- #include "sys/types.h"  /* _open, etc. */
- #include "sys/stat.h"   /* _open, etc. */
- 
-+#include <unistd.h>
-+
- #ifndef _MSC_VER
- int min(int a, int b)
- 	{
-diff --git a/lib/DiffractionImage/MAR/mar300_header.c b/lib/DiffractionImage/MAR/mar300_header.c
-index 1a933de..1c40c32 100755
---- a/lib/DiffractionImage/MAR/mar300_header.c
-+++ b/lib/DiffractionImage/MAR/mar300_header.c
-@@ -23,6 +23,9 @@
-  */
- #include "mar300_header.h"
- 
-+#include <sys/types.h>
-+#include <unistd.h>
-+
- /*
-  * Local functions
-  */
-diff --git a/lib/DiffractionImage/MAR/mar345_header.c b/lib/DiffractionImage/MAR/mar345_header.c
-index a8351ea..16d0f7b 100755
---- a/lib/DiffractionImage/MAR/mar345_header.c
-+++ b/lib/DiffractionImage/MAR/mar345_header.c
-@@ -32,6 +32,9 @@
-  */
- #include "mar345_header.h"
- 
-+#include <sys/types.h>
-+#include <unistd.h>
-+
- /*
-  * Definitions
-  */
-diff --git a/lib/DiffractionImage/MAR/nb_header.c b/lib/DiffractionImage/MAR/nb_header.c
-index 07f2741..6364ca4 100755
---- a/lib/DiffractionImage/MAR/nb_header.c
-+++ b/lib/DiffractionImage/MAR/nb_header.c
-@@ -20,6 +20,8 @@
- #include <io.h>
- #endif
- 
-+#include <sys/types.h>
-+#include <unistd.h>
- /*
-  * mar software include files
-  */
-diff --git a/lib/DiffractionImage/MAR/swap.c b/lib/DiffractionImage/MAR/swap.c
-index 443bb8c..0d96b3f 100755
---- a/lib/DiffractionImage/MAR/swap.c
-+++ b/lib/DiffractionImage/MAR/swap.c
-@@ -10,6 +10,9 @@
-  *
-  **********************************************************************/
- 
-+#define _XOPEN_SOURCE
-+#include <unistd.h>
-+
- void swaplong();
- void swapshort();
- 
-diff --git a/lib/ccif/f_interface.c b/lib/ccif/f_interface.c
-index 0f6a6b7..a09dc48 100755
---- a/lib/ccif/f_interface.c
-+++ b/lib/ccif/f_interface.c
-@@ -25,6 +25,7 @@
- ********************************************************************/
- 
- #include "stdpccts.h"
-+#include <sys/mman.h>
- 
- /* This file is terribly organised, and badly needs re-doing. There is probably
-  * scope for splitting this into three modules:
-diff --git a/lib/src/ccp4_general_f.c b/lib/src/ccp4_general_f.c
-index 8b5d04f..74ee3f7 100755
---- a/lib/src/ccp4_general_f.c
-+++ b/lib/src/ccp4_general_f.c
-@@ -26,6 +26,7 @@
- #include <string.h>
- #include <stdlib.h>
- #include <math.h>
-+#include <time.h>
- #include "ccp4_errno.h"
- #include "ccp4_fortran.h"
- #include "ccp4_parser.h"
-diff --git a/lib/src/ccp4_program.c b/lib/src/ccp4_program.c
-index 3e83d4d..bb3e975 100755
---- a/lib/src/ccp4_program.c
-+++ b/lib/src/ccp4_program.c
-@@ -25,6 +25,7 @@
- #include <stdio.h>
- #include <stdlib.h>
- #include <string.h>
-+#include <time.h>
- #include "ccp4_program.h"
- #include "ccp4_parser.h"
- #include "ccp4_utils.h"
-diff --git a/lib/src/fsplit.c b/lib/src/fsplit.c
-index ee8af24..c6fb3cd 100755
---- a/lib/src/fsplit.c
-+++ b/lib/src/fsplit.c
-@@ -50,6 +50,7 @@ static char sccsid[] = "@(#)fsplit.c	5.5 (Berkeley) 3/12/91";
- #include <string.h>
- #include <sys/types.h>
- #include <sys/stat.h>
-+#include <unistd.h>
- 
- /*
-  *	usage:		fsplit [-e efile] ... [file]
-diff --git a/src/clipper_progs/src/pirate/compress42.c b/src/clipper_progs/src/pirate/compress42.c
-index ea52e96..30dbd56 100755
---- a/src/clipper_progs/src/pirate/compress42.c
-+++ b/src/clipper_progs/src/pirate/compress42.c
-@@ -142,6 +142,7 @@
- #include	<sys/types.h>
- #include	<sys/stat.h>
- #include	<errno.h>
-+#include	<unistd.h>
- 
- #ifdef DIRENT
- #	include	<dirent.h>
-diff --git a/src/mtz2cif_/mtz2cif.c b/src/mtz2cif_/mtz2cif.c
-index e224430..c7b82f4 100755
---- a/src/mtz2cif_/mtz2cif.c
-+++ b/src/mtz2cif_/mtz2cif.c
-@@ -28,6 +28,7 @@
- #include "cmtzlib.h"
- #include "ccp4_parser.h"
- #include "ccp4_general.h"
-+#include "ccp4_program.h"
- #include "csymlib.h"
- #include "mtz2cif_lib.h"
- 
-diff --git a/x-windows/XCCPJIFFY/xplot84driver.c b/x-windows/XCCPJIFFY/xplot84driver.c
-index 67e0bf1..76526ab 100755
---- a/x-windows/XCCPJIFFY/xplot84driver.c
-+++ b/x-windows/XCCPJIFFY/xplot84driver.c
-@@ -11,6 +11,7 @@
- 
- #include <stdio.h>
- #include <sys/types.h>
-+#include <stdlib.h>
- 
- #include <X11/StringDefs.h>
- #include <X11/Intrinsic.h>
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch b/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch
deleted file mode 100644
index 62892db01147..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch
+++ /dev/null
@@ -1,597 +0,0 @@
-diff --git a/configure b/configure
-index 833f483..bcfa62d 100755
---- a/configure
-+++ b/configure
-@@ -3226,574 +3226,14 @@ else
-   echo
-   echo "Warning: this option has not been extensively tested!"
-   echo "Please report problems to ccp4@ccp4.ac.uk"
--  # Search for vendor LAPACK/BLAS first
--  if test ! "$with_netlib_lapack" ; then
--    # Initialise variables to blank
--    lapackdir=
--    XLAPACK_LIB=
--    # Possible directories to check for vendor or pre-existing LAPACK or
--    # BLAS - add to these if you want to test others
--    trydirs="`echo $LD_LIBRARY_PATH |sed -e s/:/\ /g` /lib /usr/lib /usr/local/lib"
--    # Possible library names
--    # These are the names like xxxx where the library will be libxxxx.a
--    # or libxxxx.so
--    echo
--    echo "Guessing names for native/vendor LAPACK and/or BLAS libraries"
--    echo "on this system"
--    case $system in
--      linux | linux64 | linux32 )
--        # linux users will usually have them in /usr/lib but don't call it
--        trylapack="lapack"
--        tryblas="blas"
--        # if code is non_shared then this can lead to problems. both blas and lapack
--        # need to be resolved even if they are not called!
--        if test "$non_shared" = yes; then
--          echo "You are compiling linux non_shared. This sometimes causes problems "
--          echo "  so checking for requirements." 
--          echo "Checking: try to link library against test program"
--          if test -f testlink.f || test -f testlink ; then
--            rm -f testlink*
--          fi 
--          cat > testlink.f <<EOF
--      PROGRAM TESTLINK
--C A bit of scala code to test the linking
--      real bf(3), bnorm
--c
--      integer maxbmt
--      parameter (maxbmt = 2)
--      double precision B(maxbmt,maxbmt), eigval(maxbmt),
--     $   eigvec(maxbmt,maxbmt), w(5*maxbmt)
--      integer m, ia, ix, istat
--c
--      B(1,1) = 1.00
--      B(1,2) = 1.00
--      B(2,1) = 1.00
--      B(2,2) = 1.00
--c
--      m = maxbmt
--      ia = maxbmt
--      ix = maxbmt
--      call dsyev('N', 'L', m, B, ia, eigval, w, 5*maxbmt, istat)
--      end
--EOF
--          #firstly test without -lblas
--          test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack"
--          echo $test_compile
--          if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then
--            # Compilation was okay
--            echo "... only -llapack needed"
--            XLAPACK_LIB="-llapack"
--            # Set the next two variables so that configure
--            # doesn't try to build netlib libraries
--            LAPACKLIB="lapack"
--            noblas=yes
--            trylapack=
--            tryblas=
--          else
--	    echo "more than just -llapack needed...."
--            test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas"
--            echo $test_compile
--            if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
--              # Compilation was okay
--              echo "...-llapack and -lblas were needed"
--              XLAPACK_LIB="-llapack -lblas"
--              # Set the next two variables so that configure
--              # doesn't try to build netlib libraries
--              LAPACKLIB="lapack blas"
--              noblas=no
--              trylapack=
--              tryblas=
--	    else
--              echo "....could not find either lapack or blas."
--	    fi
--          fi
--        fi
--        # add 64 bit libs
--        case $system in
--          linux64 ) trydirs="/usr/lib64 ${trydirs}" ;;
--        esac
--
--        ;;
--      osf1)
--        # OSF1 has dxml (old version) and cxml
--        # which should have both lapack and blas 
--        trylapack="dxml cxml"
--        tryblas=
--        trydirs="${trydirs} /usr/shlib"
--        ;;
--      irix)
--        # Additional search paths for IRIX
--        trydirs="${trydirs} /usr/lib32"
--        # SCSL should have both LAPACK and BLAS
--        trylapack="scs"
--        tryblas="blas"
--        ;;
--      irix64)
--        # Additional search paths for IRIX64
--        trydirs="${trydirs} /usr/lib64"
--        # SCSL should have both LAPACK and BLAS
--        trylapack="scs"
--        tryblas="blas"
--        # Extra compiler flags?
--        #XLAPACKFLAGS="-OPT:IEEE_NaN_inf=ON"
--        ;;
--      aix)
--        # Additional search paths for AIX
--        trydirs="${trydirs}" 
--        # AIX might have ESSL library - blas only I think
--        trylapack=
--        tryblas="essl"
--        ;;
--      hpux)
--        # Additional search paths for HPUX
--        trydirs="${trydirs} /opt/fortran/lib /opt/fortran/lib/pa2.0 /opt/mlib/lib/pa2.0"
--        # HPUX should have both LAPACK (part of mlib) and BLAS
--        trylapack="lapack"
--        tryblas="blas"
--        # Extra compiler flags?
--        # +U77 required for ETIME function - this is already in XFFLAGS
--        #XLAPACKFLAGS="+U77"
--        ;;
--
--      sunos | sunos64)
--        # Sun has libraries with BLAS and LAPACK invoked using
--        # -xlic_lib=sunperf
--        trylapack=
--        tryblas=
--        echo "SunOs can use the Sun Performance Library (if installed)"
--        echo "which has both BLAS and LAPACK 3.0"
--        echo 
--        echo "Looking for a valid library to use..."
--        echo
--	# Loop over the possible library names
--        try_libs="sunperf"
--        for testlib in $try_libs
--        do
--          if test ! "$XLAPACK_LIB" ; then
--            # Try running a test compile to see if this a valid library
--            if test -f testlink.f || test -f testlink ; then
--              rm -f testlink*
--            fi
--            cat > testlink.f <<EOF
--c Test fortran program to link against library
--      PROGRAM TESTLINK
--      IMPLICIT NONE
--      INTEGER A
--      A = 1
--      STOP
--      END
--EOF
--            test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -dalign -xlic_lib=$testlib"
--            echo $test_compile
--            if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
--              # Compilation was okay
--              echo "... -xlic_lib=$testlib is okay"
--              XLAPACK_LIB="-dalign -xlic_lib=$testlib"
--              # Set the next two variables so that configure
--              # doesn't try to build netlib libraries
--              LAPACKLIB="$testlib"
--              noblas=yes
--            else
--              # Compilation failed
--              echo "... cannot use -xlic_lib=$testlib"
--            fi
--            # End of test for testlib
--          fi
--          # End of loop over possible lib names
--        done
--	# Report if no suitable library was found
--        if test ! "$XLAPACK_LIB" ; then
--          echo
--          echo "No suitable LAPACK library was found."
--          echo "This may be because the Sun Performance Library is not"
--          echo "installed on your system"
--          echo "Contact your system administrator or Sun vendor"
--        fi
--        ;;
--      Darwin | Darwin32 | Darwin64 )
--        # Darwin has libraries with BLAS and LAPACK invoked using 
--        # -framework vecLib
--        echo "Darwin can use the vecLib Library (if installed)"
--        echo "which has both BLAS and LAPACK 3.0"
--        echo
--        # This is a special case so try running a test compile
--        echo "Checking: try to link library against test program"
--        if test -f testlink.f || test -f testlink ; then
--          rm -f testlink*
--        fi
--        cat > testlink.f <<EOF
--c Test fortran program to link against library
--      PROGRAM TESTLINK
--      IMPLICIT NONE     
--      INTEGER A
--      A = 1
--      STOP
--      END
--EOF
--        test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -framework vecLib"
--        echo $test_compile
--        if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
--          # Compilation was okay
--          echo "... -framework vecLib is okay"
--          XLAPACK_LIB="-framework vecLib"
--          # Set the next two variables so that configure
--          # doesn't try to build netlib libraries
--          LAPACKLIB="vecLib"
--          noblas=yes
--        else
--#alternative linking for vecLib libraries
--          case `uname -sr` in
--            *Darwin\ 7.* ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic -Wl,-framework -Wl,vecLib" ;;
--            * ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" ;;
--          esac
--
--        echo $test_compile
--        if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
--          # Compilation was okay
--          echo "... -framework vecLib is okay"
--          XLAPACK_LIB="-Wl,-framework -Wl,vecLib"
--          # Set the next two variables so that configure
--          # doesn't try to build netlib libraries
--          LAPACKLIB="-Wl,-framework -Wl,vecLib"
--          noblas=yes
--        else
--          # Compilation failed
--          echo "... cannot use -framework vecLib"
--          echo
--         fi
--        fi
--        trylapack=
--        tryblas=
--# try the fink installation
--        trydirs="${trydirs} /sw"
--        ;;
--      Darwin_ibm_compilers )
--        # Darwin has libraries with BLAS and LAPACK invoked using
--        # -framework vecLib
--        echo "Darwin can use the vecLib Library (if installed)"
--        echo "which has both BLAS and LAPACK 3.0"
--        echo
--        # This is a special case so try running a test compile
--        echo "Checking: try to link library against test program"
--        if test -f testlink.f || test -f testlink ; then
--          rm -f testlink*
--        fi
--        cat > testlink.f <<EOF
--c Test fortran program to link against library
--      PROGRAM TESTLINK
--      IMPLICIT NONE
--      INTEGER A
--      A = 1
--      STOP
--      END
--EOF
--      case `uname -sr` in
--        Darwin\ 8* )
--        XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS"
--        test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB"
--        ;;
--        Darwin\ 7* )
--        XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS"
--        test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic $XLAPACK_LIB"
--        ;;
--        *)
--        XLAPACK_LIB="/System/Library/Frameworks/vecLib.Framework/Versions/Current/VecLib"
--        test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB"
--        esac
--        echo $test_compile
--        if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
--          # Compilation was okay
--          echo "... -framework vecLib is okay"
--          # Set the next two variables so that configure
--          # doesn't try to build netlib libraries
--          LAPACKLIB="vecLib"
--          noblas=yes
--        else
--          # Compilation failed
--          XLAPACK_LIB=""
--          echo "... cannot use -framework vecLib"
--          echo
--        fi
--        trylapack=
--        tryblas=
--# try the fink installation
--        trydirs="${trydirs} /sw"
--        ;;
--
--      Darwin_intel_compilers)
--        # Darwin has libraries with BLAS and LAPACK invoked using
--        # -F vecLib
--        echo "Darwin can use the vecLib Library (if installed)"
--        echo "which has both BLAS and LAPACK 3.0"
--        echo
--        # This is a special case so try running a test compile
--        echo "Checking: try to link library against test program"
--        if test -f testlink.f || test -f testlink ; then
--          rm -f testlink*
--        fi
--        cat > testlink.f <<EOF
--c Test fortran program to link against library
--      PROGRAM TESTLINK
--      IMPLICIT NONE
--      INTEGER A
--      A = 1
--      STOP
--      END
--EOF
--        test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib"
--        echo $test_compile
--        if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
--          # Compilation was okay
--          # doesn't try to build netlib libraries
--          XLAPACK_LIB="-F /System/Library/Frameworks -Qoption,ld,-framework -Qoption,ld,vecLib"
--          LAPACKLIB="vecLib"
--          noblas=yes
--        else
--          # Compilation failed
--          echo "... cannot use -framework vecLib"
--          echo
--         fi
--        trylapack=
--        tryblas=
--# try the fink installation
--        trydirs="${trydirs} /sw"
--        ;;
--
--#       linux_ia64_sgi_altix)
--# SGI Japan
--      ia64_linux_intel) 
--        # Additional search paths for Linux/IA64
--        trydirs="${trydirs} /opt/scsl/lib /usr/lib /usr/local/lib"
--        # SCSL and MKL should have both LAPACK and BLAS
--        trylapack="mkl_lapack scs lapack"
--        tryblas="mkl scs blas"
--        ;;
--      linux_ibm_compilers )
--        trylapack="lapack"
--        tryblas="blas"
--        ;;
--      linux64_ibm_compilers )
--        trydirs="/usr/lib64 ${trydirs}"
--        trylapack="lapack"
--        tryblas="blas"
--        ;;
--      linux_intel_compilers )
--        trydirs="/usr/lib64 ${trydirs}"
--        trylapack="mkl_lapack lapack"
--        tryblas="mkl blas"
--        ;;
--      *)
--        echo "The guesses for this system may not be correct - please"
--        echo "e-mail ccp4@ccp4.ac.uk if you have any extra information"
--	echo
--        # Default guess is just libblas
--        trylapack="lapack"
--        tryblas="blas"
--        ;;
--    esac
--    #
--    # Search for LAPACK libraries
--    #
--    # Write out what the guesses are
--    if test "$trylapack" ; then
--      echo "Possible LAPACK library names for this system:"
--      for libname in $trylapack
--      do
--        echo "   lib$libname"
--      done
--      # Possible library name extensions
--      tryexts="a so dylib"
--      # Now loop over all the possibilities and see if anything
--      # turns up
--      echo
--      echo "Searching for libraries with LAPACK and BLAS:"
--      for testdir in $trydirs
--      do
--        for testlib in $trylapack
--        do
--          for ext in $tryexts
--          do
--            if test ! "$LAPACKLIB"; then
--              if test -s "$testdir/lib$testlib.$ext" ; then
--                echo "...found LAPACK library: $testdir/lib$testlib.$ext"
--                # Now try and link to a test program
--                # This is really for IRIX where libraries can be
--                # o32 or n32
--                echo "   Testing: try to link library against test program"
--                if test -f testlink.f || test -f testlink ; then
--                  rm -f testlink*
--                fi
--                cat > testlink.f <<EOF
--c Test fortran program to link against library
--      PROGRAM TESTLINK
--      IMPLICIT NONE
--      INTEGER A
--      A = 1
--      STOP
--      END
--EOF
--                test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib"
--                test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS"
--                echo $test_compile
--                if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
--                  have_lapack=yes
--                else
--# cover clapack option
--                  echo $test_ccompile
--                  if { (eval $test_ccompile ) 2>&1; } && test -s testlink ; then
--                    have_lapack=yes
--                  fi
--                fi
--                if test x$have_lapack = xyes ; then
--                # This one is okay
--                  LAPACKLIB="$testlib"
--                  LAPACKDIR="$testdir"
--                  echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR"
--		  #
--		  XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB"
--                  #
--                  # Test to see if we need BLAS too
--                  # Do this by trying to compile a test program
--                  # Use the LSAME test for now
--                  echo
--                  echo "   * Checking whether we need a separate BLAS library *"
--                  echo "   Testing: try linking library against test program"
--                  cd lib/lapack/test
--                  if test -f testlsame ; then
--                    rm -f testsame testlsame.o
--                  fi
--                  test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB"
--                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS"
--                  echo $test_compile
--                  if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then
--                    have_blas=yes
--                  else
--#cblas route
--                    echo $test_ccompile
--                    if { ( eval $test_ccompile) 2>&1;} && test -s testlsame ; then
--                      have_blas=yes
--                    fi
--                  fi
--                  if test x$have_blas = xyes ; then
--                    echo "Test program okay - additional separate BLAS not required"
--                    noblas=yes
--                  else
--                    echo "Test program failed - need a separate BLAS library"
--                  fi
--                  cd ../../..
--                else
--                # Keep looking
--                  echo "   link failed - cannot use lib$testlib"
--                fi
--              fi
--            fi
--          done
--        done
--        if test ! "$LAPACKLIB"; then
--          echo "...nothing in $testdir"
--        fi
--      done
--    fi
--
--    # If LAPACKLIB hasn't been set at this point then no LAPACK library
--    # was found 
--    if test ! "$LAPACKLIB" ; then
--      echo
--      echo "No pre-existing LAPACK library found - NetLib LAPACK will be built instead"
--      make_lapack=lapacklib
--    fi
--    # Look for possible BLAS
--    if test ! "$noblas" ; then
--      if test "$tryblas" ; then
--        echo
--        echo "Possible BLAS library names for this system:"
--        for libname in $tryblas
--        do
--          echo "   lib$libname"
--        done
--        # Possible library name extensions
--        tryexts="a so"
--        # Now loop over all the possibilities and see if anything
--        # turns up
--        echo
--        echo "Searching for libraries with BLAS:"
--        for testdir in $trydirs
--        do
--          for testlib in $tryblas
--          do
--            for ext in $tryexts
--            do
--              if test ! "$BLASLIB"; then
--                if test -s "$testdir/lib$testlib.$ext" ; then
--                  echo "...found BLAS library: $testdir/lib$testlib.$ext"
--                  # Now try and link to a test program
--                  # This is really for IRIX where libraries can be
--                  # o32 or n32
--                  echo "   Testing: try to link library against test program"
--                  if test -f testlink.f || test -f testlink ; then
--                    rm -f testlink*
--                  fi
--                  cat > testlink.f <<EOF
--c Test fortran program to link against library
--      PROGRAM TESTLINK
--      IMPLICIT NONE
--      INTEGER A
--      A = 1
--      STOP
--      END
--EOF
--                  test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib"
--                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS"
--                  echo $test_compile
--                  if { ( eval $test_compile) 2>&1;} && test -s testlink ; then
--                    have_blas=yes
--                  else
--                    echo $test_ccompile
--                    if { ( eval $test_compile) 2>&1;} && test -s testlink ; then
--                      have_blas=yes
--                    fi
--                  fi
--                  if test x$have_blas = xyes ; then
--                    # This one is okay
--                    BLASLIB="$testlib"
--                    BLASDIR="$testdir"
--                    BLASEXT="$ext"
--                    echo "Link ok - using lib$BLASLIB from $BLASDIR"
--		    XLAPACK_LIB="$XLAPACK_LIB -L$BLASDIR -l$BLASLIB"
--                  else
--                  # Keep looking
--                    echo "   link failed - cannot use lib$testlib"
--                  fi
--                fi
--              fi
--            done
--          done
--          if test ! "$BLASLIB"; then
--            echo "...nothing in $testdir"
--          fi
--        done
--      fi
--      # Do we need to build BLAS too?      
--      if test ! "$BLASLIB" ; then
--        echo
--        echo "No pre-existing BLAS library was found - NetLib BLAS will be built instead"
--        echo "This may result in poorer performance of the LAPACK routines"
--        make_blas=blaslib
--        BLASLIB=blas
--        BLASDIR="$srcdir/lib/lapack"
--        BLASEXT="a"
--      fi
--    fi
-+  # gentoo is clever
-+  make_blas=
-+  make_lapack=
-+  BLASLIB=$(${PKG_CONFIG} --libs blas)
-+  LAPACKLIB=$(${PKG_CONFIG} --libs lapack)
-+  XLAPACK_LIB="${BLASLIB} ${LAPACKLIB}"
-+  XFFLAGS_LAPACK="$(${PKG_CONFIG} --cflags lapack blas)"
-   # Otherwise force building of NetLib BLAS and LAPACK libs
--  else
--    echo
--    echo "! Force building of NetLib BLAS and LAPACK..."
--    make_blas=blaslib
--    make_lapack=lapacklib
--    BLASLIB=blas
--    BLASDIR="$srcdir/lib/lapack"
--    BLASEXT="a"
--  fi
-   # need to know if we the lapack library was linked using the C or
-   # fortran linker
-   if test -f testlink.f || test -f testlink || test -f testlink.c ; then
-@@ -3916,8 +3356,8 @@ RANLIB   = ${RANLIB}
- INSTALL_DATA = ${INSTALL_DATA}
- libdir   = $libdir
- #
--BLASLIB     = lib${BLASLIB}.${BLASEXT}
--LAPACKLIB   = liblapack.a
-+BLASLIB     = ${BLASLIB}
-+LAPACKLIB   = ${LAPACKLIB}
- #
- # These variables define targets in the main Makefile
- blaslib   = ${make_blas}
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch
deleted file mode 100644
index 9d8fefe965e5..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-diff --git a/src/pisa/sbase/Makefile.am b/src/pisa/sbase/Makefile.am
-index 053e83a..4ff3394 100755
---- a/src/pisa/sbase/Makefile.am
-+++ b/src/pisa/sbase/Makefile.am
-@@ -1,4 +1,4 @@
--pkgdatadir = $(datadir)/sbase
-+pkgdatadir = $(datadir)/pisa/sbase
- dist_pkgdata_DATA = \
- graph.sbase     index.sbase     struct.sbase
- 
-diff --git a/src/pisa/sbase/Makefile.in b/src/pisa/sbase/Makefile.in
-index faa3f7f..8630bd7 100755
---- a/src/pisa/sbase/Makefile.in
-+++ b/src/pisa/sbase/Makefile.in
-@@ -62,7 +62,7 @@ POST_UNINSTALL = :
- EXEEXT = @EXEEXT@
- OBJEXT = @OBJEXT@
- PATH_SEPARATOR = @PATH_SEPARATOR@
--pkgdatadir = $(datadir)/sbase
-+pkgdatadir = $(datadir)/pisa/sbase
- AMTAR = @AMTAR@
- AR_FLAGS = @AR_FLAGS@
- AWK = @AWK@
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch
deleted file mode 100644
index 7a012be6ef02..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch
+++ /dev/null
@@ -1,65 +0,0 @@
-diff --git a/ccp4-6.1.2/include/ccp4.setup-bash b/ccp4-6.1.2/include/ccp4.setup-bash
-index 9848101..cea8ae6 100755
---- a/ccp4-6.1.2/include/ccp4.setup-bash
-+++ b/ccp4-6.1.2/include/ccp4.setup-bash
-@@ -188,9 +188,9 @@ fi
- #Python path for the subprocess fixed module
- 
- if [ $ccp4_first_in_path -eq 1 ]; then
--    setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
-+    setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH}
- else
--    setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
-+    setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python
- fi
- 
- ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
-diff --git a/ccp4-6.1.2/include/ccp4.setup-csh b/ccp4-6.1.2/include/ccp4.setup-csh
-index 42f0820..93c2cf3 100755
---- a/ccp4-6.1.2/include/ccp4.setup-csh
-+++ b/ccp4-6.1.2/include/ccp4.setup-csh
-@@ -180,9 +180,9 @@ endif
- #Python path for the subprocess fixed module
- if (${?PYTHONPATH}) then
-   if ($ccp4_first_in_path) then
--      setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
-+      setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH}
-   else
--      setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
-+      setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python
-   endif
- else
-     setenv PYTHONPATH ${CCP4}/share/python
-diff --git a/ccp4-6.1.2/include/ccp4.setup-sh b/ccp4-6.1.2/include/ccp4.setup-sh
-index 4396ebf..a0455bd 100755
---- a/ccp4-6.1.2/include/ccp4.setup-sh
-+++ b/ccp4-6.1.2/include/ccp4.setup-sh
-@@ -228,9 +228,9 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg
- #Python path for the subprocess fixed module
- 
- if test $ccp4_first_in_path -eq 1; then
--    export PYTHONPATH=${CCP4}/share/python:${PYTHONPATH}
-+    export PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH}
- else
--    export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python
-+    export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python
- fi
- 
- ################### THE REST SHOULDN'T NEED EDITING #####################
-diff --git a/ccp4-6.1.2/include/ccp4.setup-zsh b/ccp4-6.1.2/include/ccp4.setup-zsh
-index 0e5c2ce..53523f3 100755
---- a/ccp4-6.1.2/include/ccp4.setup-zsh
-+++ b/ccp4-6.1.2/include/ccp4.setup-zsh
-@@ -157,10 +157,10 @@ export CLASSPATH
- #Python path for the subprocess fixed module
- 
- if ($ccp4_first_in_path) then
--    PYTHONPATH=${CCP4}/share/python:${PYTHONPATH}
-+    PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH}
-     export PYTHONPATH
- else
--    PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python
-+    PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python
-     export PYTHONPATH
- fi
- 
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch
deleted file mode 100644
index a5144cfa5d33..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch
+++ /dev/null
@@ -1,60 +0,0 @@
-diff --git a/src/Makefile.in b/src/Makefile.in
-index 70781f3..b2dcc25 100755
---- a/src/Makefile.in
-+++ b/src/Makefile.in
-@@ -760,7 +760,7 @@ chainsawobjs = chainsaw.o
- pdbcur : $(pdbcurobjs)
- 	@$(SETFLAGS) ; rm -f pdbcur; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o pdbcur $(pdbcurobjs) $(LDCXXFLAGS)
- ncont : $(ncontobjs)
--	@$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS)
-+	@$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) -lmmdb
- coord_format : $(coord_formatobjs)
- 	@$(SETFLAGS) xxx=1 ; \
- 	rm -f coord_format; \
-diff --git a/src/rapper/LOOP/Makefile.am b/src/rapper/LOOP/Makefile.am
-index 85f212e..2608c6d 100755
---- a/src/rapper/LOOP/Makefile.am
-+++ b/src/rapper/LOOP/Makefile.am
-@@ -15,12 +15,12 @@ params.cpp typed_value.cpp misc.cpp residue.cpp atom.cpp psa.cpp edm_sidechains.
- hash_table.cpp surface.cpp parse.cpp band.cpp edensity.cpp read_map.cpp iterator.cpp \
- residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp
- 
--rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la
-+rapper_LDADD = @GC_LIBS@ @LIBXML_LIBS@
- 
- pkgdatadir = $(datadir)/rapper
- dist_pkgdata_DATA = params.xml
- 
--INCLUDES = -I. -I../gc7.0/include -I../libxml2/include
-+INCLUDES = -I. @LIBXML_CFLAGS@ @GC_CFLAGS@
- #SUBDIRS = \
- #@PYTHON_USE_TRUE@ python
- 
-diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am
-index e78b10d..486b931 100755
---- a/src/rapper/Makefile.am
-+++ b/src/rapper/Makefile.am
-@@ -1,3 +1,3 @@
--SUBDIRS = libxml2 gc7.0 LOOP data
-+SUBDIRS = LOOP data
- 
- EXTRA_DIST =
-diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac
-index 5e4ef69..268a579 100755
---- a/src/rapper/configure.ac
-+++ b/src/rapper/configure.ac
-@@ -48,6 +48,13 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno)
- 
- AC_SUBST(rapper_LDFLAGS)
- 
--AC_CONFIG_SUBDIRS([gc7.0 libxml2])
-+PKG_CHECK_MODULES([LIBXML],[libxml-2.0])
-+AC_SUBST([LIBXML_CFLAGS])
-+AC_SUBST([LIBXML_LIBS])
-+
-+PKG_CHECK_MODULES([GC],[bdw-gc])
-+AC_SUBST([GC_CFLAGS])
-+AC_SUBST([GC_LIBS])
-+
- #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile)
- AC_OUTPUT(Makefile LOOP/Makefile data/Makefile)
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch b/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch
deleted file mode 100644
index 107cfd740238..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch
+++ /dev/null
@@ -1,131 +0,0 @@
- src/Makefile.in       |   14 +++++-----
- src/pisa/configure.ac |   67 +++++++++----------------------------------------
- 2 files changed, 19 insertions(+), 62 deletions(-)
-
-diff --git a/src/Makefile.in b/src/Makefile.in
-index 70781f3..b11db04 100755
---- a/src/Makefile.in
-+++ b/src/Makefile.in
-@@ -778,8 +778,8 @@ chainsaw : $(chainsawobjs)
- 	eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o chainsaw $(chainsawobjs) $(LDCXXFLAGS)
- pdbcur.o pcur_funcs.o ncont.o coord_format.o pdb_merge.o chainsaw.o: # dependencies at end
- 	@$(SETFLAGS) xxx=1 ; \
--	echo $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; 
--	eval $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp
-+	echo $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; 
-+	eval $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp
- 
- ### bp3, afro, gcx
- 
-@@ -813,8 +813,8 @@ gcx : libbp3 $(gcxobjs)
- 
- $(libbp3objs) $(bp3objs) $(afroobjs) $(gcxobjs) : # dependencies at end
- 	@$(SETFLAGS) xxx=1 ; \
--	echo $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \
--	eval $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C
-+	echo $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \
-+	eval $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C
- 
- ### crunch2 pmf
- 
-@@ -853,7 +853,7 @@ cif2xml : $(cif2xmlobjs)
- cross_validate : $(cross_validateobjs)
- 	@$(SETFLAGS); rm -f cross_validate; eval $(CXX) $${harvest_app_FLAGS-"$(CXXFLAGS)"} -o cross_validate $(cross_validateobjs) $(LDCXXFLAGS)
- cif2xml.o cross_validate.o : # dependencies at end
--	@$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) -I$(incdir)/mmdb $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp
-+	@$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp
- 
- pdb_extractdir = $(srcdir)/harvest_app_/pdb_extract
- pdb_extract_suite :
-@@ -873,8 +873,8 @@ $(dev_tools_ctargets) :
- $(dev_tools_cxxtargets) :
- 	@$(SETFLAGS) xxx=1; \
- 	  rm -f $@; \
--	  echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS) ;\
--	  eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS)
-+	  echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS) ;\
-+	  eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS)
- 
- ### mlphare
- mlphare:
-diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac
-index 81afdda..044b6f8 100755
---- a/src/pisa/configure.ac
-+++ b/src/pisa/configure.ac
-@@ -31,64 +31,21 @@ AC_CHECK_FUNCS([floor pow rint sqrt])
- # test for function in m
- AC_CHECK_LIB([m], [sqrt])
- 
--dnl Optional: Check for MMDB.
--AM_PATH_MMDB(,
--  [ if test "x$mmdb_prefix" != x ; then
--      if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then 
--        case "$ac_MMDB_CXXFLAGS" in
--        *src/mmdb )
--        ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g`
--        ;;
--        *include/mmdb )
--        ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g`
--        ;;
--        *)
--        esac
--	MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS"
--        MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#`
--        AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
--      else
--        MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb"
--        MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb"
--        AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
--      fi
--    else
--     AC_MSG_ERROR([mmdb not found])
--    fi
--  ]
--)
-+PKG_CHECK_MODULES([MMDB],[mmdb])
-+PKG_CHECK_MODULES([SSM],[ssm])
-+
-+MMDB_CXXFLAGS=${MMDB_CFLAGS}
-+
-+AC_SUBST([MMDB_CFLAGS])
-+AC_SUBST([MMDB_CXXFLAGS])
-+AC_SUBST([SSM_CFLAGS])
-+
-+AC_SUBST([MMDB_LIBS])
-+AC_SUBST([SSM_LIBS])
- 
--ac_saved_CXXFLAGS=$CXXFLAGS
--ac_saved_LIBS=$LIBS
- CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS"
- LIBS="$MMDB_LIBS $LIBS"
--AM_PATH_SSM(,
--  [ if test "x$ssm_prefix" != x ; then
--      if test "x$ac_SSM_CXXFLAGS" != x && test "x$ac_SSM_LDOPTS" = x ; then 
--        case "$ac_SSM_CXXFLAGS" in
--        *lib/ssm )
--        ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#lib/ssm#lib#g`
--        ;;
--        *include/ssm )
--        ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#include/ssm#lib#g`
--        ;;
--        *)
--        esac
--        SSM_CXXFLAGS="$ac_SSM_CXXFLAGS"
--        SSM_LIBS=`echo "$ac_SSM_LDOPTS -lssm" | sed s#-I#-L#`
--        AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS])
--      else
--        SSM_CXXFLAGS="-I$ssm_prefix/include/ssm -I$ssm_prefix/lib/ssm"
--        SSM_LIBS="-L$ssm_prefix/lib -L$ssm_prefix/lib/ssm -lssm"
--        AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS])
--      fi
--    else
--     AC_MSG_ERROR([ssm not found])
--    fi
--  ]
--)
--CXXFLAGS=$ac_saved_CXXFLAGS
--LIBS=$ac_saved_LIBS
-+
- 
- # Checks for typedefs, structures, and compiler characteristics.
- #
diff --git a/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch b/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch
deleted file mode 100644
index 4b98545eec83..000000000000
--- a/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch
+++ /dev/null
@@ -1,130 +0,0 @@
- src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c | 34 ++++++++++++++---------------
- 1 file changed, 17 insertions(+), 17 deletions(-)
-
-diff --git a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c
-index 2c9f02f..98d814a 100755
---- a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c
-+++ b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c
-@@ -297,7 +297,7 @@ int canvas_draw_line(char *canvas, int npts, float *x, float *y, char *tags,
-     puts("canvas_draw_line: about to evaluate the command...");
-   }
-   if (Tcl_Eval(interp,command) != TCL_OK) {
--    printf("canvas_draw_line: error from Tcl_Eval: %s",interp->result);
-+    printf("canvas_draw_line: error from Tcl_Eval: %s",Tcl_GetStringResult(interp));
-     return 0;
-   }
-   if (CCP4MAPWISH_CANVAS_DIAG)
-@@ -432,7 +432,7 @@ int canvas_draw_rectangle(char *canvas, int npts, float *x, float *y,
-     puts("canvas_draw_rectangle: about to evaluate the command...");
-   }
-   if (Tcl_Eval(interp,command) != TCL_OK) {
--    printf("canvas_draw_rectangle: error from Tcl_Eval: %s",interp->result);
-+    printf("canvas_draw_rectangle: error from Tcl_Eval: %s",Tcl_GetStringResult(interp));
-     printf("canvas_draw_rectangle:\ncanvas = \"%s\"\ntags = \"%s\"\ncolor = \"%s\"\nunits = \"%c\"\n",canvas,tags,color,units);
-     return 0;
-   }
-@@ -536,7 +536,7 @@ int canvas_draw_label(char *canvas, char *text, float x, float y,
-   /* Execute the command which draws the label */
-   if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_draw_label: command is: %s\n",command);
-   if (Tcl_Eval(interp,command) != TCL_OK) {
--    printf("canvas_draw_label: error from Tcl_Eval: %s\n",interp->result);
-+    printf("canvas_draw_label: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
-     return 0;
-   }
- 
-@@ -617,7 +617,7 @@ int canvas_scale_canvas(char *canvas, char *tag, float scale)
-   /* Execute the command which scales the canvas */
-   if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_scale_canvas: command is: %s\n",command);
-   if (Tcl_Eval(interp,command) != TCL_OK) {
--    printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result);
-+    printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
-     return 0;
-   }
- 
-@@ -706,7 +706,7 @@ int canvas_shift_canvas(char *canvas)
-   /* Execute the command which resizes the canvas */
-   if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command);
-   if (Tcl_Eval(interp,command) != TCL_OK) {
--    printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",interp->result);
-+    printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
-     return 0;
-   }
- 
-@@ -789,7 +789,7 @@ int canvas_shift_element(char *canvas, char *tag, int shiftx, int shifty)
-   /* Execute the command which resizes the canvas */
-   if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command);
-   if (Tcl_Eval(interp,command) != TCL_OK) {
--    printf("canvas_shift_element: error from Tcl_Eval: %s\n",interp->result);
-+    printf("canvas_shift_element: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
-     return 0;
-   }
- 
-@@ -861,7 +861,7 @@ int canvas_delete(char *canvas, char *tag)
-   /* Execute the command which deletes the tagged items */
-   if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_delete: command is: %s\n",command);
-   if (Tcl_Eval(interp,command) != TCL_OK) {
--    printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result);
-+    printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
-     return 0;
-   }
- 
-@@ -892,15 +892,15 @@ int canvas_exists(char *canvas)
- 
-   sprintf(tmpstr,"winfo exists %s",canvas);
-   if (Tcl_Eval(interp,tmpstr) != TCL_OK) {
--    printf("canvas_exists: error from Tcl_Eval: %s",interp->result);
-+    printf("canvas_exists: error from Tcl_Eval: %s",Tcl_GetStringResult(interp));
-     return 0;
-   }
-   /* Extract a long int using strtol
-      If no conversion takes place then "endptr" will be equal
-      to "result" */
--  istatus = (int) strtol(interp->result,&endptr,10);
--  if (strcmp(interp->result,endptr) == 0) {
--    printf("canvas_exists: bad return status from winfo command \"%s\"\n",interp->result);
-+  istatus = (int) strtol(Tcl_GetStringResult(interp),&endptr,10);
-+  if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) {
-+    printf("canvas_exists: bad return status from winfo command \"%s\"\n",Tcl_GetStringResult(interp));
-     return 0;
-   }
-   if (!istatus) {
-@@ -930,13 +930,13 @@ float canvas_get_tk_scaling(char *canvas, char units)
- 
-   /* Execute the tk scaling command */
-   if (Tcl_Eval(interp,"tk scaling") != TCL_OK) {
--    printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",interp->result);
-+    printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",Tcl_GetStringResult(interp));
-     return (float) 0.0;
-   }
- 
-   /* Extract a float from the result */
--  tkscale = ((float) strtod(interp->result,&endptr));
--  if (strcmp(interp->result,endptr) == 0) {
-+  tkscale = ((float) strtod(Tcl_GetStringResult(interp),&endptr));
-+  if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) {
-     printf("canvas_get_tk_scaling: couldn't extract scale factor\n");
-     return (float) 0.0;
-   }
-@@ -1021,19 +1021,19 @@ int canvas_get_limits(char *canvas, int limits[4])
- 
-   /* Evaluate the command */
-   if (Tcl_Eval(interp,command) != TCL_OK) {
--    printf("canvas_get_limits: error from Tcl_Eval: %s\n",interp->result);
-+    printf("canvas_get_limits: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
-     return 0;
-   }
- 
-   /* Process the result - it should consist of 4 integers */
-   /* Use strtok which can split the string based on tokens
-      set by the programmer - in this case a space */
--  if (!interp->result) {
-+  if (!Tcl_GetStringResult(interp)) {
-     puts("canvas_get_limits: failed to fetch canvas limits");
-     return TCL_ERROR;
-   }
-   i = 0;
--  p = strtok(interp->result," ");
-+  p = strtok(Tcl_GetStringResult(interp)," ");
-   if (p == NULL) {
-     return 0;
-   }
diff --git a/sci-chemistry/ccp4-apps/metadata.xml b/sci-chemistry/ccp4-apps/metadata.xml
deleted file mode 100644
index 51fdedab1b38..000000000000
--- a/sci-chemistry/ccp4-apps/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-</pkgmetadata>
diff --git a/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild b/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild
deleted file mode 100644
index eea4a408b472..000000000000
--- a/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit fortran-2
-
-DESCRIPTION="Protein X-ray crystallography toolkit -- meta package"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI=""
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE="X arpwarp +balbes"
-
-RDEPEND="
-	~sci-chemistry/ccp4-apps-${PV}[X?]
-	!<=sci-chemistry/ccp4-apps-${PV}-r2
-	>=sci-chemistry/molrep-11.0.00-r1
-	>=sci-chemistry/mosflm-7.0.6-r2
-	sci-chemistry/mrbump[X?]
-	>=sci-chemistry/oasis-4.0-r1
-	>=sci-chemistry/pdb-extract-3.004-r2
-	>=sci-chemistry/refmac-5.5.0110-r1
-	>=sci-chemistry/scala-3.3.18-r1
-	>=sci-chemistry/sfcheck-7.03.18-r1
-	sci-chemistry/xia2
-	arpwarp? ( sci-chemistry/arp-warp-bin )
-	balbes? ( sci-chemistry/balbes )
-	X? (
-		~sci-chemistry/ccp4i-${PV}
-		sci-chemistry/imosflm
-		sci-chemistry/pymol
-		sci-chemistry/rasmol
-		)"
-DEPEND=""
diff --git a/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch
deleted file mode 100644
index 1420419ffab0..000000000000
--- a/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch
+++ /dev/null
@@ -1,87 +0,0 @@
---- ccp4-6.0.1.orig/configure	2006-06-10 17:30:02.000000000 -0700
-+++ ccp4-6.0.1/configure	2006-06-10 17:45:43.000000000 -0700
-@@ -623,45 +623,45 @@
- #     echo "! Beware -- the $system installation isn't properly tested." ; }
- syswarn='echo; echo "! Beware -- the $system installation is not properly tested."'
- 
--if test -z "$onlylibs" ; then 
--   for i in CCP4_SCR BINSORT_SCR; do
--     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
--     else
--       eval echo "! No directory \$$i and can\'t create it."
--       echo "  Check the value of $i."
--       badvar=1
--     fi
--   done
--
--   for i in libdir bindir; do
--     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
--     else
--       eval echo "! No directory \$$i and can\'t create it."
--       echo "  Check the argument of --$i."
--       badvar=1
--     fi
--   done
--
--   for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
--     if test -d $i || mkdir $i; then :
--     else
--       eval echo "! No directory $i and can\'t create it."
--       badvar=1
--     fi
--   done
--else
--   # Kludge to fool the "Makefile" target in the top-level CCP4
--   # Makefile into not trying to remake src/Makefile.in
--   for i in $srcdir/src $srcdir/lib/src ; do
--     if test -d $i || mkdir $i; then
--       if ! test -f $i/Makefile.in ; then
--         echo
--         echo "onlylibs: making dummy file $i/Makefile.in"
--	 touch $i/Makefile.in
--       fi
--     fi
--   done
--fi
-+#if test -z "$onlylibs" ; then 
-+#   for i in CCP4_SCR BINSORT_SCR; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the value of $i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in libdir bindir; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the argument of --$i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
-+#     if test -d $i || mkdir $i; then :
-+#     else
-+#       eval echo "! No directory $i and can\'t create it."
-+#       badvar=1
-+#     fi
-+#   done
-+#else
-+#   # Kludge to fool the "Makefile" target in the top-level CCP4
-+#   # Makefile into not trying to remake src/Makefile.in
-+#   for i in $srcdir/src $srcdir/lib/src ; do
-+#     if test -d $i || mkdir $i; then
-+#       if ! test -f $i/Makefile.in ; then
-+#         echo
-+#         echo "onlylibs: making dummy file $i/Makefile.in"
-+#	 touch $i/Makefile.in
-+#       fi
-+#     fi
-+#   done
-+#fi
- 
- ### sanity checks
- 
diff --git a/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch b/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch
deleted file mode 100644
index a77d9494a05c..000000000000
--- a/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4-6.0.1.orig/lib/src/library_f.c	2006-06-12 07:06:22.000000000 -0700
-+++ ccp4-6.0.1/lib/src/library_f.c	2006-06-12 07:21:56.000000000 -0700
-@@ -716,7 +716,7 @@
- 
- #endif /* end of apple xlf support */
- 
--#if ( defined (__linux__) && defined (_CALL_SYSV) )
-+#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) )
- /* linuxppc xlf support */
- void gerror_ (str, Lstr)
- char *str;
diff --git a/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch
deleted file mode 100644
index 1420419ffab0..000000000000
--- a/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch
+++ /dev/null
@@ -1,87 +0,0 @@
---- ccp4-6.0.1.orig/configure	2006-06-10 17:30:02.000000000 -0700
-+++ ccp4-6.0.1/configure	2006-06-10 17:45:43.000000000 -0700
-@@ -623,45 +623,45 @@
- #     echo "! Beware -- the $system installation isn't properly tested." ; }
- syswarn='echo; echo "! Beware -- the $system installation is not properly tested."'
- 
--if test -z "$onlylibs" ; then 
--   for i in CCP4_SCR BINSORT_SCR; do
--     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
--     else
--       eval echo "! No directory \$$i and can\'t create it."
--       echo "  Check the value of $i."
--       badvar=1
--     fi
--   done
--
--   for i in libdir bindir; do
--     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
--     else
--       eval echo "! No directory \$$i and can\'t create it."
--       echo "  Check the argument of --$i."
--       badvar=1
--     fi
--   done
--
--   for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
--     if test -d $i || mkdir $i; then :
--     else
--       eval echo "! No directory $i and can\'t create it."
--       badvar=1
--     fi
--   done
--else
--   # Kludge to fool the "Makefile" target in the top-level CCP4
--   # Makefile into not trying to remake src/Makefile.in
--   for i in $srcdir/src $srcdir/lib/src ; do
--     if test -d $i || mkdir $i; then
--       if ! test -f $i/Makefile.in ; then
--         echo
--         echo "onlylibs: making dummy file $i/Makefile.in"
--	 touch $i/Makefile.in
--       fi
--     fi
--   done
--fi
-+#if test -z "$onlylibs" ; then 
-+#   for i in CCP4_SCR BINSORT_SCR; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the value of $i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in libdir bindir; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the argument of --$i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
-+#     if test -d $i || mkdir $i; then :
-+#     else
-+#       eval echo "! No directory $i and can\'t create it."
-+#       badvar=1
-+#     fi
-+#   done
-+#else
-+#   # Kludge to fool the "Makefile" target in the top-level CCP4
-+#   # Makefile into not trying to remake src/Makefile.in
-+#   for i in $srcdir/src $srcdir/lib/src ; do
-+#     if test -d $i || mkdir $i; then
-+#       if ! test -f $i/Makefile.in ; then
-+#         echo
-+#         echo "onlylibs: making dummy file $i/Makefile.in"
-+#	 touch $i/Makefile.in
-+#       fi
-+#     fi
-+#   done
-+#fi
- 
- ### sanity checks
- 
diff --git a/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch b/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch
deleted file mode 100644
index c118cc53baff..000000000000
--- a/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-https://bugs.gentoo.org/show_bug.cgi?id=175630
-JTRiley
-
---- ccp4-6.0.2.orig/src/refmac5_/make_unix_ccp4.f	2005-09-06 07:29:56.000000000 -0400
-+++ ccp4-6.0.2.new/src/refmac5_/make_unix_ccp4.f	2007-05-02 20:03:46.000000000 -0400
-@@ -97,7 +97,7 @@
- 
-       READ(CID,'(I2,1X,I2,1X,I2,2X)') IH(4),IH(3),IH(2)
- 
--      CALL IDATE(IMON,IDAY,IYR)
-+      CALL UIDATE(IMON,IDAY,IYR)
-       IF(IYR.GE.99) THEN
-         IYR=IYR+1900
-       ELSE
diff --git a/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch b/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch
deleted file mode 100644
index a77d9494a05c..000000000000
--- a/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4-6.0.1.orig/lib/src/library_f.c	2006-06-12 07:06:22.000000000 -0700
-+++ ccp4-6.0.1/lib/src/library_f.c	2006-06-12 07:21:56.000000000 -0700
-@@ -716,7 +716,7 @@
- 
- #endif /* end of apple xlf support */
- 
--#if ( defined (__linux__) && defined (_CALL_SYSV) )
-+#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) )
- /* linuxppc xlf support */
- void gerror_ (str, Lstr)
- char *str;
diff --git a/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch
deleted file mode 100644
index 106db895b775..000000000000
--- a/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- ccp4-5.99.5.orig/ccp4i/etc/configure.def.dist	2006-01-06 17:54:17.000000000 -0800
-+++ ccp4-5.99.5/ccp4i/etc/configure.def.dist	2006-01-06 17:54:47.000000000 -0800
-@@ -54,8 +54,8 @@
- MESSAGE                   _text				""
- BLT_LIBRARY               _text                     ""
- MENU_LENGTH               _positiveint              25
--HYPERTEXT_VIEWER          _text                     netscape
--START_NETSCAPE	          _text			    netscape
-+HYPERTEXT_VIEWER          _text                     firefox
-+START_NETSCAPE	          _text			    firefox
- O_MAPMAN                  _text                     mapman
- MAPMAN_MAXSIZE		  _positiveint		    4194304
- QUANTA_MBKALL             _text                     mbkall
diff --git a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch
deleted file mode 100644
index 02a2aa6d8877..000000000000
--- a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch
+++ /dev/null
@@ -1,103 +0,0 @@
---- ccp4-5.99.5.orig/configure	2006-01-17 00:35:36.000000000 -0800
-+++ ccp4-5.99.5/configure	2006-01-17 10:44:39.000000000 -0800
-@@ -2410,12 +2410,12 @@
-       end
- EOF
-           #firslty test without -lblas
--          test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack"
-+          test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lpthread"
-           echo $test_compile
-           if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then
-             # Compilation was okay
--            echo "... only -llapack needed"
--            XLAPACK_LIB="-llapack"
-+            echo "... only -llapack -lpthread needed"
-+            XLAPACK_LIB="-llapack -lpthread"
-             # Set the next two variables so that configure
-             # doesn't try to build netlib libraries
-             LAPACKLIB="lapack"
-@@ -2424,12 +2424,12 @@
-             tryblas=
-           else
- 	    echo "more than just -llapack needed...."
--            test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas"
-+            test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas -lpthread"
-             echo $test_compile
-             if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-               # Compilation was okay
--              echo "...-llapack and -lblas were needed"
--              XLAPACK_LIB="-llapack -lblas"
-+              echo "...-llapack, -lpthread and -lblas were needed"
-+              XLAPACK_LIB="-llapack -lpthread -lblas"
-               # Set the next two variables so that configure
-               # doesn't try to build netlib libraries
-               LAPACKLIB="lapack blas"
-@@ -2720,8 +2720,8 @@
-       STOP
-       END
- EOF
--                test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib"
--                test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS"
-+                test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread"
-+                test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread"
-                 echo $test_compile
-                 if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-                   have_lapack=yes
-@@ -2738,7 +2738,7 @@
-                   LAPACKDIR="$testdir"
-                   echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR"
- 		  #
--		  XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB"
-+		  XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB -lpthread"
-                   #
-                   # Test to see if we need BLAS too
-                   # Do this by trying to compile a test program
-@@ -2750,8 +2750,8 @@
-                   if test -f testlsame ; then
-                     rm -f testsame testlsame.o
-                   fi
--                  test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB"
--                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS"
-+                  test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB -lpthread"
-+                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS -lpthread"
-                   echo $test_compile
-                   if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then
-                     have_blas=yes
-@@ -2830,8 +2830,8 @@
-       STOP
-       END
- EOF
--                  test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib"
--                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS"
-+                  test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread"
-+                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread"
-                   echo $test_compile
-                   if { ( eval $test_compile) 2>&1;} && test -s testlink ; then
-                     have_blas=yes
-@@ -3033,7 +3033,7 @@
-         if test -f testlsame ; then
-           rm -f testsame testlsame.o
-         fi
--        test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB"
-+        test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB -lpthread"
-         echo $test_compile
-         if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then
-           echo "Found LSAME in lib$BLASLIB"
-@@ -3046,7 +3046,7 @@
-         if test -f testxerbla ; then
-           rm -f testxerbla testxerbla.o
-         fi
--        test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB"
-+        test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB -lpthread"
-         echo $test_compile
-         if { ( eval $test_compile) 2>&1;} && test -s testxerbla ; then
-           # Found lsame
-@@ -3080,7 +3080,7 @@
-     cd ../..
-     #
-     lapackdir=lib/lapack
--    XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB"
-+    XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB -lpthread"
- # netlib lapack is in fortran, so we may need the fortran libraries when
- # we are linking using the C or C++ compilers
-     case $system in 
diff --git a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch
deleted file mode 100644
index 3bf5a0652247..000000000000
--- a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4-5.99.5/lib/clipper/configure.orig	2006-01-07 16:54:13.000000000 -0800
-+++ ccp4-5.99.5/lib/clipper/configure	2006-01-07 16:54:31.000000000 -0800
-@@ -21751,7 +21751,7 @@
- 
- if test "x$mccp4_prefix" != x; then
-  # ie. mccp4=thing was given (thing is what we're checking for)
-- ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include"
-+ ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include -I$mccp4_prefix/include/mccp4"
-  ac_MCCP4_LDOPTS="-L$mccp4_prefix/lib -lmccp4"
- else
-  # treat as standard lib/include
diff --git a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch
deleted file mode 100644
index 34d6197572fc..000000000000
--- a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- ccp4-5.99.5.orig/x-windows/Makefile.in	2006-01-06 12:31:02.000000000 -0800
-+++ ccp4-5.99.5/x-windows/Makefile.in	2006-01-06 12:31:30.000000000 -0800
-@@ -158,6 +158,7 @@
- install_obj = ipdisp.exe hklview xdldataman xdlmapman \
- rotgen ipmosflm
- install: all
-+	mkdir -p $(bindir)
- 	$(INSTALL_PROGRAM) $(srcdir)/ipdisp.exe $(bindir)
- 	$(INSTALL_PROGRAM) $(srcdir)/ipdisp/ipdisp $(bindir)
- 	$(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir)
diff --git a/sci-chemistry/ccp4/files/dont-build-rasmol.patch b/sci-chemistry/ccp4/files/dont-build-rasmol.patch
deleted file mode 100644
index 8da54fd26de8..000000000000
--- a/sci-chemistry/ccp4/files/dont-build-rasmol.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- ccp4-5.99.5.orig/x-windows/Makefile.in	2005-12-05 03:06:57.000000000 -0800
-+++ ccp4-5.99.5/x-windows/Makefile.in	2005-12-05 03:07:23.000000000 -0800
-@@ -35,7 +35,7 @@
- #
- # all
- #
--all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy rasmol2 ipmosflm
-+all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy ipmosflm
- #
- # xdl_view
- #
-@@ -161,7 +161,6 @@
- 	$(INSTALL_PROGRAM) $(srcdir)/xdldataman $(bindir)
- 	$(INSTALL_PROGRAM) $(srcdir)/xdlmapman $(bindir)
- 	cd $(srcdir)/XCCPJIFFY ; $(MAKE) install
--	$(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir)
- 	cd $(rotgen_dir); $(MAKE) install
- 	$(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir)
- 	cd $(xdlview_dir); $(MAKE) install
diff --git a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch
deleted file mode 100644
index 7813141b2ec2..000000000000
--- a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- ccp4-5.99.5.orig/x-windows/Mosflm/mosflm/Makefile.in	2006-01-06 00:04:12.000000000 -0800
-+++ ccp4-5.99.5/x-windows/Mosflm/mosflm/Makefile.in	2006-01-06 00:04:41.000000000 -0800
-@@ -37,6 +37,7 @@
- 	${F77} ${FFLAGS} -o $@ $<
- 
- ipmosflm:	${OBJS}
-+		mkdir -p ${DPSBIN}
- 		${FLINK} ${FFLAGS} ${OBJS} ${LOCALLIBS} ${LIBS} \
-                 -o ${DPSBIN}/ipmosflm ${LDFLAGS}
- 
diff --git a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch
deleted file mode 100644
index ae4b7633b105..000000000000
--- a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4-5.99.5.orig/x-windows/Mosflm/cbf/Makefile.in	2006-01-05 23:42:19.000000000 -0800
-+++ ccp4-5.99.5/x-windows/Mosflm/cbf/Makefile.in	2006-01-05 23:43:35.000000000 -0800
-@@ -132,7 +132,7 @@
- #
- # CBF library
- #
--$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP)
-+$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB)
- 	$(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
- 	$(AR) cr $@ *.o
- 	$(RANLIB) $@
diff --git a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch
deleted file mode 100644
index 97607b689672..000000000000
--- a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- ccp4-5.99.5.orig/x-windows/Mosflm/index/Makefile.in	2006-01-05 23:15:09.000000000 -0800
-+++ ccp4-5.99.5/x-windows/Mosflm/index/Makefile.in	2006-01-05 23:15:30.000000000 -0800
-@@ -76,6 +76,7 @@
- 
- # local version of libdps_index.a
- ${LIB}/dps_index.a: ${IOBJS} ${HOBJS}
-+	mkdir -p ${LIB}
- 	ar ru ${LIB}/dps_index.a ${IOBJS} ${HOBJS}
- 
- ${LIB}/libpeak.a: 
diff --git a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch
deleted file mode 100644
index eac1b9f1721e..000000000000
--- a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- ccp4-5.99.5.orig/x-windows/Mosflm/src/dps/index/Makefile.in	2006-01-05 22:48:47.000000000 -0800
-+++ ccp4-5.99.5/x-windows/Mosflm/src/dps/index/Makefile.in	2006-01-05 22:49:02.000000000 -0800
-@@ -42,6 +42,7 @@
- 	$(LOCALLIBS) $(LIBS) 
- 
- index: $(IOBJS) 
-+	mkdir -p $(LIBDIR)
- 	${AR} $(AR_FLAGS) $(LIBDIR)/libdps_index.a $(IOBJS)
- 	chmod 644 $(LIBDIR)/libdps_index.a
- 
diff --git a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch
deleted file mode 100644
index 3e1a8b0e6be8..000000000000
--- a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4-5.99.5.orig/configure	2006-01-06 11:45:43.000000000 -0800
-+++ ccp4-5.99.5/configure	2006-01-06 11:46:53.000000000 -0800
-@@ -3210,7 +3210,7 @@
- #ccp4 setup
-   xopts="${xopts} --with-ccp4=${srcdir}"
- #interface setup
--  xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol"
-+  xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol --enable-mmdbold --enable-mtz --with-mccp4=/usr"
-   echo   
-   echo "********* CLIPPER CONFIGURATION ***********"
-   echo
diff --git a/sci-chemistry/ccp4/metadata.xml b/sci-chemistry/ccp4/metadata.xml
deleted file mode 100644
index d37774eb9ada..000000000000
--- a/sci-chemistry/ccp4/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>sci-chemistry</herd>
-	<use>
-		<flag name="balbes">Install sci-chemistry/balbes</flag>
-		<flag name="arpwarp">Add binary arp-warp for molecular replacement</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-chemistry/ccp4i/Manifest b/sci-chemistry/ccp4i/Manifest
deleted file mode 100644
index e082cb44f7fb..000000000000
--- a/sci-chemistry/ccp4i/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST 6.1.3-oasis4.0.patch.bz2 946 SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b SHA512 7c7bf4ef90550708bf41b1831dbe71c38418b46455adb3d42ec609d287894ac9260d9671f1759f71c713ced72fa004b9808391ea6874007ac8b7d7637f349d32 WHIRLPOOL a2bc27e1e054e1717c387f3800533fa490c03d1d18d3fe3cff4676f0ec47799a1681a206e01013c1b8f8e41162303446a824b86effeef2ed73f059feb07fb820
-DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c
-DIST ccp4i-6.1.3-arpwarp.patch.bz2 58498 SHA256 297e6f75354f3a1932302f7039bf449484c95eb41b8634ae96d93c754b47c687 SHA512 0bf18d9768b722c553e79eed04de316f6b0b4695f7678e1d850d5e22735ecc79cdb961ea76b6482457fff232892b81ce191cd48fa588ded8058184a871dffb65 WHIRLPOOL f24625941e31e951f13c94cf31e2ca061840b016aa3fd038d29710d9ca400d364467dc3fa1e42a55944d63ac7e42a0a6baa39a596c55b18610eeb552d232d1b8
diff --git a/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild b/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild
deleted file mode 100644
index bdfba7800493..000000000000
--- a/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild
+++ /dev/null
@@ -1,99 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils multilib python-single-r1 virtualx
-
-MY_PN="${PN%i}"
-MY_P="${MY_PN}-${PV}"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-DESCRIPTION="Protein X-ray crystallography toolkit -- graphical interface"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI="
-	${SRC}/${PV}/${MY_P}-core-src.tar.gz
-	mirror://gentoo/${P}-arpwarp.patch.bz2
-	https://dev.gentoo.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2"
-[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
-[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} https://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
-
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-LICENSE="ccp4"
-IUSE=""
-
-RDEPEND="
-	app-shells/tcsh
-	media-gfx/graphviz
-	>=dev-lang/tk-8.3:0
-	>=dev-tcltk/blt-2.4
-	sci-libs/ccp4-libs"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-fix-baubles.patch
-	"${WORKDIR}"/${P}-arpwarp.patch
-	)
-
-src_prepare() {
-	epatch ${PATCHES[@]}
-
-	[[ ! -z ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	epatch "${WORKDIR}"/${PV}-oasis4.0.patch
-	python_fix_shebang ccp4i/ share/dbccp4i/
-}
-
-src_configure() {
-	:
-}
-
-src_compile() {
-	:
-}
-
-src_install() {
-	# rm imosflm stuff
-	rm -rf "${S}"/ccp4i/{bin/imosflm,imosflm} || die
-
-	rm -rf "${S}"/ccp4i/{bin,etc}/WINDOWS || die
-
-	# This is installed by mrbump
-	rm -rf "${S}"/ccp4i/{tasks/{dbviewer.tcl,mrbump.*},templates/mrbump.com,scripts/mrbump.script} || die
-
-	# CCP4Interface - GUI
-	insinto /usr/$(get_libdir)/ccp4
-	doins -r "${S}"/ccp4i
-	exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin
-	doexe "${S}"/ccp4i/bin/*
-	dosym ../$(get_libdir)/ccp4/ccp4i/bin/ccp4i /usr/bin/ccp4i
-
-	dodir /usr/$(get_libdir)/ccp4/ccp4i/unix
-
-	# dbccp4i
-	insinto /usr/share/ccp4
-	doins -r "${S}"/share/dbccp4i
-}
-
-pkg_postinst() {
-	_ccp4-setup() {
-		source "${EPREFIX}/etc/profile"
-		export USER=root
-		bash "${EPREFIX}"/usr/$(get_libdir)/ccp4/ccp4i/bin/ccp4i -h > /dev/null
-	}
-	VIRTUALX_COMMAND="_ccp4-setup" virtualmake
-	echo ""
-	elog "ccp4i needs some enviromental settings. So please"
-	elog "\t source ${EPREFIX}/etc/profile"
-	echo ""
-}
diff --git a/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch b/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch
deleted file mode 100644
index 2c5f659b8018..000000000000
--- a/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- ccp4i/etc/configure.def.dist	2009-01-09 16:45:08.000000000 +0100
-+++ ccp4i/etc/configure.def.dist.new	2009-07-07 23:17:26.000000000 +0200
-@@ -53,8 +53,8 @@
- RUN_IMOSFLM               _text "ccp4iwish [file join [GetEnvPath CCP4I_TOP] imosflm imosflm.tcl] project [GetCurrentProjectDir [GetCurrentProject]]"
- RUN_CCP4MG                _text                     "ccp4mg"
- RUN_COOT                  _text                     "coot"
--RUN_BAUBLES               _text                     "python [file join [GetEnvPath CCP4] share smartie baubles.py]"
--RUN_DBVIEWER              _text                     "wish [file join [GetEnvPath CCP4] share dbccp4i application viewer.tcl]"
-+RUN_BAUBLES               _text                     "python [file join [GetEnvPath CCP4] share ccp4 smartie baubles.py]"
-+RUN_DBVIEWER              _text                     "wish [file join [GetEnvPath DBCCP4I_TOP] application viewer.tcl]"
- ENABLE_BUBBLE_HELP        _logical                  1
- DISABLE_TASKS             _logical                  1
- CCP4_SETUP_COMMAND        _text                     setup_ccp4
-@@ -62,7 +62,7 @@
- BLT_LIBRARY               _text                     ""
- MENU_LENGTH               _positiveint              25
- HYPERTEXT_VIEWER          _text                     firefox
--START_NETSCAPE	          _text			    netscape
-+START_NETSCAPE	          _text			    firefox
- O_MAPMAN                  _text                     mapman
- MAPMAN_MAXSIZE		  _positiveint		    4194304
- QUANTA_MBKALL             _text                     mbkall
diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch
deleted file mode 100644
index 9f5cfb4b635f..000000000000
--- a/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff --git a/ccp4i/scripts/check.script b/ccp4i/scripts/check.script
-index def44bc..dd4bb7e 100755
---- a/ccp4i/scripts/check.script
-+++ b/ccp4i/scripts/check.script
-@@ -24,7 +24,7 @@
-   if $RUN_RAMPAGE {
- 
-     # Generate command line
--    set cmd "[BinPath rapper]"
-+    set cmd "[BinPath rappermc]"
- 
-     set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper]
-     set paramsfile [FileJoin $rapperdatadir params.xml]
-diff --git a/ccp4i/scripts/rapper.script b/ccp4i/scripts/rapper.script
-index cdae1e2..faae226 100755
---- a/ccp4i/scripts/rapper.script
-+++ b/ccp4i/scripts/rapper.script
-@@ -17,7 +17,7 @@
- 
- #set up command line 
- 
--set cmd "[BinPath rapper]"
-+set cmd "[BinPath rappermc]"
- 
- set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper]
- set paramsfile [FileJoin [GetEnvPath CCP4] share rapper params.xml]
-@@ -180,7 +180,7 @@ append outfiles " $XYZOUT PROJECT"
- 
- # Run RAPPER to join loop back to framework and out put to defined pdb file
- # Also need to sort out multimodel files join - FIX ME
--set cmd2 "[BinPath rapper]"
-+set cmd2 "[BinPath rappermc]"
- append cmd2 " $paramsfile joinpdb "
- append cmd2 " --pdb2 \"$root\-loop.pdb\" "
- append cmd2 " --pdb  \"$root\-framework.pdb\" "
-diff --git a/ccp4i/tasks/check.tcl b/ccp4i/tasks/check.tcl
-index ae88ff2..ee3307b 100755
---- a/ccp4i/tasks/check.tcl
-+++ b/ccp4i/tasks/check.tcl
-@@ -46,7 +46,7 @@ proc check_run { arrayname } {
-  # Check for Rampage program. If it is not found, we switch off the option.
-  # If it was the only option, script will fail with next check.
-  if { $array(RUN_RAMPAGE) == 1 } {
--   if { [FindExecutable "rapper"] == "" } {
-+   if { [FindExecutable "rappermc"] == "" } {
-       WarningMessage "Input Error: Rapper_Rampage program not found in system path."
-       set array(RUN_RAMPAGE) 0
-     }
-diff --git a/ccp4i/tasks/rapper.tcl b/ccp4i/tasks/rapper.tcl
-index e299057..8843a3f 100755
---- a/ccp4i/tasks/rapper.tcl
-+++ b/ccp4i/tasks/rapper.tcl
-@@ -28,7 +28,7 @@ proc rapper_run { arrayname } {
-  # Check for RAPPER program. If it is not found, we switch off the option.
-  # If it was the only option, script will fail with next check.
-   if { [regexp MODEL $build_type ] && $prog_type == "RAPPER"} {
--   if { [FindExecutable "rapper"] == "" } {
-+   if { [FindExecutable "rappermc"] == "" } {
-       WarningMessage "Input Error: RAPPER program not found in system path."
-       set build_type 0
-     }
diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch
deleted file mode 100644
index 74cd2b946601..000000000000
--- a/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-diff --git a/ccp4i/scripts/superpose.script b/ccp4i/scripts/superpose.script
-index 3483c97..5027536 100755
---- a/ccp4i/scripts/superpose.script
-+++ b/ccp4i/scripts/superpose.script
-@@ -21,7 +21,7 @@
- 
-   if { [regexp SSM $SUPERPOSE_MODE ] } {
- 
--    set cmd "[BinPath superpose] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\""
-+    set cmd "[BinPath superpose-ccp4] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\""
-     set status [Execute $cmd "" program_status report ]
- 
-   } elseif { [regexp TOP $SUPERPOSE_MODE ] } {
-diff --git a/ccp4i/tasks/superpose.tcl b/ccp4i/tasks/superpose.tcl
-index 748bf6e..c92122a 100755
---- a/ccp4i/tasks/superpose.tcl
-+++ b/ccp4i/tasks/superpose.tcl
-@@ -100,7 +100,7 @@ proc superpose_run { arrayname } {
- # If user is match equivalent named residues/atoms then fit in the match fields
-   switch [GetValue $arrayname SUPERPOSE_MODE] \
-   SSM {
--    if { ![file exists [FindExecutable superpose]] } {
-+    if { ![file exists [FindExecutable superpose-ccp4]] } {
-        WarningMessage "The program \"superpose\" is not on your path. 
- Check your installation for \"superpose\" program and \"ssm\" library."
-        return 0
diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch
deleted file mode 100644
index 9af60b7c5152..000000000000
--- a/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch
+++ /dev/null
@@ -1,91 +0,0 @@
-diff --git a/ccp4i/crank/plugins/prep/crank_prep.tcl b/ccp4i/crank/plugins/prep/crank_prep.tcl
-index 7d05905..d01f1dc 100755
---- a/ccp4i/crank/plugins/prep/crank_prep.tcl
-+++ b/ccp4i/crank/plugins/prep/crank_prep.tcl
-@@ -226,7 +226,7 @@ proc run_truncate { i j } {
-     set script "$script\n$labout"
-     set script "$script\nEND\n"
- 	
--    set run_command "truncate $command << \"$script\""
-+    set run_command "ftruncate $command << \"$script\""
-     puts $run_command
-     catch {eval exec $run_command } output 
-     puts $output
-diff --git a/ccp4i/scripts/dtrek2mtz.script b/ccp4i/scripts/dtrek2mtz.script
-index e74aa0d..a2a1adb 100755
---- a/ccp4i/scripts/dtrek2mtz.script
-+++ b/ccp4i/scripts/dtrek2mtz.script
-@@ -36,7 +36,7 @@
-     set HKL_TRUNCATE [GetTmpFileName -ext mtz]
- 
-     CreateComScript truncate truncate_script
--    set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
-+    set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
-     set status [Execute $cmd $truncate_script program_status report]
- 
-     HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate
-diff --git a/ccp4i/scripts/import.script b/ccp4i/scripts/import.script
-index 90cba83..1c90c33 100755
---- a/ccp4i/scripts/import.script
-+++ b/ccp4i/scripts/import.script
-@@ -144,7 +144,7 @@ if { $FORMAT ==  "MTZ" } {
- 
-     set truncatemtz [GetTmpFileName -ext mtz ]
-     CreateComScript truncate truncate_script
--    set cmd "[BinPath truncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\""
-+    set cmd "[BinPath ftruncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\""
-     set status [Execute $cmd $truncate_script program_status report]
- 
- 
-diff --git a/ccp4i/scripts/import_scaled.script b/ccp4i/scripts/import_scaled.script
-index dcc619b..7250513 100755
---- a/ccp4i/scripts/import_scaled.script
-+++ b/ccp4i/scripts/import_scaled.script
-@@ -62,7 +62,7 @@
- 
-     } else {
-       CreateComScript truncate truncate_script
--      set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
-+      set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
-       set status [Execute $cmd $truncate_script program_status report]
- 
-       HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate
-diff --git a/ccp4i/scripts/scala.script b/ccp4i/scripts/scala.script
-index 6940ccd..bde10d6 100755
---- a/ccp4i/scripts/scala.script
-+++ b/ccp4i/scripts/scala.script
-@@ -275,7 +275,7 @@ END"
- 
-       } else {
-         CreateComScript truncate truncate_script
--        set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""  
-+        set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""  
-         set status [Execute $cmd $truncate_script $LOG_FILE  program_status report  ]
-       }
-           
-diff --git a/ccp4i/scripts/scalepack2mtz.script b/ccp4i/scripts/scalepack2mtz.script
-index 986e06c..a1947a6 100755
---- a/ccp4i/scripts/scalepack2mtz.script
-+++ b/ccp4i/scripts/scalepack2mtz.script
-@@ -35,7 +35,7 @@
- 
-     set HKL_TRUNCATE [GetTmpFileName -ext mtz]
-     CreateComScript truncate truncate_script
--    set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
-+    set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
-     set status [Execute $cmd $truncate_script program_status report]
- 
-     HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate
-diff --git a/ccp4i/scripts/truncate.script b/ccp4i/scripts/truncate.script
-index e0e09ce..2d448a2 100755
---- a/ccp4i/scripts/truncate.script
-+++ b/ccp4i/scripts/truncate.script
-@@ -45,7 +45,7 @@
- 
-   CreateComScript truncate truncate_script
- 
--  set cmd "[BinPath truncate] HKLIN \"$HKLIN\""
-+  set cmd "[BinPath ftruncate] HKLIN \"$HKLIN\""
-   if { ![StringSame $INPUT_DATA AMPLITUDES] } {
-     append cmd " HKLOUT \"$HKL_TRUNCATE\""
-   }
diff --git a/sci-chemistry/ccp4i/metadata.xml b/sci-chemistry/ccp4i/metadata.xml
deleted file mode 100644
index 51fdedab1b38..000000000000
--- a/sci-chemistry/ccp4i/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-</pkgmetadata>
diff --git a/sci-chemistry/coot/coot-0.7.1-r1.ebuild b/sci-chemistry/coot/coot-0.7.1-r1.ebuild
deleted file mode 100644
index 001145ee18ee..000000000000
--- a/sci-chemistry/coot/coot-0.7.1-r1.ebuild
+++ /dev/null
@@ -1,167 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-AUTOTOOLS_AUTORECONF="true"
-
-inherit autotools-utils python-single-r1 toolchain-funcs versionator
-
-MY_S2_PV=$(replace_version_separator 2 - ${PV})
-MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
-MY_S_P=${MY_S2_P}-${PR/r/revision-}
-MY_PV=${PV}
-MY_P=${PN}-${MY_PV}
-
-DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
-HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/"
-SRC_URI="
-	http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/${MY_P}.tar.gz
-	test? ( https://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz  )"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+openmp static-libs test"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-SCIDEPS="
-	>=sci-libs/ccp4-libs-6.1
-	sci-libs/clipper
-	>=sci-libs/coot-data-2
-	>=sci-libs/gsl-1.3
-	>=sci-libs/mmdb-1.23:0
-	sci-libs/ssm
-	sci-libs/monomer-db
-	sci-chemistry/reduce
-	sci-chemistry/refmac
-	sci-chemistry/probe"
-
-XDEPS="
-	gnome-base/libgnomecanvas
-	gnome-base/librsvg:2
-	media-libs/libpng
-	media-libs/freeglut
-	x11-libs/gtk+:2
-	x11-libs/goocanvas:0
-	x11-libs/gtkglext"
-
-SCHEMEDEPS="
-	dev-scheme/net-http
-	dev-scheme/guile-gui
-	>=dev-scheme/guile-lib-0.1.6
-	dev-scheme/guile-www
-	>=x11-libs/guile-gtk-2.1"
-
-RDEPEND="
-	${SCIDEPS}
-	${XDEPS}
-	${SCHEMEDEPS}
-	${PYTHON_DEPS}
-	dev-python/pygtk:2[${PYTHON_USEDEP}]
-	>=dev-libs/gmp-4.2.2-r2
-	>=net-misc/curl-7.19.6
-	net-dns/libidn"
-DEPEND="${RDEPEND}
-	>=sys-devel/libtool-2.4-r2
-	dev-lang/swig
-	sys-devel/bc
-	test? ( dev-scheme/greg )"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
-	if use openmp; then
-		tc-has-openmp || die "Please use an OPENMP capable compiler"
-	fi
-	python-single-r1_pkg_setup
-}
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-0.7-clipper-config.patch
-	"${FILESDIR}"/${PN}-0.7-goocanvas.patch
-	"${FILESDIR}"/${PN}-0.7-mmdb-config.patch
-	"${FILESDIR}"/${PN}-0.7-ssm.patch
-	)
-
-src_prepare() {
-	sed \
-		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
-		-i configure.in || die
-
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	# All the --with's are used to activate various parts.
-	# Yes, this is broken behavior.
-	local myeconfargs=(
-		--includedir='${prefix}/include/coot'
-		--with-goocanvas-prefix="${EPREFIX}/usr"
-		--with-guile
-		--with-python="${EPREFIX}/usr"
-		--with-guile-gtk
-		--with-gtk2
-		--with-pygtk
-		$(use_enable openmp)
-		)
-	autotools-utils_src_configure
-}
-
-src_test() {
-	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
-	mkdir "${T}"/coot_test
-
-	export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
-	export COOT_SCHEME_DIR="${S}/scheme/"
-	export COOT_RESOURCES_FILE="${S}/cootrc"
-	export COOT_PIXMAPS_DIR="${S}/pixmaps/"
-	export COOT_DATA_DIR="${S}/"
-	export COOT_PYTHON_DIR="${S}/python/"
-	export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
-	export PYTHONHOME="${EPREFIX}"/usr/
-	export CCP4_SCR="${T}"/coot_test/
-	export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/"
-	export SYMINFO="${S}/syminfo.lib"
-
-	export COOT_TEST_DATA_DIR="${WORKDIR}"/greg-data
-
-	cat > command-line-greg.scm <<- EOF
-	(use-modules (ice-9 greg))
-		(set! greg-tools (list "greg-tests"))
-			(set! greg-debug #t)
-			(set! greg-verbose 5)
-			(let ((r (greg-test-run)))
-				(if r
-				(coot-real-exit 0)
-				(coot-real-exit 1)))
-	EOF
-
-	einfo "Running test with following paths ..."
-	einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES"
-	einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR"
-	einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE"
-	einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR"
-	einfo "COOT_DATA_DIR $COOT_DATA_DIR"
-	einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR"
-	einfo "PYTHONPATH $PYTHONPATH"
-	einfo "PYTHONHOME $PYTHONHOME"
-	einfo "CCP4_SCR ${CCP4_SCR}"
-	einfo "CLIBD_MON ${CLIBD_MON}"
-	einfo "SYMINFO ${SYMINFO}"
-
-	"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
-	"${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die
-}
-
-src_install() {
-	autotools-utils_src_install
-	insinto /usr/share/${PN}
-	doins syminfo.lib
-}
diff --git a/sci-chemistry/coot/coot-0.7.2.ebuild b/sci-chemistry/coot/coot-0.7.2.ebuild
deleted file mode 100644
index 0e14d4464539..000000000000
--- a/sci-chemistry/coot/coot-0.7.2.ebuild
+++ /dev/null
@@ -1,165 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-AUTOTOOLS_AUTORECONF="true"
-
-inherit autotools-utils python-single-r1 toolchain-funcs versionator
-
-MY_S2_PV=$(replace_version_separator 2 - ${PV})
-MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
-MY_S_P=${MY_S2_P}-${PR/r/revision-}
-MY_PV=${PV}
-MY_P=${PN}-${MY_PV}
-
-DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
-HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/"
-SRC_URI="
-	http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/${MY_P}.tar.gz
-	test? ( https://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz  )"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="+openmp static-libs test"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-SCIDEPS="
-	>=sci-libs/ccp4-libs-6.1
-	sci-libs/clipper
-	>=sci-libs/coot-data-2
-	>=sci-libs/gsl-1.3
-	>=sci-libs/mmdb-1.23:0
-	sci-libs/ssm
-	sci-libs/monomer-db
-	sci-chemistry/reduce
-	sci-chemistry/refmac
-	sci-chemistry/probe"
-
-XDEPS="
-	gnome-base/libgnomecanvas
-	gnome-base/librsvg:2
-	media-libs/libpng
-	media-libs/freeglut
-	x11-libs/gtk+:2
-	x11-libs/goocanvas:0
-	x11-libs/gtkglext"
-
-SCHEMEDEPS="
-	dev-scheme/net-http
-	dev-scheme/guile-gui
-	>=dev-scheme/guile-lib-0.1.6
-	dev-scheme/guile-www
-	>=x11-libs/guile-gtk-2.1"
-
-RDEPEND="
-	${SCIDEPS}
-	${XDEPS}
-	${SCHEMEDEPS}
-	${PYTHON_DEPS}
-	dev-python/pygtk:2[${PYTHON_USEDEP}]
-	>=dev-libs/gmp-4.2.2-r2
-	>=net-misc/curl-7.19.6
-	net-dns/libidn"
-DEPEND="${RDEPEND}
-	>=sys-devel/libtool-2.4-r2
-	dev-lang/swig
-	sys-devel/bc
-	test? ( dev-scheme/greg )"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
-	if use openmp; then
-		tc-has-openmp || die "Please use an OPENMP capable compiler"
-	fi
-	python-single-r1_pkg_setup
-}
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-0.7-clipper-config.patch
-	"${FILESDIR}"/${PN}-0.7-goocanvas.patch
-	"${FILESDIR}"/${PN}-0.7-mmdb-config.patch
-	)
-
-src_prepare() {
-	sed \
-		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
-		-i configure.in || die
-
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	# All the --with's are used to activate various parts.
-	# Yes, this is broken behavior.
-	local myeconfargs=(
-		--includedir='${prefix}/include/coot'
-		--with-goocanvas-prefix="${EPREFIX}/usr"
-		--with-guile
-		--with-python="${EPREFIX}/usr"
-		--with-guile-gtk
-		--with-gtk2
-		--with-pygtk
-		$(use_enable openmp)
-		)
-	autotools-utils_src_configure
-}
-
-src_compile() {
-	autotools-utils_src_compile
-	cp "${S}"/src/coot_gtk2.py python/coot.py || die
-}
-
-src_test() {
-	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
-	mkdir "${T}"/coot_test
-
-	export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
-	export COOT_SCHEME_DIR="${S}/scheme/"
-	export COOT_RESOURCES_FILE="${S}/cootrc"
-	export COOT_PIXMAPS_DIR="${S}/pixmaps/"
-	export COOT_DATA_DIR="${S}/"
-	export COOT_PYTHON_DIR="${S}/python/"
-	export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
-	export PYTHONHOME="${EPREFIX}"/usr/
-	export CCP4_SCR="${T}"/coot_test/
-	export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/"
-	export SYMINFO="${S}/syminfo.lib"
-
-	export COOT_TEST_DATA_DIR="${WORKDIR}"/greg-data
-
-	cat > command-line-greg.scm <<- EOF
-	(use-modules (ice-9 greg))
-		(set! greg-tools (list "greg-tests"))
-			(set! greg-debug #t)
-			(set! greg-verbose 5)
-			(let ((r (greg-test-run)))
-				(if r
-				(coot-real-exit 0)
-				(coot-real-exit 1)))
-	EOF
-
-	einfo "Running test with following paths ..."
-	einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES"
-	einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR"
-	einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE"
-	einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR"
-	einfo "COOT_DATA_DIR $COOT_DATA_DIR"
-	einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR"
-	einfo "PYTHONPATH $PYTHONPATH"
-	einfo "PYTHONHOME $PYTHONHOME"
-	einfo "CCP4_SCR ${CCP4_SCR}"
-	einfo "CLIBD_MON ${CLIBD_MON}"
-	einfo "SYMINFO ${SYMINFO}"
-
-	"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
-	"${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die
-}
diff --git a/sci-chemistry/coot/coot-0.7.ebuild b/sci-chemistry/coot/coot-0.7.ebuild
deleted file mode 100644
index f5cdfa54b525..000000000000
--- a/sci-chemistry/coot/coot-0.7.ebuild
+++ /dev/null
@@ -1,159 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-PYTHON_DEPEND="2"
-
-AUTOTOOLS_AUTORECONF="true"
-
-inherit autotools-utils python toolchain-funcs versionator
-
-MY_S2_PV=$(replace_version_separator 2 - ${PV})
-MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
-MY_S_P=${MY_S2_P}-${PR/r/revision-}
-MY_PV=${PV}
-MY_P=${PN}-${MY_PV}
-
-DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
-HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/"
-SRC_URI="
-	http://www.biop.ox.ac.uk/coot/software/source/releases/${MY_P}.tar.gz
-	test? ( https://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz  )"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="+openmp static-libs test"
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-SCIDEPS="
-	>=sci-libs/ccp4-libs-6.1
-	sci-libs/clipper
-	>=sci-libs/coot-data-2
-	>=sci-libs/gsl-1.3
-	>=sci-libs/mmdb-1.23:0
-	sci-libs/ssm
-	<sci-libs/monomer-db-1
-	sci-chemistry/reduce
-	<sci-chemistry/refmac-5.6
-	sci-chemistry/probe"
-
-XDEPS="
-	gnome-base/libgnomecanvas
-	gnome-base/librsvg:2
-	media-libs/libpng
-	media-libs/freeglut
-	x11-libs/gtk+:2
-	x11-libs/goocanvas:0
-	x11-libs/gtkglext"
-
-SCHEMEDEPS="
-	dev-scheme/net-http
-	dev-scheme/guile-gui
-	>=dev-scheme/guile-lib-0.1.6
-	dev-scheme/guile-www
-	>=x11-libs/guile-gtk-2.1"
-
-RDEPEND="
-	${SCIDEPS}
-	${XDEPS}
-	${SCHEMEDEPS}
-	dev-python/pygtk:2
-	>=dev-libs/gmp-4.2.2-r2
-	>=net-misc/curl-7.19.6
-	net-dns/libidn"
-DEPEND="${RDEPEND}
-	>=sys-devel/libtool-2.4-r2
-	dev-lang/swig
-	sys-devel/bc
-	test? ( dev-scheme/greg )"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
-	if use openmp; then
-		tc-has-openmp || die "Please use an OPENMP capable compiler"
-	fi
-	python_set_active_version 2
-	python_pkg_setup
-}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-clipper-config.patch
-	"${FILESDIR}"/${P}-goocanvas.patch
-	"${FILESDIR}"/${P}-mmdb-config.patch
-	"${FILESDIR}"/${P}-ssm.patch
-	)
-
-src_prepare() {
-	sed \
-		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-$(PYTHON)-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
-		-i configure.in || die
-
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	# All the --with's are used to activate various parts.
-	# Yes, this is broken behavior.
-	local myeconfargs=(
-		--includedir='${prefix}/include/coot'
-		--with-goocanvas-prefix="${EPREFIX}/usr"
-		--with-guile
-		--with-python="${EPREFIX}/usr"
-		--with-guile-gtk
-		--with-gtk2
-		--with-pygtk
-		$(use_enable openmp)
-		)
-	autotools-utils_src_configure
-}
-
-src_test() {
-	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
-	mkdir "${T}"/coot_test
-
-	export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
-	export COOT_SCHEME_DIR="${S}/scheme/"
-	export COOT_RESOURCES_FILE="${S}/cootrc"
-	export COOT_PIXMAPS_DIR="${S}/pixmaps/"
-	export COOT_DATA_DIR="${S}/"
-	export COOT_PYTHON_DIR="${S}/python/"
-	export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
-	export PYTHONHOME="${EPREFIX}"/usr/
-	export CCP4_SCR="${T}"/coot_test/
-	export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/"
-	export SYMINFO="${S}/syminfo.lib"
-
-	export COOT_TEST_DATA_DIR="${WORKDIR}"/data/greg-data
-
-	cat > command-line-greg.scm <<- EOF
-	(use-modules (ice-9 greg))
-		(set! greg-tools (list "greg-tests"))
-			(set! greg-debug #t)
-			(set! greg-verbose 5)
-			(let ((r (greg-test-run)))
-				(if r
-				(coot-real-exit 0)
-				(coot-real-exit 1)))
-	EOF
-
-	einfo "Running test with following paths ..."
-	einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES"
-	einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR"
-	einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE"
-	einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR"
-	einfo "COOT_DATA_DIR $COOT_DATA_DIR"
-	einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR"
-	einfo "PYTHONPATH $PYTHONPATH"
-	einfo "PYTHONHOME $PYTHONHOME"
-	einfo "CCP4_SCR ${CCP4_SCR}"
-	einfo "CLIBD_MON ${CLIBD_MON}"
-	einfo "SYMINFO ${SYMINFO}"
-
-	"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
-	"${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die
-}
diff --git a/sci-chemistry/imosflm/Manifest b/sci-chemistry/imosflm/Manifest
deleted file mode 100644
index 2ce7d893b7fd..000000000000
--- a/sci-chemistry/imosflm/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST imosflm-1.0.7.zip 941784 SHA256 b067261b4d7ef2f1f7581ddeaa08252d29f889acf89ce190eb0d8b30aa94b107 SHA512 f3163e1f71c5b1e24d6b3fbd5a040bbcebae25485d1258eef4b2725821f5f96c1260adb2bcc3ab57179d7b9b9e538ddf0494ab9b5be259b98d138fddacec8c77 WHIRLPOOL bd2b6bcdcc241fde41fe2ba99bd1e2f47bc444c46ee36a5b332d5c018b81a9d649378110a8bffa48ffc67a19b04ede7e61846b53a250e5fe3058ec0313fda80c
diff --git a/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch b/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch
deleted file mode 100644
index 5d0dd7010910..000000000000
--- a/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/c/tkImageLoad.c b/c/tkImageLoad.c
-index e7c46f0..1496a15 100755
---- a/c/tkImageLoad.c
-+++ b/c/tkImageLoad.c
-@@ -12,6 +12,7 @@
- #include <tcl.h>
- #include <tk.h>
- #include <assert.h>
-+#include <stdlib.h>
- 
- #define HEADER_LINE_LENGTH 512
- #define BYTES_PER_PIXEL 2
diff --git a/sci-chemistry/imosflm/files/1.0.4-tk.patch b/sci-chemistry/imosflm/files/1.0.4-tk.patch
deleted file mode 100644
index a90175194eb4..000000000000
--- a/sci-chemistry/imosflm/files/1.0.4-tk.patch
+++ /dev/null
@@ -1,50 +0,0 @@
---- c/tkImageLoad.c	2009-08-14 21:10:19.000000000 +0200
-+++ c/tkImageLoad.c.new	2009-08-14 21:10:55.000000000 +0200
-@@ -19,6 +19,7 @@
- //#define BLOCKED 1
- //#define UNBLOCKED 1
- #define IN_BLOCK_FLIP 1
-+#define USE_COMPOSITELESS_PHOTO_PUT_BLOCK
- 
- /* *********************************************************************/
- 
---- c/tkImageLoad.c	2009-08-14 21:13:29.000000000 +0200
-+++ c/tkImageLoad.c.new	2009-08-14 21:14:59.000000000 +0200
-@@ -272,9 +272,11 @@
-   }
-   /* put the photo block into the image */
- #ifdef __alpha
--  Tk_PhotoPutBlock(dp, &db, 0, 0, width, height);
-+  Tk_PhotoPutBlock(dp, &db, 0, 0, width, height,
-+  TK_PHOTO_COMPOSITE_OVERLAY);
- #else
--  Tk_PhotoPutBlock(dp, &db, 0, 0, width, height, TK_PHOTO_COMPOSITE_SET);
-+  Tk_PhotoPutBlock(dp, &db, 0, 0, width, height, TK_PHOTO_COMPOSITE_SET,
-+  TK_PHOTO_COMPOSITE_OVERLAY);
- #endif
- 
-   /* Free the photo block's memory now it is finished with */
-@@ -417,9 +419,11 @@
- 
-   /* put the photo block back into the image */
- #ifdef __alpha
-- Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height);
-+ Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height,
-+ TK_PHOTO_COMPOSITE_OVERLAY);
- #else
-- Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height,TK_PHOTO_COMPOSITE_SET);
-+ Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height,TK_PHOTO_COMPOSITE_SET,
-+ TK_PHOTO_COMPOSITE_OVERLAY);
- #endif
-   /* Free the photo block's memory now it is finished with */
-   if (block.pixelPtr) {
---- c/tkImageLoad.c	2009-08-14 21:15:06.000000000 +0200
-+++ c/tkImageLoad.c.new	2009-08-14 21:16:53.000000000 +0200
-@@ -9,6 +9,7 @@
- \************************************************************************/
- 
- #include <stdio.h>
-+#include <string.h>
- #include <tcl.h>
- #include <tk.h>
- #include <assert.h>
diff --git a/sci-chemistry/imosflm/files/1.0.7-libpng16.patch b/sci-chemistry/imosflm/files/1.0.7-libpng16.patch
deleted file mode 100644
index 27efc6f36f4b..000000000000
--- a/sci-chemistry/imosflm/files/1.0.7-libpng16.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-http://bugs.gentoo.org/467036
-
---- src/contrast.tcl
-+++ src/contrast.tcl
-@@ -3,7 +3,7 @@
- 
- package require palette
- 
--image create photo ::img::pixel_count_v -data "iVBORw0KGgoAAAANSUhEUgAAAA4AAABCCAIAAAGft0AHAAAABGdBTUEAAYagMeiWXwAAASFJREFUKJGtVFEWhCAINJ9H4f4n4jD7YauAA1jGT2EwAxNyMXMppZZu3bv6Q3t3iH7ob3fOPz3wdLoi7y8V1SOZp0NE02Hm7quc6VSVaokFKzMD8qKUUd0tyEQ0z1DchNQaud+JCHclzeIDOUCle7EjcA/XPZU4Klb9y2GDY68LVe8YiAihmXT052G9SQ0+m4yN2J7EZqrvnZpheMdGRLnq5/ViddTusPeux9o5G7fdsskrV9ej8rw3I80LhNUUgqmvwCY8izozZcvo5tGt1owfoGJhoEVtgcXg2da2gJa0JYESseRJ8gvyOYSGlxUkScYFoBoJB+RZrR+H2sWx2vEQrnv0pa4HYkFqF7UHrefRdjE5zQQFAp/Nqwf8XNePZ+AHq5sOPlXtupMAAAAASUVORK5CYII="
-+image create photo ::img::pixel_count_v -data "iVBORw0KGgoAAAANSUhEUgAAAA4AAABCCAIAAAGft0AHAAAABGdBTUEAAYagMeiWXwAAASFJREFUeJytVFEWhCAINJ9H4f4n4jD7YauAA1jGT2EwAxNyMXMppZZu3bv6Q3t3iH7ob3fOPz3wdLoi7y8V1SOZp0NE02Hm7quc6VSVaokFKzMD8qKUUd0tyEQ0z1DchNQaud+JCHclzeIDOUCle7EjcA/XPZU4Klb9y2GDY68LVe8YiAihmXT052G9SQ0+m4yN2J7EZqrvnZpheMdGRLnq5/ViddTusPeux9o5G7fdsskrV9ej8rw3I80LhNUUgqmvwCY8izozZcvo5tGt1owfoGJhoEVtgcXg2da2gJa0JYESseRJ8gvyOYSGlxUkScYFoBoJB+RZrR+H2sWx2vEQrnv0pa4HYkFqF7UHrefRdjE5zQQFAp/Nqwf8XNePZ+AHq5sOPv4fGP4AAAAASUVORK5CYII="
- 
- class Contrast {
-     inherit Palette
diff --git a/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild b/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild
deleted file mode 100644
index e49667e50dc7..000000000000
--- a/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils multilib toolchain-funcs versionator
-
-MY_PV="$(delete_all_version_separators ${PV})"
-
-DESCRIPTION="A new GUI for the Mosflm crystallographic data processing tool"
-HOMEPAGE="http://www.mrc-lmb.cam.ac.uk/harry/imosflm"
-SRC_URI="${HOMEPAGE}/ver${MY_PV}/downloads/${P}.zip"
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	dev-lang/tcl:0=
-	>=dev-tcltk/itcl-3.3
-	>=dev-tcltk/itk-3.3
-	>=dev-tcltk/iwidgets-4
-	>=dev-tcltk/tdom-0.8
-	>=dev-tcltk/tkimg-1.3
-	>=dev-tcltk/tktreectrl-2.1
-	dev-tcltk/anigif
-	dev-tcltk/combobox
-	dev-tcltk/tablelist
-	>=sci-chemistry/mosflm-7.0.9"
-DEPEND="app-arch/unzip"
-
-S=${WORKDIR}/${PN}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-libpng16.patch
-}
-
-src_install(){
-	rm -rf lib/{*.so,anigif,combobox}
-
-	insinto /usr/$(get_libdir)/${PN}
-	doins -r "${S}"/{src,bitmaps,lib}
-	fperms 775 /usr/$(get_libdir)/${PN}/src/imosflm
-
-	cat >> "${T}"/23imosflm <<- EOF
-	IMOSFLM_VERSION="${PV}"
-	EOF
-
-	doenvd "${T}"/23imosflm
-
-	make_wrapper imosflm /usr/$(get_libdir)/${PN}/src/imosflm
-}
diff --git a/sci-chemistry/imosflm/metadata.xml b/sci-chemistry/imosflm/metadata.xml
deleted file mode 100644
index 51fdedab1b38..000000000000
--- a/sci-chemistry/imosflm/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-</pkgmetadata>
diff --git a/sci-chemistry/makecif/Manifest b/sci-chemistry/makecif/Manifest
deleted file mode 100644
index b489a33454fd..000000000000
--- a/sci-chemistry/makecif/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST makecif-5.6.6.tar.gz 3797710 SHA256 fdcc1bee70583da3161f0d46eb792d965c04f08f0ad3033f730486550e859d1f SHA512 874c69d85b55ef22057c1113418218d7fd0a1e795f04673f3d64cd015230ab47ad8bdb0277ca9b389cc3edf397dc63c2c1cdd35837a86bc5d2a595d9ae534dbc WHIRLPOOL 5ecc1f7d06445d34e1d5d97ad98fd4c9d21db1e1611a9d89e25f0228a7b2cce5fa631b470687b3e6f7085c932cee6c5d8d4da2e6473406a22d63a26645f56be7
diff --git a/sci-chemistry/makecif/files/5.6.6-makefile.patch b/sci-chemistry/makecif/files/5.6.6-makefile.patch
deleted file mode 100644
index 186abb92b7d8..000000000000
--- a/sci-chemistry/makecif/files/5.6.6-makefile.patch
+++ /dev/null
@@ -1,49 +0,0 @@
-diff --git a/src/makefile b/src/makefile
-index 6c8264a..acdec20 100755
---- a/src/makefile
-+++ b/src/makefile
-@@ -22,6 +22,8 @@ MAKEDIC = $(MAKECIF)/dic/
- # setenv BLANC_FORT "f77  -O1" 
- #
- 
-+all: makecif_all libcheck_all modcheck_all emin_all
-+
- clean:
- 	rm -f temp_makecif_path.fh
- 	rm -f ../bin/*
-@@ -118,7 +120,7 @@ makecif.o: makecif.f  lib_com.fh crd_com.fh
- 	$(BLANC_FORT) -c makecif.f  
- 
- mkcif: main_makecif.o make_lib11.o make_lib12.o make_lib2.o make_vdw.o make_CIF.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_PDB.o makecif.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o libcheck.o 
--	$(BLANC_FORT) -o ../bin/makecif main_makecif.o makecif.o make_vdw.o make_CIF.o make_PDB.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_unix.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o  libcheck.o 
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/makecif main_makecif.o makecif.o make_vdw.o make_CIF.o make_PDB.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_unix.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o  libcheck.o 
- # -------------
- libcheck.o: libcheck.f  lib_com.fh crd_com.fh 
- 	$(BLANC_FORT) -c libcheck.f
-@@ -130,7 +132,7 @@ main_libcheck.o: main_libcheck.f libcheck_version.fh
- 	$(BLANC_FORT) -c main_libcheck.f
- 
- lbcheck: main_libcheck.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o libcheck.o  make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_unix.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o
--	$(BLANC_FORT) -o ../bin/libcheck main_libcheck.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_lib11.o make_lib12.o make_lib2.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o  mol2_file.o sdf_files.o 
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/libcheck main_libcheck.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_lib11.o make_lib12.o make_lib2.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o  mol2_file.o sdf_files.o 
- # ------------
- 
- emin.o: emin.f crd_com.fh atom_com.fh
-@@ -143,7 +145,7 @@ main_emin.o: main_emin.f
- 	$(BLANC_FORT) -c main_emin.f 
- 
- emn: main_emin.o emin_new.o angle_subr.o make_unix.o make_CIF.o make_subr_2.o make_subr.o
--	$(BLANC_FORT) -o ../bin/emin main_emin.o emin_new.o make_CIF.o angle_subr.o make_unix.o make_subr_2.o make_subr.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/emin main_emin.o emin_new.o make_CIF.o angle_subr.o make_unix.o make_subr_2.o make_subr.o
- 
- # -------------
- 
-@@ -155,7 +157,7 @@ main_modcheck.o: main_modcheck.f
- 	$(BLANC_FORT) -c main_modcheck.f 
- 
- mdcheck: main_modcheck.o modcheck.o mod_subr.o make_CIF.o make_unix.o make_subr_2.o make_subr.o 
--	$(BLANC_FORT) -o ../bin/modcheck main_modcheck.o make_CIF.o modcheck.o mod_subr.o make_unix.o make_subr_2.o make_subr.o  
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/modcheck main_modcheck.o make_CIF.o modcheck.o mod_subr.o make_unix.o make_subr_2.o make_subr.o  
- 
- 
- # ======================================
diff --git a/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild b/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild
deleted file mode 100644
index 509117f300af..000000000000
--- a/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils fortran-2 toolchain-funcs
-
-DESCRIPTION="PDB --> CIF convertor"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/makecif.html"
-SRC_URI="mirror://gentoo/${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~amd64 ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-LICENSE="ccp4"
-IUSE=""
-
-S="${WORKDIR}"/${PN}
-
-DEPEND=""
-RDEPEND="
-	!>=sci-chemistry/refmac-5.6
-	sci-libs/monomer-db"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-makefile.patch
-}
-
-src_compile() {
-	emake -C src clean
-	emake \
-		-C src \
-		BLANC_FORT="$(tc-getFC) ${FFLAGS}" \
-		LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dobin bin/*
-	dodoc readme
-}
diff --git a/sci-chemistry/makecif/makecif-5.6.6.ebuild b/sci-chemistry/makecif/makecif-5.6.6.ebuild
deleted file mode 100644
index 3a5f70a8b259..000000000000
--- a/sci-chemistry/makecif/makecif-5.6.6.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils fortran-2 toolchain-funcs
-
-DESCRIPTION="PDB --> CIF convertor"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/makecif.html"
-SRC_URI="mirror://gentoo/${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-LICENSE="ccp4"
-IUSE=""
-
-S="${WORKDIR}"/${PN}
-
-DEPEND=""
-RDEPEND="
-	!>=sci-chemistry/refmac-5.6
-	sci-libs/monomer-db"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-makefile.patch
-}
-
-src_compile() {
-	cd src && emake clean
-	emake \
-		BLANC_FORT="$(tc-getFC) ${FFLAGS}" \
-		LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dobin bin/*
-	dodoc readme
-}
diff --git a/sci-chemistry/makecif/metadata.xml b/sci-chemistry/makecif/metadata.xml
deleted file mode 100644
index 993c1d1ffcda..000000000000
--- a/sci-chemistry/makecif/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>sci-chemistry</herd>
-	<maintainer>
-		<email>jlec@gentoo.org</email>
-	</maintainer>
-	<longdescription>
-PDB - CIF convertor
-check and create correct structure description
-create the list of restraints
-create dictionary description of new ligands
-rebuild missing atoms
-create tree like structure
-also the part of REFMAC
-can use additional user's dictionary
-</longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/molrep/Manifest b/sci-chemistry/molrep/Manifest
deleted file mode 100644
index d91b8a448acd..000000000000
--- a/sci-chemistry/molrep/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST molrep-11.0.02.tar.gz 3594084 SHA256 6acb00bc91ad76027461ce6055eda72c8de34e5243449a31d5ede9e537e9adce SHA512 e22636e2d6b5558b66877960a64c0b990bb50d9e1b42016981b64e1311f83d5942fde7c1cd2dc8462ef1be814ce94ef566028079a7a091c9b3d7300f2d6ce03f WHIRLPOOL e507108a38be703e882ab3fd25e817c53c2d57b76fce578de3d308f10a85fce7a9febed39f748667a01c631b35787955d7d0290c944d4bfabfc936eab620daaf
-DIST molrep-11.0.03.tar.gz 3643087 SHA256 f4c317713b0dddf0ca883734f0bfe27600b50f8d4dd354ea8ae8245e21ce4392 SHA512 d9ff351e3754871d100c41aa9b8af48e3588768320f5ed92e536fac5e24114ca5df6497103d0b077455fc4e30e2d3d085aeb63854eb88dc8e74259b4e1683dc8 WHIRLPOOL b16e128e3ca7f1734ca79f70decab3e262d47b6a37c49e46c4c7d51f3fd8093cd3a0f20e487caeb5e9aa0a37a9fd050588cad3e99ad46e1866d05ff4a8ed0bb6
diff --git a/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch b/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch
deleted file mode 100644
index d81ec793b510..000000000000
--- a/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch
+++ /dev/null
@@ -1,61 +0,0 @@
---- src/makefile	2009-02-27 16:51:46.492890717 +0100
-+++ src/makefile.new	2009-02-27 16:52:18.295619642 +0100
-@@ -5,8 +5,8 @@
- 
- BIN = $(MOLREP)/bin
- 
--OBJS =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym.o molrep_unix.o
--OBJSL =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym.o molrep_unix.o
-+OBJS =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym_ccp4.o molrep_unix_ccp4.o
-+OBJSL =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym_ccp4.o molrep_unix_ccp4.o
- 
- 
- all: molrep
-@@ -19,31 +19,31 @@
- # -----------------------------
- 
- molrep.o: molrep.f 
--	$(MR_FORT) -c molrep.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep.f
- molrep1.o: molrep1.f 
--	$(MR_FORT) -c molrep1.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep1.f
- molrep2.o: molrep2.f 
--	$(MR_FORT) -c molrep2.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep2.f
- molrep3.o: molrep3.f 
--	$(MR_FORT) -c molrep3.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep3.f
- molrep_prog.o: molrep_prog.f 
--	$(MR_FORT) -c molrep_prog.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep_prog.f
- molrep_prog1.o: molrep_prog1.f 
--	$(MR_FORT) -c molrep_prog1.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep_prog1.f
- molrep_prog2.o: molrep_prog2.f 
--	$(MR_FORT) -c molrep_prog2.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep_prog2.f
- molrep_subr.o: molrep_subr.f  
--	$(MR_FORT) -c molrep_subr.f 
--molrep_sym.o: molrep_sym.f  
--	$(MR_FORT) -c molrep_sym.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep_subr.f
-+molrep_sym_ccp4.o: molrep_sym.f  
-+	$(MR_FORT) $(FFLAGS) -c molrep_sym_ccp4.f 
- main_molrep_mtz.o: main_molrep_mtz.f molrep_version.fh molrep_keywords.fh 
--	$(MR_FORT) -c main_molrep_mtz.f 
--molrep_unix.o: molrep_unix.f 
--	$(MR_FORT) -c molrep_unix.f 
-+	$(MR_FORT) $(FFLAGS) -c main_molrep_mtz.f 
-+molrep_unix_ccp4.o: molrep_unix.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep_unix_ccp4.f 
- molrep_dummy.o: molrep_dummy.f 
--	$(MR_FORT) -c molrep_dummy.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep_dummy.f 
- 
- molrep: $(OBJS)
--	$(MR_FORT) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
-+	$(MR_FORT) $(FFLAGS) $(LDFLAGS) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
- 
- # --------------------------------
-
diff --git a/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch b/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch
deleted file mode 100644
index c18b9a1e3f0d..000000000000
--- a/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/src/makefile b/src/makefile
-index 30d0de7..10dd68f 100755
---- a/src/makefile
-+++ b/src/makefile
-@@ -46,6 +46,6 @@ molrep_dummy.o: molrep_dummy.f
- 	$(MR_FORT) -c molrep_dummy.f 
- 
- molrep: $(OBJS)
--	$(MR_FORT) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
-+	$(MR_FORT) $(LDFLAGS) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
- 
- # --------------------------------
diff --git a/sci-chemistry/molrep/files/11.0.00-test.patch b/sci-chemistry/molrep/files/11.0.00-test.patch
deleted file mode 100644
index d90cfb8c7b35..000000000000
--- a/sci-chemistry/molrep/files/11.0.00-test.patch
+++ /dev/null
@@ -1,191 +0,0 @@
-diff --git a/molrep_check/em.bat b/molrep_check/em.bat
-index 2f0f992..96ddd75 100755
---- a/molrep_check/em.bat
-+++ b/molrep_check/em.bat
-@@ -8,6 +8,8 @@ $MR_TEST/molrep -m ../em/model.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop
- # --------------------------------
- _NMON  6
- stop
-+echo $?
-+[[ $? ]] || exit 1
- # --------------------------------
- #
- # 2. Atomic model --> EM map
-@@ -20,6 +22,7 @@ $MR_TEST/molrep -m ../em/model.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop
- _NMON  6
- _prf  y
- stop
-+[[ $? ]] || exit 1
- # --------------------------------
- #
- # 3. Atomic model --> EM map
-@@ -36,6 +39,7 @@ _ncs  322
- _centre  0.500 0.490 0.490
- _angles  0.0 0.0 90.0  
- stop
-+[[ $? ]] || exit 1
- # --------------------------------
- #
- cp out/molrep.pdb hexamer.pdb
-@@ -52,6 +56,7 @@ $MR_TEST/molrep -mx hexamer.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop
- # --------------------------------
- _DOM s
- stop
-+[[ $? ]] || exit 1
- # --------------------------------
- #
- # 5. EM --> X-ray     
-@@ -60,6 +65,7 @@ stop
- $MR_TEST/molrep -f ../em/p2.cif  -m ../em/pel.map -po out/ -ps scr/ -i <<stop
- # --------------------------------
- stop
-+[[ $? ]] || exit 1
- # --------------------------------
- #
- # 6. Placing  the model to a particular orientation and position.
-@@ -72,4 +78,5 @@ $MR_TEST/molrep -f ../em/p2.cif  -m ../em/pel.map -po out/ -ps scr/ -i <<stop
- _fun  s
- _file_t ../em/tab
- stop
-+[[ $? ]] || exit 1
- #==========================================
-diff --git a/molrep_check/mr.bat b/molrep_check/mr.bat
-index 284a4cd..6e00695 100755
---- a/molrep_check/mr.bat
-+++ b/molrep_check/mr.bat
-@@ -10,6 +10,7 @@
- $MR_TEST/molrep -f ../data/test.mtz -m ../data/test_mod.pdb -po out/ -ps scr/ -i <<stop
- # --------------------------------
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -26,6 +27,7 @@ _nmon   2
- _COMPL  .5
- _SIM    .7
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -46,6 +48,7 @@ $MR_TEST/molrep -f ../data/test.cif -m ../data/test_mod.pdb -mx ../data/test_mod
- # --------------------------------
- _NP    3
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -67,6 +70,7 @@ $MR_TEST/molrep -f ../data/test.cif -m ../data/test_mod.pdb -po out/ -ps scr/ -i
- _NMON   2
- _NP     3
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -85,6 +89,7 @@ _NPT    3
- _NPTD   3
- _DYAD   D
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -103,6 +108,7 @@ _NP    3
- _NPT   10
- _NMR   3
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -118,6 +124,7 @@ _PRF Y
- _compl 1.
- _sim   .2
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -136,6 +143,7 @@ _ph   PH
- _fom  FOM
- #
- stop
-+[[ $? ]] || exit 1
- # =================================================================
- #
- #   9. use sequence
-@@ -145,6 +153,7 @@ stop
- $MR_TEST/molrep -f ../data/s100.mtz -m ../data/monomer.pdb -s ../data/s100.seq -po out/ -ps scr/ -i <<stop 
- # --------------------------------
- stop
-+[[ $? ]] || exit 1
- # =================================================================
- #
- #   10. Locked RF
-@@ -157,6 +166,7 @@ _lock y
- _file_tsrf ../data/srf.tab
- _nsrf 1
- stop
-+[[ $? ]] || exit 1
- # =================================================================
- #
- #   11. Multi-monomer search using NCS, SELF = 'A' means to compute Self RF and 
-@@ -169,6 +179,7 @@ $MR_TEST/molrep -f ../data/s100.mtz -m ../data/monomer.pdb -m2 ../data/monomer.p
- _self a
- _nsrf 1
- stop
-+[[ $? ]] || exit 1
- # =================================================================
- #
- #   12.  use pst
-@@ -179,6 +190,7 @@ $MR_TEST/molrep -f ../data/pst.mtz -m ../data/model_pst.pdb -po out/ -ps scr/ -i
- # --------------------------------
- #
- stop
-+[[ $? ]] || exit 1
- # =================================================================
- #
- #   13. space group check
-@@ -189,7 +201,8 @@ $MR_TEST/molrep -f ../data/test.mtz -m ../data/test_mod.pdb -po out/ -ps scr/ -i
- # --------------------------------
- _sg all
- #
--stop
-+s[[ $? ]] || exit 1
-+top
- # ==========================================================
- #  
- #  14. Example for finding HA position by MR solution.
-@@ -206,6 +219,7 @@ _SIGFD  SIGFD3
- #
- _FUN   d
- stop
-+[[ $? ]] || exit 1
- # ==========================================================
- #  
- #  15. Example for HA search by multi-copy search
-@@ -225,6 +239,7 @@ _diff h
- _dyad y
- _nmon 4
- stop
-+[[ $? ]] || exit 1
- # ==========================================================
- #  
- #  16. Example HA for search by translation function
-@@ -242,6 +257,7 @@ _FUN  t
- _diff  h
- _nmon  4
- stop
-+[[ $? ]] || exit 1
- # ==========================================================
- #  
- #  17. Example for Self RF for Heavy Atom structure in derivative.
-@@ -258,4 +274,5 @@ _SIGFD  SIGFD3
- _FUN  r
- _diff  h
- stop
-+[[ $? ]] || exit 1
- # ==========================================================
diff --git a/sci-chemistry/molrep/files/11.0.03-EOR.patch b/sci-chemistry/molrep/files/11.0.03-EOR.patch
deleted file mode 100644
index 430629e8dcc1..000000000000
--- a/sci-chemistry/molrep/files/11.0.03-EOR.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/molrep.f |    2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-diff --git a/src/molrep.f b/src/molrep.f
-index eac0cfc..94f74c6 100755
---- a/src/molrep.f
-+++ b/src/molrep.f
-@@ -1257,7 +1257,7 @@ C         CHECK_DENS_FILE( 2 )
-         LEN1 = 1
-         IF(LEN.GT.60) LEN1 = LEN - 59
-         WRITE(LINE,'(''Input MODEL_2(fixed)_file:'',A)') 
--     *                                 NAME2(LEN11:LEN)
-+     *                                 NAME2(LEN1:LEN)
-         CALL MSGDOC(MDoc,LINE)
- 
-       ENDIF
diff --git a/sci-chemistry/molrep/metadata.xml b/sci-chemistry/molrep/metadata.xml
deleted file mode 100644
index ae9ec7c5f6a4..000000000000
--- a/sci-chemistry/molrep/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-  <maintainer>
-    <email>jlec@gentoo.org</email>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/molrep/molrep-11.0.02.ebuild b/sci-chemistry/molrep/molrep-11.0.02.ebuild
deleted file mode 100644
index 51ff6cb26524..000000000000
--- a/sci-chemistry/molrep/molrep-11.0.02.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="molecular replacement program"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html"
-SRC_URI="mirror://gentoo/${P}.tar.gz"
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	>=sci-libs/ccp4-libs-6.1.3
-	sci-libs/mmdb
-	virtual/lapack"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/11.0.00-respect-FLAGS.patch \
-		"${FILESDIR}"/11.0.00-test.patch
-}
-
-src_compile() {
-	cd "${S}"/src
-	emake clean
-	emake \
-		MR_FORT="$(tc-getFC) ${FFLAGS}" \
-		FFLAGS="${FFLAGS}" \
-		LDFLAGS="${LDFLAGS}" \
-		MR_LIBRARY="-L${EPREFIX}/usr/$(get_libdir) -lccp4f -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb lapack) -lccif -lstdc++ -lm"
-}
-
-src_test() {
-	export MR_TEST="${S}/bin/"
-	cd "${S}"/molrep_check/work
-	mkdir out scr
-	cp ../*.bat .
-	bash em.bat || die
-	bash mr.bat || die
-}
-
-src_install() {
-	exeinto /usr/libexec/ccp4/bin/
-	doexe bin/${PN}
-	dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN}
-	dodoc readme doc/${PN}.rtf
-}
diff --git a/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild b/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild
deleted file mode 100644
index 3373bbba6f97..000000000000
--- a/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils flag-o-matic fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="molecular replacement program"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.gz"
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	>=sci-libs/ccp4-libs-6.1.3
-	sci-libs/mmdb
-	virtual/lapack"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/11.0.00-respect-FLAGS.patch \
-		"${FILESDIR}"/11.0.00-test.patch \
-		"${FILESDIR}"/${PV}-EOR.patch
-	[[ $(tc-getFC) =~ gfortran ]] && append-fflags -fno-second-underscore
-}
-
-src_compile() {
-	cd "${S}"/src
-	emake clean
-	emake \
-		MR_FORT="$(tc-getFC) ${FFLAGS}" \
-		FFLAGS="${FFLAGS}" \
-		LDFLAGS="${LDFLAGS}" \
-		MR_LIBRARY="-L${EPREFIX}/usr/$(get_libdir) -lccp4f -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb lapack) -lccif -lstdc++ -lm"
-}
-
-src_test() {
-	export MR_TEST="${S}/bin/"
-	cd "${S}"/molrep_check/work
-	mkdir out scr
-	cp ../*.bat .
-	bash em.bat || die
-	bash mr.bat || die
-}
-
-src_install() {
-	exeinto /usr/libexec/ccp4/bin/
-	doexe bin/${PN}
-	dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN}
-	dodoc readme doc/${PN}.rtf
-}
diff --git a/sci-chemistry/mosflm/Manifest b/sci-chemistry/mosflm/Manifest
deleted file mode 100644
index 80df134c833e..000000000000
--- a/sci-chemistry/mosflm/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mosflm709.tgz 3324010 SHA256 d22b05211f274b50c284d4c14fcb456c52b13344e2a48d5f45855fe87f82f6d1 SHA512 aa85f8459f280e0e1d2d54041029ef072346ecef3ffcc7724eb524469e1b77dfbd95aac8b46f2b9682d605a4e5931d9c13f1162d5f3bcff08644db7e79a6316c WHIRLPOOL b3a82858a8d2a3162bc0fcfb3bf7fb7b01cfc6bca80b34643e7c6caae54b1ef1e2b24a58617ffe2b0423ca6626d51e31b49c0dba6a82ed5c61fa10d044e0d3b8
diff --git a/sci-chemistry/mosflm/files/7.0.6-Makefile.patch b/sci-chemistry/mosflm/files/7.0.6-Makefile.patch
deleted file mode 100644
index a35232f6e8c0..000000000000
--- a/sci-chemistry/mosflm/files/7.0.6-Makefile.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- Makefile	2008-10-17 16:15:30.000000000 +0200
-+++ Makefile.new	2009-02-20 21:52:34.000000000 +0100
-@@ -22,7 +22,7 @@
- CBFLIBS = cbf/lib/libcbf.a
- JPGLIBS = jpg/libjpeg.a
- 
--all:	$(DPSLIBS) $(CBFLIBS) $(JPGLIBS)
--	cd mosflm ; make
-+all:	dpslibs cbflibs
-+	+make -C mosflm
- 
- ##########################################################################
-
diff --git a/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch b/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch
deleted file mode 100644
index da393eb93fe6..000000000000
--- a/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-diff --git a/mosflm/bravais_fortran.c b/mosflm/bravais_fortran.c
-index 3d68cad..800bd0e 100644
---- a/mosflm/bravais_fortran.c
-+++ b/mosflm/bravais_fortran.c
-@@ -2,6 +2,7 @@
- #include <stdlib.h>
- #include <math.h>
- #include "../util/util.h"
-+#include "../util/bravais.h"
- 
- /* bravais_fortran_(): This routine converts array from FORTRAN program
-                        to structure for call to bravais
-diff --git a/mosflm/chelp.c b/mosflm/chelp.c
-index b2aaefc..fa44ab0 100644
---- a/mosflm/chelp.c
-+++ b/mosflm/chelp.c
-@@ -5,6 +5,7 @@
- /* modified for Linux by Joachim Meyer jmeyer@embl-heidelberg.de 1998.05.19 */
- 
- #include "chelp.h"
-+#include <stdio.h>
- 
- #if CALL_LIKE_HPUX
-   void chelp ()
-diff --git a/mosflm/pck.c b/mosflm/pck.c
-index ec094fc..288671d 100644
---- a/mosflm/pck.c
-+++ b/mosflm/pck.c
-@@ -17,6 +17,7 @@
- #include <math.h>
- #include <ctype.h>
- #include <string.h>
-+#include <unistd.h>
- 
- #define BYTE char
- #define WORD short int
diff --git a/sci-chemistry/mosflm/files/7.0.6-parallel.patch b/sci-chemistry/mosflm/files/7.0.6-parallel.patch
deleted file mode 100644
index f735c7ce5cf7..000000000000
--- a/sci-chemistry/mosflm/files/7.0.6-parallel.patch
+++ /dev/null
@@ -1,28 +0,0 @@
---- cbf/Makefile	2009-08-31 09:35:06.000000000 +0200
-+++ cbf/Makefile.new	2009-08-31 10:44:46.000000000 +0200
-@@ -362,6 +362,8 @@
-              $(EXAMPLES)/img.h               \
-              $(INCLUDE)/md5.h
- 
-+OBJ = $(subst .c,.o,$(SOURCE))
-+
- #
- # Compile the library and examples
- #
-@@ -379,11 +381,14 @@
- $(LIB):
- 	mkdir $(LIB)
- 
-+
-+.c.o: $(SOURCE) $(HEADERS)
-+	$(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $<
-+
- #
- # CBF library
- #
--$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP)
--	$(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
-+$(LIB)/libcbf.a: $(OBJ) $(COMMONDEP)
- 	$(AR) cr $@ *.o
- 	rm *.o
- 	if [ -f $(RANLIB) ]; then $(RANLIB) $@ ; fi
diff --git a/sci-chemistry/mosflm/files/7.0.7-parallel.patch b/sci-chemistry/mosflm/files/7.0.7-parallel.patch
deleted file mode 100644
index df0a8b63273a..000000000000
--- a/sci-chemistry/mosflm/files/7.0.7-parallel.patch
+++ /dev/null
@@ -1,92 +0,0 @@
- Makefile     |   21 ++++++++++-----------
- cbf/Makefile |    9 +++++++--
- 2 files changed, 17 insertions(+), 13 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 37f4c7e..51d4164 100644
---- a/Makefile
-+++ b/Makefile
-@@ -22,8 +22,8 @@ DPSLIBS = lib/DPSLIB.a
- CBFLIBS = cbf/lib/libcbf.a
- JPGLIBS = jpg/libjpeg.a
- 
--all:	$(DPSLIBS) $(CBFLIBS) $(JPGLIBS)
--	cd mosflm ; make
-+all:	$(DPSLIBS)
-+	$(MAKE) -C mosflm
- 
- ##########################################################################
- #                                                                        #
-@@ -47,22 +47,21 @@ dpslibs:
- 
- cbflibs: 
- 	rm -f `find ./cbf -name "*.a" -print`
--	cd cbf ; make all ; if [ -f $(RANLIB) ]; \
--	then $(RANLIB) lib/libcbf.a; fi
-+	$(MAKE) -C cbf all
- 
- jpglibs: 
--	cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; make libjpeg.a
-+	cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; $(MAKE) libjpeg.a
- 
- ${DPSLIBS}:
--	make dpslibs
-+	$(MAKE) dpslibs
- 
- ${CBFLIBS}:
--	make cbflibs
-+	$(MAKE) cbflibs
- 
- ${JPGLIBS}:
--	make jpglibs
-+	$(MAKE) jpglibs
- 
--libs:	${DPSLIBS} ${CBFLIBS} ${JPGLIBS}
-+libs:	${DPSLIBS} ${CBFLIBS}
- 	@echo "****************************************************************"
- 	@echo "             Making libraries for system ${HOSTTYPE}"
- 	@echo "****************************************************************"
-@@ -71,11 +70,11 @@ ipmosflm: libs
- 	@echo "****************************************************************"
- 	@echo "           Making IPMOSFLM for system ${HOSTTYPE}"
- 	@echo "****************************************************************"
--	cd mosflm ; make ipmosflm
-+	$(MAKE) -C mosflm ipmosflm
- 
- force:
- 	rm bin/ipmosflm
--	make ipmosflm
-+	$(MAKE) ipmosflm
- 
- install:
- 	@echo "the executable is in ${MOSHOME}/bin/ipmosflm"
-diff --git a/cbf/Makefile b/cbf/Makefile
-index e61497c..c3c94ac 100644
---- a/cbf/Makefile
-+++ b/cbf/Makefile
-@@ -362,6 +362,8 @@ HEADERS   =  $(INCLUDE)/cbf.h                  \
-              $(EXAMPLES)/img.h               \
-              $(INCLUDE)/md5.h
- 
-+OBJ = $(subst .c,.o,$(SOURCE))
-+
- #
- # Compile the library and examples
- #
-@@ -379,11 +381,14 @@ $(INSTALLDIR):
- $(LIB):
- 	mkdir $(LIB)
- 
-+
-+.c.o: $(SOURCE) $(HEADERS)
-+	$(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $<
-+
- #
- # CBF library
- #
--$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP)
--	$(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
-+$(LIB)/libcbf.a: $(OBJ) $(COMMONDEP)
- 	$(AR) cr $@ *.o
- 	rm *.o
- 	if [ -f $(RANLIB) ]; then $(RANLIB) $@ ; fi
diff --git a/sci-chemistry/mosflm/files/7.0.9-parallel.patch b/sci-chemistry/mosflm/files/7.0.9-parallel.patch
deleted file mode 100644
index 38c6fc45a5c0..000000000000
--- a/sci-chemistry/mosflm/files/7.0.9-parallel.patch
+++ /dev/null
@@ -1,92 +0,0 @@
- Makefile     |   21 ++++++++++-----------
- cbf/Makefile |    9 +++++++--
- 2 files changed, 17 insertions(+), 13 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 3d2f543..2219d8d 100644
---- a/Makefile
-+++ b/Makefile
-@@ -22,8 +22,8 @@ DPSLIBS = lib/DPSLIB.a
- CBFLIBS = cbf/lib/libcbf.a
- JPGLIBS = jpg/libjpeg.a
- 
--all:	$(DPSLIBS) $(CBFLIBS) $(JPGLIBS)
--	cd mosflm ; make
-+all:	$(DPSLIBS)
-+	$(MAKE) -C mosflm
- 
- dpslibs:
- 	@-find . -name "*a" -delete
-@@ -32,22 +32,21 @@ dpslibs:
- 
- cbflibs: 
- 	@-find ./cbf -name "*.a" -delete
--	cd cbf ; make all ; if [ -f $(RANLIB) ]; \
--	then $(RANLIB) lib/libcbf.a; fi
-+	$(MAKE) -C cbf all
- 
- jpglibs: 
--	cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; make libjpeg.a
-+	cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; $(MAKE) libjpeg.a
- 
- ${DPSLIBS}:
--	make dpslibs
-+	$(MAKE) dpslibs
- 
- ${CBFLIBS}:
--	make cbflibs
-+	$(MAKE) cbflibs
- 
- ${JPGLIBS}:
--	make jpglibs
-+	$(MAKE) jpglibs
- 
--libs:	${DPSLIBS} ${CBFLIBS} ${JPGLIBS}
-+libs:	${DPSLIBS} ${CBFLIBS}
- 	@echo "****************************************************************"
- 	@echo "             Making libraries for system ${HOSTTYPE}"
- 	@echo "****************************************************************"
-@@ -56,11 +55,11 @@ ipmosflm: libs
- 	@echo "****************************************************************"
- 	@echo "           Making IPMOSFLM for system ${HOSTTYPE}"
- 	@echo "****************************************************************"
--	cd mosflm ; make ipmosflm
-+	$(MAKE) -C mosflm ipmosflm
- 
- force:
- 	@-rm -f bin/ipmosflm
--	make ipmosflm
-+	$(MAKE) ipmosflm
- 
- install:
- 	@echo "the executable is in ${MOSHOME}/bin/ipmosflm"
-diff --git a/cbf/Makefile b/cbf/Makefile
-index e61497c..c3c94ac 100644
---- a/cbf/Makefile
-+++ b/cbf/Makefile
-@@ -362,6 +362,8 @@ HEADERS   =  $(INCLUDE)/cbf.h                  \
-              $(EXAMPLES)/img.h               \
-              $(INCLUDE)/md5.h
- 
-+OBJ = $(subst .c,.o,$(SOURCE))
-+
- #
- # Compile the library and examples
- #
-@@ -379,11 +381,14 @@ $(INSTALLDIR):
- $(LIB):
- 	mkdir $(LIB)
- 
-+
-+.c.o: $(SOURCE) $(HEADERS)
-+	$(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $<
-+
- #
- # CBF library
- #
--$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP)
--	$(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
-+$(LIB)/libcbf.a: $(OBJ) $(COMMONDEP)
- 	$(AR) cr $@ *.o
- 	rm *.o
- 	if [ -f $(RANLIB) ]; then $(RANLIB) $@ ; fi
diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch b/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch
deleted file mode 100644
index 90158eb458d5..000000000000
--- a/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- mosflm/pilatus_c.c |    2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-diff --git a/mosflm/pilatus_c.c b/mosflm/pilatus_c.c
-index 1eaae26..cce5a02 100644
---- a/mosflm/pilatus_c.c
-+++ b/mosflm/pilatus_c.c
-@@ -34,7 +34,7 @@ delete them later */
-   int cbf_int[16];
-   long cbf_int4[16];
-   double cbf_double[16];
--  char cbf_char[16][24];
-+  char cbf_char[16][32];
-   /* temporary from cbfwrap.c - pilatus doesn't have these, so we'll 
- delete them later */
-   int id, index, iindex;
diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch b/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch
deleted file mode 100644
index 32f251f8e00c..000000000000
--- a/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch
+++ /dev/null
@@ -1,29 +0,0 @@
- mosflm/mosflm_jpeg.c           |    1 +
- src/dps/index/ind_gen_direct.c |    2 ++
- 2 files changed, 3 insertions(+), 0 deletions(-)
-
-diff --git a/mosflm/mosflm_jpeg.c b/mosflm/mosflm_jpeg.c
-index 2b32b2e..54684d0 100644
---- a/mosflm/mosflm_jpeg.c
-+++ b/mosflm/mosflm_jpeg.c
-@@ -76,6 +76,7 @@ G. Winter
- #include <fcntl.h>
- #include <stdio.h>
- #include <stdlib.h>
-+#include <string.h>
- #if (defined _MSC_VER) 
- /* no need to do this for __MINGW_ (Mingw gcc) this is just about unique!*/
- #define S_IRWXU S_IREAD|S_IWRITE|S_IEXEC
-diff --git a/src/dps/index/ind_gen_direct.c b/src/dps/index/ind_gen_direct.c
-index 6e143df..2eea61b 100644
---- a/src/dps/index/ind_gen_direct.c
-+++ b/src/dps/index/ind_gen_direct.c
-@@ -41,6 +41,8 @@
- /* #include <malloc.h> */
- #include "util.h"
- #include "ind_gen_direct.h"
-+#include "ind_help.h"
-+#include "ind_sort_merge.h"
- /* char *strcat( char *, const char *); */
- 
- 
diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch b/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch
deleted file mode 100644
index bb4a16bf30fc..000000000000
--- a/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- mosflm/pilatus_c.c |    2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-diff --git a/mosflm/pilatus_c.c b/mosflm/pilatus_c.c
-index 4a85b26..9893e0c 100644
---- a/mosflm/pilatus_c.c
-+++ b/mosflm/pilatus_c.c
-@@ -34,7 +34,7 @@ delete them later */
-   int cbf_int[16] = {0};
-   long cbf_int4[16] = {0};
-   double cbf_double[16] = {0};
--  char cbf_char[16][24] = {' '};
-+  char cbf_char[16][32] = {' '};
-   /* temporary from cbfwrap.c - pilatus doesn't have these, so we'll 
- delete them later */
-   int id, index, iindex;
diff --git a/sci-chemistry/mosflm/metadata.xml b/sci-chemistry/mosflm/metadata.xml
deleted file mode 100644
index ae9ec7c5f6a4..000000000000
--- a/sci-chemistry/mosflm/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-  <maintainer>
-    <email>jlec@gentoo.org</email>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mosflm/mosflm-7.0.9.ebuild b/sci-chemistry/mosflm/mosflm-7.0.9.ebuild
deleted file mode 100644
index 3aa74ced3d94..000000000000
--- a/sci-chemistry/mosflm/mosflm-7.0.9.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils fortran-2 toolchain-funcs versionator
-
-MY_PV="$(delete_all_version_separators)"
-MY_P="${PN}${MY_PV}"
-
-DESCRIPTION="A program for integrating single crystal diffraction data from area detectors"
-HOMEPAGE="http://www.mrc-lmb.cam.ac.uk/harry/mosflm/"
-SRC_URI="${HOMEPAGE}ver${MY_PV}/build-it-yourself/${MY_P}.tgz"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	app-shells/tcsh
-	sci-libs/cbflib
-	sci-libs/ccp4-libs
-	sys-libs/ncurses
-	virtual/jpeg:0=
-	x11-libs/libxdl_view"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	sed \
-		-e "s:../cbf/lib/libcbf.a:-lcbf -limg:g" \
-		-e "s:../jpg/libjpeg.a:-ljpeg:g" \
-		-i ${PN}/Makefile || die
-
-	sed \
-		-e '/jinclude.h/d' \
-		-i mosflm/mosflm_jpeg.c || die
-
-	cp DATETIME.C mosflm/datetime.c || die
-
-	epatch \
-		"${FILESDIR}"/${PV}-parallel.patch \
-		"${FILESDIR}"/7.0.6-impl-dec.patch \
-		"${FILESDIR}"/${P}-buffer-overflow.patch \
-		"${FILESDIR}"/${PN}-7.0.7-impl-dec.patch
-
-	rm -rf test.f {cbf,jpg}/*.{h,c} || die
-}
-
-src_compile() {
-	emake \
-		MOSHOME="${S}" \
-		DPS="${S}" \
-		FC=$(tc-getFC) \
-		FLINK=$(tc-getFC) \
-		CC=$(tc-getCC) \
-		AR_FLAGS=vru \
-		MOSLIBS="-lccp4f -lccp4c -lxdl_view $($(tc-getPKG_CONFIG) --libs ncurses) -lXt -lmmdb -lccif -lstdc++" \
-		MCFLAGS="-O0 -fno-second-underscore" \
-		MOSFLAGS="${FFLAGS} -fno-second-underscore" \
-		FFLAGS="${FFLAGS} -fno-second-underscore" \
-		CFLAGS="${CFLAGS}" \
-		MOSCFLAGS="${CFLAGS}" \
-		LFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	exeinto /usr/libexec/ccp4/bin/
-	doexe bin/ipmosflm
-	dosym ../libexec/ccp4/bin/ip${PN} /usr/bin/ip${PN}
-}
diff --git a/sci-chemistry/mrbump/Manifest b/sci-chemistry/mrbump/Manifest
deleted file mode 100644
index f9887a6071b2..000000000000
--- a/sci-chemistry/mrbump/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mrbump-0.4.4.tar.gz 9220116 SHA256 499634815cf316ca273900252dab16b91f6421b0f85a548108258f9934dccd6a SHA512 3a39159d78c4310f5a04efc7bb10ed81f6f260baa65db3615d5065c94175e33de3dbe2073de057a699efe541d59674cc927699229a4af5e8102600caea4c03d3 WHIRLPOOL adb8c583b81cce8ec7e29f203b0a33de41f42c0fae77317671593f661db8c06c56106ed4fcfdeb503c9594c8802dc1dd1a0c7da290b7d3046e8f3d8d6911f60d
diff --git a/sci-chemistry/mrbump/files/0.4.4-superpose.patch b/sci-chemistry/mrbump/files/0.4.4-superpose.patch
deleted file mode 100644
index c9941e9ece2a..000000000000
--- a/sci-chemistry/mrbump/files/0.4.4-superpose.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- share/mrbump/include/mr/Ensemble.py	2008-07-28 16:40:47.000000000 +0200
-+++ share/mrbump/include/mr/Ensemble.py.new	2009-08-26 22:26:44.000000000 +0200
-@@ -29,7 +29,7 @@
-          self.superposeEXE=os.path.join(os.environ['CBIN'], 'superpose.exe') 
-          self.pdbsetEXE=os.path.join(os.environ['CBIN'], 'pdbset.exe') 
-       else:
--         self.superposeEXE=os.path.join(os.environ['CBIN'], 'superpose') 
-+         self.superposeEXE=os.path.join(os.environ['CBIN'], 'superpose-ccp4') 
-          self.pdbsetEXE=os.path.join(os.environ['CBIN'], 'pdbset') 
-  
-       self.SPxyz_template=''
diff --git a/sci-chemistry/mrbump/metadata.xml b/sci-chemistry/mrbump/metadata.xml
deleted file mode 100644
index 4aaae064be71..000000000000
--- a/sci-chemistry/mrbump/metadata.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>sci-chemistry</herd>
-	<maintainer>
-		<email>jlec@gentoo.org</email>
-		<name>Justin Lecher (jlec)</name>
-	</maintainer>
-</pkgmetadata>
-
diff --git a/sci-chemistry/mrbump/mrbump-0.4.4.ebuild b/sci-chemistry/mrbump/mrbump-0.4.4.ebuild
deleted file mode 100644
index 66ec9309e1cd..000000000000
--- a/sci-chemistry/mrbump/mrbump-0.4.4.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="3"
-
-PYTHON_DEPEND="2"
-
-inherit eutils multilib python
-
-DESCRIPTION="An automated scheme for Molecular Replacement"
-HOMEPAGE="http://www.ccp4.ac.uk/MrBUMP"
-SRC_URI="${HOMEPAGE}/release/${P}.tar.gz"
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE="X perl"
-
-RDEPEND=">=sci-chemistry/ccp4-apps-6.1.3[X?]
-	|| ( sci-biology/mafft
-		sci-biology/clustalw:2
-		sci-biology/probcons
-		sci-biology/t-coffee )
-	sci-biology/fasta
-	X? ( media-gfx/graphviz )
-	perl? ( dev-perl/SOAP-Lite )"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
-	python_set_active_version 2
-}
-
-src_unpack(){
-	unpack ${A}
-	cd "${S}"
-	unpack ./"${PN}".tar.gz
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-superpose.patch
-	python_convert_shebangs 2 setup_lib/*
-}
-
-src_install(){
-	insinto /usr/$(get_libdir)/ccp4/ccp4i
-	doins -r ccp4i/{MrBUMP-ccp4i.tar.gz,MrBUMP/{help,scripts,tasks,templates}} || \
-	die "failed to install interface"
-
-	insinto /usr/share/${PN}
-	doins -r share/${PN}/{data,include} || die "failed to install mrbump data"
-
-	dobin share/${PN}/bin/* || die "failed to install binaries"
-
-	dodoc README.txt || die
-	dohtml html/mrbump_doc.html || die
-}
diff --git a/sci-chemistry/oasis/Manifest b/sci-chemistry/oasis/Manifest
deleted file mode 100644
index e87a831c1fe3..000000000000
--- a/sci-chemistry/oasis/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST oasis4.0_Linux.zip 6714528 SHA256 56da70ce0c2750aaddf64ad2cd7852fc341d2022209484beb356b4e73dec61ba SHA512 b43b8315e8e3bc8531e11021605100f231635e2363256a19ed0f51015913221eb9e37b3891b9b1239bf83c9ada8f65a1bdc79ec5745201436f8c3b5019bd4bf7 WHIRLPOOL 24d337391997d036bd657ab22aecc77d36f7fa0af573d17433869a29640a8a10368c75ebee114071c577cc0cce34d838271147599d99e2c389088b8c6185f41b
diff --git a/sci-chemistry/oasis/files/4.0-makefile.patch b/sci-chemistry/oasis/files/4.0-makefile.patch
deleted file mode 100644
index f27a350a1fd2..000000000000
--- a/sci-chemistry/oasis/files/4.0-makefile.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-diff --git a/src/Makefile b/src/Makefile
-index 1e9128f..eb9edaf 100644
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -20,8 +20,8 @@ IRIX:
- 	@ ${F77} -O2 -mips3 -nocpp -OPT:Olimit=1500 -w -rpath ${CCP4_LIB} -o oasis4-0 oasis4-0.f -L${CCP4_LIB}/src -lccp4f -lccp4c -lmmdb -lC -lm -L/usr/lib32 -lblas
- 	@ ${F77} -O2 -mips3 -nocpp -OPT:Olimit=1500 -w -rpath ${CCP4_LIB} -o fnp2fp fnp2fp.f -L${CCP4_LIB}/src -lccp4f -lccp4c -lmmdb -lC -lm -L/usr/lib32 -lblas
- Linux:
--	@ ${F77} -O -w -fno-second-underscore -fno-globals -fno-automatic -o oasis4-0 oasis4-0.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lg2c -lm -L${CCP4_LIB}
--	@ ${F77} -O -w -fno-second-underscore -fno-globals -fno-automatic -o fnp2fp fnp2fp.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lg2c -lm -L${CCP4_LIB}
-+	${F77} $(CFLAGS) $(LDFLAGS) -o oasis oasis4-0.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lm -L${CCP4_LIB}
-+	${F77} $(CFLAGS) $(LDFLAGS) -o fnp2fp fnp2fp.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lm -L${CCP4_LIB}
- Darwin:
- 	@ ${F77} -O2 -fno-second-underscore -o fnp2fp fnp2fp.f   -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lgcc_s.10.5 -lSystem -lm
- 	@ ${F77} -O2 -fno-second-underscore -o oasis4-0 oasis4-0.f   -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lgcc_s.10.5 -lSystem -lm
diff --git a/sci-chemistry/oasis/metadata.xml b/sci-chemistry/oasis/metadata.xml
deleted file mode 100644
index 8412c2f3d312..000000000000
--- a/sci-chemistry/oasis/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-  <use>
-    <flag name="minimal">Restricts functionality on free software</flag>
-  </use>
-</pkgmetadata>
diff --git a/sci-chemistry/oasis/oasis-4.0-r3.ebuild b/sci-chemistry/oasis/oasis-4.0-r3.ebuild
deleted file mode 100644
index 98c8aaef47b4..000000000000
--- a/sci-chemistry/oasis/oasis-4.0-r3.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils fortran-2 multilib toolchain-funcs
-
-MY_P="${PN}${PV}_Linux"
-
-DESCRIPTION="A direct-method program for SAD/SIR phasing"
-HOMEPAGE="http://cryst.iphy.ac.cn/Project/protein/protein-I.html"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${MY_P}.zip"
-
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-LICENSE="ccp4 oasis"
-IUSE="examples +minimal"
-
-RDEPEND="
-	sci-chemistry/ccp4-apps
-	sci-chemistry/pymol
-	sci-libs/mmdb:0
-	sci-visualization/gnuplot
-	!minimal? (
-		sci-chemistry/solve-resolve-bin
-		sci-chemistry/arp-warp-bin
-	)"
-DEPEND="${RDEPEND}
-	sci-libs/ccp4-libs"
-
-S="${WORKDIR}"/${MY_P}
-
-src_prepare() {
-	rm bin/{fnp2fp,gnuplot,oasis4-0,seq} || die
-	epatch "${FILESDIR}"/${PV}-makefile.patch
-}
-
-src_compile() {
-	emake \
-		-C src \
-		F77="$(tc-getFC)" \
-		CFLAGS="${FFLAGS}" \
-		CCP4_LIB="${EPREFIX}/usr/$(get_libdir)" \
-		Linux
-}
-
-src_install() {
-	exeinto /usr/libexec/ccp4/bin/
-	doexe src/{${PN},fnp2fp}
-
-	exeinto /usr/$(get_libdir)/${PN}
-	doexe bin/*.*sh
-
-	insinto /usr/share/doc/${PF}/html
-	doins bin/html/*
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/${PN}/html
-	chmod 755 "${ED}"/usr/share/doc/${PF}/html/*.{*sh,awk} || die
-
-	if use examples; then
-		insinto /usr/share/${PN}
-		doins -r examples
-	fi
-
-	cat >> "${T}"/25oasis <<- EOF
-	oasisbin="${EPREFIX}/usr/$(get_libdir)/${PN}"
-	EOF
-
-	doenvd "${T}"/25oasis
-}
diff --git a/sci-chemistry/pdb-extract/Manifest b/sci-chemistry/pdb-extract/Manifest
deleted file mode 100644
index 9036c79e3e7c..000000000000
--- a/sci-chemistry/pdb-extract/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST pdb-extract-v3.004-prod-src.tar.gz 942450 SHA256 58bef2aba4869cdd16a79ddc588da5596a2ccd1f5c925f300b63b6d8299bb953 SHA512 4505fd615324982e741a3656d8a36ffc2cd6524c825d254e0a1ff44b3464aaf63cbdbe4f614a6ace6c0e56af8f452634152edadd0ed5305f0148856affa8cb60 WHIRLPOOL b7077431d75a31a9ac4ea41f7cb76874aa49626a19c1290126405a8cdac4d210f56929f9213512ae4f542286be5cbedc972642b9ef07a4e461ac969c6c0d965f
-DIST pdb-extract-v3.11-prod-src.tar.gz 1016140 SHA256 cc56ab58e4b4f0914dcd61834cae673ade5b12688861ea5f0197a33f5939d131 SHA512 06ef4110f873d23bcf878877a8b9f714b895a5b269f8d33312387c0bcb569adb2b1d1577eebc30200d5f0d3648959450912911609dab3749e7d5eb4c84d7e12f WHIRLPOOL ea0e643e1d64f344fdd643348b0ce35143e29f27a64b9153d6645c8dbf914e193f700217c0caecb30ea300ae10f47ea09bed61811c3bb293ef63d9e45acf74d3
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch
deleted file mode 100644
index 3a6f5498ffba..000000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch
+++ /dev/null
@@ -1,46 +0,0 @@
---- Makefile	2008-12-05 14:36:44.000000000 +0100
-+++ Makefile.new	2008-12-05 14:37:21.000000000 +0100
-@@ -19,13 +19,7 @@
- CHECKOUT_SCRIPT_MODULE = util
- CHECKOUT_SCRIPT = checkout.sh
- 
--LIBDIRS =  cifobj-common-v4.1 \
--           tables-v8.0 \
--           regex-v2.2 \
--           cif-file-v1.0 \
--           misclib-v2.2 \
--           cifparse-obj-v7.0 \
--           $(EXTRACT)
-+LIBDIRS =  $(EXTRACT)
- 
- all:	compile
- 
---- pdb-extract-v3.0/Makefile	2008-12-05 14:42:58.000000000 +0100
-+++ pdb-extract-v3.0/Makefile.new	2008-12-05 14:42:15.510315392 +0100
-@@ -6,6 +6,7 @@
- 
- M_INCL_DIR = ../include
- M_LIB_DIR  = ../lib
-+M_LIB_DIR_GENTOO = @GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
- M_BIN_DIR  = ../bin
- 
- PROJ_DIR   = .
-@@ -37,12 +38,12 @@
- include ../etc/Makefile.platform
- 
- # Dependent libraries for the pdbml-parser
--CIF_FILE_LIB      = $(M_LIB_DIR)/cif-file.a
--CIFPARSE_LIB      = $(M_LIB_DIR)/cifparse-obj.a
--CIF_TABLE_LIB     = $(M_LIB_DIR)/cif-table-obj.a
--CIFOBJ_COMMON_LIB = $(M_LIB_DIR)/cifobj-common.a
--REGEX_LIB         = $(M_LIB_DIR)/regex.a
--MISCLIB_LIB       = $(M_LIB_DIR)/misclib.a
-+CIF_FILE_LIB      = $(M_LIB_DIR_GENTOO)/cif-file.a
-+CIFPARSE_LIB      = $(M_LIB_DIR_GENTOO)/cifparse-obj.a
-+CIF_TABLE_LIB     = $(M_LIB_DIR_GENTOO)/tables.a
-+CIFOBJ_COMMON_LIB = $(M_LIB_DIR_GENTOO)/common.a
-+REGEX_LIB         = $(M_LIB_DIR_GENTOO)/regex.a
-+MISCLIB_LIB       = $(M_LIB_DIR_GENTOO)/misclib.a
- 
- ALL_DEP_LIBS = $(CIF_FILE_LIB) $(CIFPARSE_LIB) \
-   $(CIF_TABLE_LIB) $(CIFOBJ_COMMON_LIB) $(REGEX_LIB) $(MISCLIB_LIB)
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch
deleted file mode 100644
index cdf48e4784c6..000000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch
+++ /dev/null
@@ -1,199 +0,0 @@
-diff -Naur pdb-extract-v3.004-prod-src/Makefile pdb-extract-v3.004-prod-src.new/Makefile
---- pdb-extract-v3.004-prod-src/Makefile	2007-09-11 11:19:46.000000000 -0400
-+++ pdb-extract-v3.004-prod-src.new/Makefile	2009-12-03 21:34:10.000000000 -0500
-@@ -52,7 +52,7 @@
- 		echo "------------------------------------------------------------"; \
- 		echo "**** Making $$libdir ****"; \
- 		echo "------------------------------------------------------------"; \
--		(cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \
-+		(cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LDFLAGS_OPT="${LDFLAGS}" install) || exit 1; \
- 	done
- 
- beta:
-diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.darwin3 pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin3
---- pdb-extract-v3.004-prod-src/etc/make.platform.darwin3	2007-09-11 11:19:46.000000000 -0400
-+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin3	2009-12-03 21:34:10.000000000 -0500
-@@ -91,7 +91,7 @@
- DEFINES=$(GDEFINES) $(LDEFINES)
- 
- ## Global include directories
--GINCLUDES= 
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
- 
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -159,7 +159,7 @@
- STATIC_LINKING=
- 
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
- 
- # Fortran linker
- F77_LINKER=f77
-diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.darwin4 pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin4
---- pdb-extract-v3.004-prod-src/etc/make.platform.darwin4	2007-09-11 11:19:46.000000000 -0400
-+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin4	2009-12-03 21:34:10.000000000 -0500
-@@ -92,7 +92,7 @@
- DEFINES=$(GDEFINES) $(LDEFINES)
- 
- ## Global include directories
--GINCLUDES= 
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
- 
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -160,7 +160,7 @@
- STATIC_LINKING=
- 
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
- 
- # Fortran linker
- F77_LINKER=f77
-diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu3 pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu3
---- pdb-extract-v3.004-prod-src/etc/make.platform.gnu3	2007-09-11 11:19:46.000000000 -0400
-+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu3	2009-12-03 21:34:10.000000000 -0500
-@@ -6,6 +6,8 @@
- ##
- ##########################################################################
- 
-+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
-+
- #-----Lexer and Parser section-------------------------------------------#
- 
- # Lexer executable
-@@ -89,7 +91,7 @@
- DEFINES=$(GDEFINES) $(LDEFINES)
- 
- ## Global include directories
--GINCLUDES= 
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
- 
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -107,8 +109,8 @@
- C_WARNINGS=$(WARNINGS)
- 
- # C compiler flags
--CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
--CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
-+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
-                $(INCLUDES) 
- 
- ## C++ compiler
-@@ -128,9 +130,9 @@
- EXT=C
- 
- # C++ compiler flags
--C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
-+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
-         $(INCLUDES)
--C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-                  $(DEFINES) $(INCLUDES)
- # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
- # source code that is not maintained by PDB
-@@ -144,7 +146,7 @@
- F77=f77
- 
- # Fortran compiler flags
--FFLAGS=-O -u
-+FFLAGS=$(F_OPT)
- 
- # Additional Fortran libraries
- F77LIBS=
-@@ -154,11 +156,11 @@
- #-----Linkers section----------------------------------------------------#
- 
- # Static linking option. If not defined, dynamic linking is used.
--STATIC_LINKING=-static
-+STATIC_LINKING= 
- 
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
--LDFLAGS_NO_STATIC=$(ABI) -w
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
-+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w
- 
- # Fortran linker
- F77_LINKER=f77
-diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu4 pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu4
---- pdb-extract-v3.004-prod-src/etc/make.platform.gnu4	2007-09-11 11:19:46.000000000 -0400
-+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu4	2009-12-03 21:34:10.000000000 -0500
-@@ -6,6 +6,8 @@
- ##
- ##########################################################################
- 
-+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
-+
- #-----Lexer and Parser section-------------------------------------------#
- 
- # Lexer executable
-@@ -34,7 +36,7 @@
- 
- # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all
- # warnings as errors.
--WARNINGS_AS_ERRORS=-Werror
-+WARNINGS_AS_ERRORS=
- 
- # ALL_WARNINGS defines flags to instruct all compilers to report all
- # warnings.
-@@ -90,7 +92,7 @@
- DEFINES=$(GDEFINES) $(LDEFINES)
- 
- ## Global include directories
--GINCLUDES= 
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
- 
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -108,8 +110,8 @@
- C_WARNINGS=$(WARNINGS)
- 
- # C compiler flags
--CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
--CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
-+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
-                $(INCLUDES) 
- 
- ## C++ compiler
-@@ -129,9 +131,9 @@
- EXT=C
- 
- # C++ compiler flags
--C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
-+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
-         $(INCLUDES)
--C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-                  $(DEFINES) $(INCLUDES)
- # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
- # source code that is not maintained by PDB
-@@ -145,7 +147,7 @@
- F77=f77
- 
- # Fortran compiler flags
--FFLAGS=-O -u
-+FFLAGS=$(F_OPT)
- 
- # Additional Fortran libraries
- F77LIBS=
-@@ -155,11 +157,11 @@
- #-----Linkers section----------------------------------------------------#
- 
- # Static linking option. If not defined, dynamic linking is used.
--STATIC_LINKING=-static
-+STATIC_LINKING= 
- 
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
--LDFLAGS_NO_STATIC=$(ABI) -w
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
-+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w
- 
- # Fortran linker
- F77_LINKER=f77
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch
deleted file mode 100644
index 6506713742b6..000000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- pdb-extract-v3.0/src/extract.C	2007-09-11 17:19:48.000000000 +0200
-+++ pdb-extract-v3.0/src/extract.C.new	2008-12-05 17:49:59.000000000 +0100
-@@ -1689,7 +1689,7 @@
-         open_file_error(inpfile, "get_mmcif");
-     }
-     
--    (!strcmp_case(CCP4,"yes"))? temp = getenv("CCP4"): temp = getenv("PDB_EXTRACT");
-+    (!strcmp_case(CCP4,"yes"))? temp = getenv("CCP4"): temp = getenv("PDB_EXTRACT_ROOT");
-     if(temp != NULL) {
-         strcpy(pdb_extract, "");
-         strcpy(pdb_extract_sf, "");
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch
deleted file mode 100644
index 6907399c27df..000000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- cifobj-common-v4.1/src/GenString.C	2008-11-13 10:44:01.000000000 +0100
-+++ cifobj-common-v4.1/src/GenString.C.new	2008-11-13 10:43:54.000000000 +0100
-@@ -144,6 +144,7 @@
- #include <string>
- #include <algorithm>
- #include <sstream>
-+#include <string.h>
- 
- #include "GenString.h"
- 
---- tables-v8.0/src/ISTable.C	2007-09-11 17:19:47.000000000 +0200
-+++ tables-v8.0/src/ISTable.C.new	2008-11-13 10:48:18.000000000 +0100
-@@ -150,6 +150,7 @@
- #include <sstream>
- #include <iostream>
- #include <iomanip>
-+#include <limits.h>
- 
- #include "Exceptions.h"
- #include "GenString.h"
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch
deleted file mode 100644
index 7383811b5bfd..000000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch
+++ /dev/null
@@ -1,207 +0,0 @@
- Makefile                  |    2 +-
- etc/make.platform.darwin3 |    4 ++--
- etc/make.platform.darwin4 |    4 ++--
- etc/make.platform.gnu3    |   20 +++++++++++---------
- etc/make.platform.gnu4    |   20 +++++++++++---------
- 5 files changed, 27 insertions(+), 23 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 627d256..72c7e59 100644
---- a/Makefile
-+++ b/Makefile
-@@ -52,7 +52,7 @@ compile:
- 		echo "------------------------------------------------------------"; \
- 		echo "**** Making $$libdir ****"; \
- 		echo "------------------------------------------------------------"; \
--		(cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \
-+		(cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LDFLAGS_OPT="${LDFLAGS}" install) || exit 1; \
- 	done
- 
- beta:
-diff --git a/etc/make.platform.darwin3 b/etc/make.platform.darwin3
-index c5f7b06..4c1c97c 100644
---- a/etc/make.platform.darwin3
-+++ b/etc/make.platform.darwin3
-@@ -91,7 +91,7 @@ GDEFINES=$(PLATFORM) $(COMPILER)
- DEFINES=$(GDEFINES) $(LDEFINES)
- 
- ## Global include directories
--GINCLUDES= 
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
- 
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -159,7 +159,7 @@ F77LIBS=
- STATIC_LINKING=
- 
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
- 
- # Fortran linker
- F77_LINKER=f77
-diff --git a/etc/make.platform.darwin4 b/etc/make.platform.darwin4
-index 4619b34..f481fdb 100644
---- a/etc/make.platform.darwin4
-+++ b/etc/make.platform.darwin4
-@@ -92,7 +92,7 @@ GDEFINES=$(PLATFORM) $(COMPILER)
- DEFINES=$(GDEFINES) $(LDEFINES)
- 
- ## Global include directories
--GINCLUDES= 
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
- 
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -160,7 +160,7 @@ F77LIBS=
- STATIC_LINKING=
- 
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
- 
- # Fortran linker
- F77_LINKER=f77
-diff --git a/etc/make.platform.gnu3 b/etc/make.platform.gnu3
-index 7fd442e..9bec4dc 100644
---- a/etc/make.platform.gnu3
-+++ b/etc/make.platform.gnu3
-@@ -6,6 +6,8 @@
- ##
- ##########################################################################
- 
-+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
-+
- #-----Lexer and Parser section-------------------------------------------#
- 
- # Lexer executable
-@@ -89,7 +91,7 @@ GDEFINES=$(PLATFORM) $(COMPILER)
- DEFINES=$(GDEFINES) $(LDEFINES)
- 
- ## Global include directories
--GINCLUDES= 
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
- 
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -107,8 +109,8 @@ NON_ANSI_C_FLAG=
- C_WARNINGS=$(WARNINGS)
- 
- # C compiler flags
--CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
--CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
-+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
-                $(INCLUDES) 
- 
- ## C++ compiler
-@@ -128,9 +130,9 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED)
- EXT=C
- 
- # C++ compiler flags
--C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
-+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
-         $(INCLUDES)
--C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-                  $(DEFINES) $(INCLUDES)
- # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
- # source code that is not maintained by PDB
-@@ -144,7 +146,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \
- F77=f77
- 
- # Fortran compiler flags
--FFLAGS=-O -u
-+FFLAGS=$(F_OPT)
- 
- # Additional Fortran libraries
- F77LIBS=
-@@ -154,11 +156,11 @@ F77LIBS=
- #-----Linkers section----------------------------------------------------#
- 
- # Static linking option. If not defined, dynamic linking is used.
--STATIC_LINKING=-static
-+STATIC_LINKING= 
- 
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
--LDFLAGS_NO_STATIC=$(ABI) -w
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
-+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w
- 
- # Fortran linker
- F77_LINKER=f77
-diff --git a/etc/make.platform.gnu4 b/etc/make.platform.gnu4
-index 78a0007..bc85308 100644
---- a/etc/make.platform.gnu4
-+++ b/etc/make.platform.gnu4
-@@ -6,6 +6,8 @@
- ##
- ##########################################################################
- 
-+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
-+
- #-----Lexer and Parser section-------------------------------------------#
- 
- # Lexer executable
-@@ -34,7 +36,7 @@ ABI=
- 
- # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all
- # warnings as errors.
--WARNINGS_AS_ERRORS=-Werror
-+WARNINGS_AS_ERRORS=
- 
- # ALL_WARNINGS defines flags to instruct all compilers to report all
- # warnings.
-@@ -90,7 +92,7 @@ GDEFINES=$(PLATFORM) $(COMPILER)
- DEFINES=$(GDEFINES) $(LDEFINES)
- 
- ## Global include directories
--GINCLUDES= 
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
- 
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -108,8 +110,8 @@ NON_ANSI_C_FLAG=
- C_WARNINGS=$(WARNINGS)
- 
- # C compiler flags
--CFLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
--CFLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) 
-+CFLAGS=$(C_OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) 
- 
- ## C++ compiler
- ## This part defines C++ compiler information
-@@ -128,9 +130,9 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED)
- EXT=C
- 
- # C++ compiler flags
--C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-+C++FLAGS=$(CCC_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-   $(DEFINES) $(INCLUDES)
--C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \
-+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \
-   $(C_PLUS_WARNINGS) $(DEFINES) $(INCLUDES)
- 
- # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
-@@ -145,7 +147,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
- F77=f77
- 
- # Fortran compiler flags
--FFLAGS=-O -u
-+FFLAGS=$(F_OPT)
- 
- # Additional Fortran libraries
- F77LIBS=
-@@ -158,8 +160,8 @@ F77LIBS=
- STATIC_LINKING=
- 
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
--LDFLAGS_NO_STATIC=$(ABI) -w
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
-+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w
- 
- # Fortran linker
- F77_LINKER=f77
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch
deleted file mode 100644
index 5284bd745d53..000000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch
+++ /dev/null
@@ -1,64 +0,0 @@
- common-v4.5/src/mapped_ptr_vector.C |   14 +++++++-------
- 1 files changed, 7 insertions(+), 7 deletions(-)
-
-diff --git a/common-v4.5/src/mapped_ptr_vector.C b/common-v4.5/src/mapped_ptr_vector.C
-index d7c61f3..e20a236 100644
---- a/common-v4.5/src/mapped_ptr_vector.C
-+++ b/common-v4.5/src/mapped_ptr_vector.C
-@@ -263,12 +263,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(T* inP,
-     _vector.push_back(inP);
- 
-     typename tIndex::value_type valuePair(inP->GetName(),
--      make_pair(_vector.size() - 1, fileIndex));
-+      std::make_pair(_vector.size() - 1, fileIndex));
- 
-     _index.insert(valuePair);
- 
-     _currentName = inP->GetName();
--    _currentIndices = make_pair(_vector.size() - 1, fileIndex);
-+    _currentIndices = std::make_pair(_vector.size() - 1, fileIndex);
- 
- }
- 
-@@ -281,12 +281,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(const string& name,
-     _vector.push_back(NULL);
- 
-     typename tIndex::value_type valuePair(name,
--      make_pair(_vector.size() - 1, fileIndex));
-+      std::make_pair(_vector.size() - 1, fileIndex));
- 
-     _index.insert(valuePair);
- 
-     _currentName = name;
--    _currentIndices = make_pair(_vector.size() - 1, fileIndex);
-+    _currentIndices = std::make_pair(_vector.size() - 1, fileIndex);
- }
- 
- 
-@@ -454,7 +454,7 @@ void mapped_ptr_vector<T, StringCompareT>::erase(const string& name)
-     if (is_equal(_currentName, name, keyComp))
-     {
-         _currentName.clear();
--        _currentIndices = make_pair(_vector.size(), (unsigned int)0);
-+        _currentIndices = std::make_pair(_vector.size(), (unsigned int)0);
-     }
- 
- }
-@@ -539,7 +539,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic
-     if (_vector.empty())
-     {
-         // Empty container. Return invalid index.
--        return(make_pair(_vector.size(), (unsigned int)0));
-+        return(std::make_pair(_vector.size(), (unsigned int)0));
-     }
- 
-     typename tIndex::key_compare keyComp = _index.key_comp();
-@@ -563,7 +563,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic
-         else
-         {
-             // Not found. Return invalid index.
--            return(make_pair(_vector.size(), (unsigned int)0));
-+            return(std::make_pair(_vector.size(), (unsigned int)0));
-         } 
-     }
-     
diff --git a/sci-chemistry/pdb-extract/metadata.xml b/sci-chemistry/pdb-extract/metadata.xml
deleted file mode 100644
index e42d0af60f42..000000000000
--- a/sci-chemistry/pdb-extract/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>sci-chemistry</herd>
-</pkgmetadata>
diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild
deleted file mode 100644
index 836d76f5c007..000000000000
--- a/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-inherit eutils toolchain-funcs multilib prefix
-
-MY_P="${PN}-v${PV}-prod-src"
-
-DESCRIPTION="Tools for extracting mmCIF data from structure determination applications"
-HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html"
-SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz"
-
-LICENSE="PDB"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="!<app-text/html-xml-utils-5.3"
-DEPEND="${RDEPEND}
-	>=sci-libs/cifparse-obj-7.025"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-cflags-install.patch \
-		"${FILESDIR}"/${P}-gcc-4.3.patch \
-		"${FILESDIR}"/${P}-Makefile.patch \
-		"${FILESDIR}"/${P}-env.patch
-
-	sed -i "s:GENTOOLIBDIR:$(get_libdir):g" \
-		pdb-extract-v3.0/Makefile \
-		|| die "Failed to fix libdir"
-
-	# Get rid of unneeded directories, to make sure we use system files
-	ebegin "Deleting redundant directories"
-	rm -rf cif-file-v1.0 cifobj-common-v4.1 cifparse-obj-v7.0 \
-		misclib-v2.2 regex-v2.2 tables-v8.0
-	eend
-
-	sed -i \
-		-e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
-		-e "s:^\(CC=\).*:\1$(tc-getCC):g" \
-		-e "s:^\(GINCLUDES=\).*:\1-I${EPREFIX}/usr/include/cifparse-obj:g" \
-		-e "s:^\(LIBDIR=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		"${S}"/etc/make.* \
-		|| die "Failed to fix makefiles"
-
-	eprefixify pdb-extract-v3.0/Makefile etc/*
-}
-
-src_install() {
-	exeinto /usr/libexec/ccp4/bin
-	doexe bin/pdb_extract{,_sf} bin/extract \
-		|| die "failed to install binaries"
-	insinto /usr/include/rcsb
-	doins include/* || die "failed to install include files"
-	dodoc README* || die "failed to install docs"
-	insinto /usr/share/rcsb/
-	doins -r pdb-extract-data || die "failed to install data files"
-
-	cat >> "${T}"/envd <<- EOF
-	PDB_EXTRACT="${EPREFIX}/usr/share/rcsb/"
-	PDB_EXTRACT_ROOT="${EPREFIX}/usr/"
-	EOF
-
-	newenvd "${T}"/envd 20pdb-extract \
-		|| die "failed to install env files"
-}
diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild
deleted file mode 100644
index 04351c8a125a..000000000000
--- a/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils toolchain-funcs multilib prefix
-
-MY_P="${PN}-v${PV}-prod-src"
-
-DESCRIPTION="Tools for extracting mmCIF data from structure determination applications"
-HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html"
-SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz"
-
-LICENSE="PDB"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="!<app-text/html-xml-utils-5.3"
-DEPEND="${RDEPEND}
-	>=sci-libs/cifparse-obj-7.025"
-
-S="${WORKDIR}/${MY_P}"
-
-MAKEOPTS+=" -j1"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-cflags-install.patch \
-		"${FILESDIR}"/${P}-gcc-4.7.patch \
-		"${FILESDIR}"/${PN}-3.004-env.patch
-
-	sed -i \
-		-e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
-		-e "s:^\(CC=\).*:\1$(tc-getCC):g" \
-		-e "s:^\(GINCLUDES=\).*:\1-I${EPREFIX}/usr/include/cifparse-obj:g" \
-		-e "s:^\(LIBDIR=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		"${S}"/etc/make.* \
-		|| die "Failed to fix makefiles"
-
-	eprefixify pdb-extract-v3.0/Makefile etc/*
-}
-
-src_install() {
-	exeinto /usr/libexec/ccp4/bin
-	doexe bin/pdb_extract{,_sf} bin/extract
-	insinto /usr/include/rcsb
-	doins include/*
-	dodoc README*
-	insinto /usr/share/rcsb/
-	doins -r pdb-extract-data
-
-	cat >> "${T}"/envd <<- EOF
-	PDB_EXTRACT="${EPREFIX}/usr/share/rcsb/"
-	PDB_EXTRACT_ROOT="${EPREFIX}/usr/"
-	EOF
-
-	newenvd "${T}"/envd 20pdb-extract
-}
diff --git a/sci-chemistry/phaser/Manifest b/sci-chemistry/phaser/Manifest
deleted file mode 100644
index deb3ba972a75..000000000000
--- a/sci-chemistry/phaser/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ccp4-6.1.13-phaser-cctbx-src.tar.gz 22021353 SHA256 e6c4365cb34da5ce2dd5f1e74b8927258064016194446163418c8a3139a4b804 SHA512 cdf36572613a6e400af0f29da501ccfd2a9f1a7e2d89162aad3fe14929816b41790bb57ba1e77976b9046c6e06a29df2748999db93a2cd0a4d1fde95ac1f9e8b WHIRLPOOL 5aa1a1c6520be90ef02be0e9de9c111a9835cda05a3549c390f62ceef7e68c8392670d91941b823c0ee94f29e6aab9d34a61b90e8bd3d4820a83daa547463fdb
diff --git a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch b/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch
deleted file mode 100644
index 5311cb332785..000000000000
--- a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py
-index 3b1bd3a..8939a74 100755
---- a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py
-+++ b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py
-@@ -802,8 +802,6 @@ class environment:
-     else:
-       action = self.write_bin_sh_dispatcher
-       ext = ""
--      try: os.chmod(source_file, 0755)
--      except OSError: pass
-     target_file_ext = target_file + ext
-     remove_or_rename(target_file_ext)
-     try: action(source_file, target_file_ext)
diff --git a/sci-chemistry/phaser/metadata.xml b/sci-chemistry/phaser/metadata.xml
deleted file mode 100644
index 6b4826474daa..000000000000
--- a/sci-chemistry/phaser/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-  <maintainer>
-    <email>jlec@gentoo.org</email>
-    <description>ccp4 maintainer</description>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/phaser/phaser-2.1.4.ebuild b/sci-chemistry/phaser/phaser-2.1.4.ebuild
deleted file mode 100644
index 86fa57f52603..000000000000
--- a/sci-chemistry/phaser/phaser-2.1.4.ebuild
+++ /dev/null
@@ -1,115 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic python-single-r1 toolchain-funcs
-
-CCP4VER="6.1.13"
-
-DESCRIPTION="A program for phasing macromolecular crystal structures"
-HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser"
-SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/${CCP4VER}/ccp4-${CCP4VER}-${PN}-cctbx-src.tar.gz"
-
-LICENSE="|| ( phaser phaser-com ccp4 )"
-SLOT="0"
-#KEYWORDS="~amd64 ~x86"
-KEYWORDS=""
-IUSE="openmp"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-		  app-shells/tcsh"
-
-S="${WORKDIR}"/ccp4-${CCP4VER}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/phaser-2.1.4-chmod.patch \
-		"${FILESDIR}"/phaser-2.1.4-ldflags.patch
-
-	use openmp && append-flags -fopenmp
-
-	for i in ${CXXFLAGS}; do
-		OPTS="${OPTS} \"${i}\","
-	done
-
-	OPTS=${OPTS%,}
-
-	sed -i \
-		-e "s:opts = \[.*\]$:opts = \[${OPTS}\]:g" \
-		"${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die
-
-	for i in ${LDFLAGS}; do
-		OPTSLD="${OPTSLD} \"${i}\","
-	done
-
-	sed -i \
-		-e "s:env_etc.shlinkflags .* \"-shared\":env_etc.shlinkflags = \[ ${OPTSLD} \"-shared\"\]:g" \
-		-e "s:\[\"-static:\[${OPTSLD} \"-static:g" \
-		"${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die
-
-}
-
-src_configure() {
-	local compiler
-	local mtype
-	local mversion
-	local nproc
-
-	# Valid compilers are win32_cl, sunos_CC, unix_gcc, unix_ecc,
-	# unix_icc, unix_icpc, tru64_cxx, hp_ux11_aCC, irix_CC,
-	# darwin_c++, darwin_gcc.  The build systems seems to prepend
-	# unix_ all by itself.  Can this be derived from $(tc-getCC)?
-	compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
-
-	# Breaks cross compilation.
-	mtype=$(src/${PN}/bin/machine_type)
-	mversion=$(src/${PN}/bin/machine_version)
-
-	einfo "Creating build directory"
-	mkdir build
-	cd build
-	ln -sf "${S}/lib/cctbx/cctbx_sources/scons"  scons
-	ln -sf "${S}/lib/cctbx/cctbx_sources/libtbx" libtbx
-
-	einfo "Configuring phaser components"
-	$(PYTHON) "libtbx/configure.py" \
-		--build=release \
-		--compiler=${compiler} \
-		--repository="${S}"/src/${PN}/source \
-		--repository="${S}"/lib/cctbx/cctbx_sources \
-		--static_libraries \
-		ccp4io="${S}" \
-		mmtbx \
-		phaser || die "configure.py failed"
-}
-
-src_compile() {
-	nproc=`echo "-j1 ${MAKEOPTS}" \
-		| sed -e "s/.*\(-j\s*\|--jobs=\)\([0-9]\+\).*/\2/"`
-
-	cd build
-	einfo "Setting up build environment"
-	source setpaths.sh
-
-	einfo "Compiling phaser components"
-	libtbx.scons -j ${nproc} || die "libtbx.scons failed"
-}
-
-src_install() {
-	dobin build/exe/phaser || die
-
-	cat >> "${T}"/53${PN} <<- EOF
-	PHASER="${EPREFIX}/usr/bin"
-	PHASER_ENVIRONMENT="1"
-	PHASER_MTYPE="${mtype}"
-	PHASER_MVERSION="${mversion}"
-	PHASER_VERSION="${PV}"
-	EOF
-
-	doenvd "${T}"/53${PN} || die
-}
diff --git a/sci-chemistry/pointless/Manifest b/sci-chemistry/pointless/Manifest
deleted file mode 100644
index 911c44875112..000000000000
--- a/sci-chemistry/pointless/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST pointless-1.6.14.tar.gz 423657 SHA256 68f0c1f65239b1451310fe885c2b9d51fc558de7b43af1e584750e05dc5635d8 SHA512 9dd524a7c842edc01206450c52ca1a01e8e3ee6f9ff71742789943ee10e006b5452b0be3aa509dd16bb85f1b9c3d7954616a78ec2fef2daea7c0ab42cdaa42b9 WHIRLPOOL 5085afbd88713384039ef2c2b4b2f7fddd8f078dca9df54062b0415e970791868c61df98f4044b4e061077a73b4e129b6e5db34852d64cace48108db9c6ae50f
-DIST pointless-1.6.2.tar.gz 412244 SHA256 5e09ca592ea565e8ace142fc0edff39d0ab723f4ac6e2cadd6ba571d667c80f6 SHA512 2e897a7302ba4d43da69c8ee91254b0632d8a0ae301140a144472f7e466078f0b1abd10362343d7d50d04bd86ae8b83265a20302f7aeae3dc8845f1581211ddd WHIRLPOOL 8953806f68684e882717673ec18263f0ac2093f3cb2cac573b20886f5f0d60c67b756f74bdb3555342bb3d287021b7c70b20c53f0e38e687a5914df935ae35cd
diff --git a/sci-chemistry/pointless/files/1.5.1-gcc4.4.patch b/sci-chemistry/pointless/files/1.5.1-gcc4.4.patch
deleted file mode 100644
index ca67dbd3f336..000000000000
--- a/sci-chemistry/pointless/files/1.5.1-gcc4.4.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/string_util.hh b/string_util.hh
-index 66af6f3..047512b 100644
---- a/string_util.hh
-+++ b/string_util.hh
-@@ -3,6 +3,7 @@
- 
- #include <string>
- #include <vector>
-+#include <stdio.h>
- #include "range.hh"
- 
- //======================================================================
diff --git a/sci-chemistry/pointless/metadata.xml b/sci-chemistry/pointless/metadata.xml
deleted file mode 100644
index ae9ec7c5f6a4..000000000000
--- a/sci-chemistry/pointless/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-  <maintainer>
-    <email>jlec@gentoo.org</email>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/pointless/pointless-1.6.14-r1.ebuild b/sci-chemistry/pointless/pointless-1.6.14-r1.ebuild
deleted file mode 100644
index d983cb290242..000000000000
--- a/sci-chemistry/pointless/pointless-1.6.14-r1.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils fortran-2 multilib python-single-r1 toolchain-funcs
-
-DESCRIPTION="Scores crystallographic Laue and space groups"
-HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html"
-SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="
-	sci-chemistry/ccp4-apps
-	>=sci-libs/ccp4-libs-6.1.3-r10
-	sci-libs/clipper
-	sci-libs/fftw:2.1
-	sci-libs/mmdb
-	>=sci-libs/cctbx-2010.03.29.2334-r3[${PYTHON_USEDEP}]"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/1.5.1-gcc4.4.patch
-}
-
-src_compile() {
-	emake  \
-		-f Makefile.make \
-		CC=$(tc-getCC) \
-		CXX=$(tc-getCXX) \
-		CFLAGS="${CFLAGS}" \
-		CXXFLAGS="${CXXFLAGS}" \
-		LFLAGS="${LDFLAGS}" \
-		CLIB="${EPREFIX}/usr/$(get_libdir)" \
-		CCTBX_VERSION=2010 \
-		ICCP4=-I"${EPREFIX}/usr/include/ccp4" \
-		ITBX="-I${EPREFIX}/usr/include" \
-		ICLPR="-I${EPREFIX}/$(python_get_sitedir)/" \
-		LTBX="-L${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \
-		SLIB="-L${EPREFIX}/usr/$(get_libdir) -lgfortran"
-}
-
-src_install() {
-	dobin pointless othercell
-}
diff --git a/sci-chemistry/pointless/pointless-1.6.14.ebuild b/sci-chemistry/pointless/pointless-1.6.14.ebuild
deleted file mode 100644
index 158bde017aea..000000000000
--- a/sci-chemistry/pointless/pointless-1.6.14.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="3"
-
-PYTHON_DEPEND="2"
-
-inherit eutils fortran-2 multilib python toolchain-funcs
-
-DESCRIPTION="Scores crystallographic Laue and space groups"
-HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html"
-SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="
-	sci-chemistry/ccp4-apps
-	>=sci-libs/ccp4-libs-6.1.3-r10
-	sci-libs/clipper
-	sci-libs/fftw:2.1
-	sci-libs/mmdb
-	>=sci-libs/cctbx-2010.03.29.2334-r3"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python_set_active_version 2
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/1.5.1-gcc4.4.patch
-}
-
-src_compile() {
-	emake  \
-		-f Makefile.make \
-		CC=$(tc-getCC) \
-		CXX=$(tc-getCXX) \
-		CFLAGS="${CFLAGS}" \
-		CXXFLAGS="${CXXFLAGS}" \
-		LFLAGS="${LDFLAGS}" \
-		CLIB="${EPREFIX}/usr/$(get_libdir)" \
-		CCTBX_VERSION=2010 \
-		ICCP4=-I"${EPREFIX}/usr/include/ccp4" \
-		ITBX="-I${EPREFIX}/usr/include" \
-		ICLPR="-I${EPREFIX}/$(python_get_sitedir)/" \
-		LTBX="-L${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \
-		SLIB="-L${EPREFIX}/usr/$(get_libdir) -lgfortran" \
-		|| die
-}
-
-src_install() {
-	dobin pointless othercell || die
-}
diff --git a/sci-chemistry/pointless/pointless-1.6.2.ebuild b/sci-chemistry/pointless/pointless-1.6.2.ebuild
deleted file mode 100644
index 2b9f0ad4faa0..000000000000
--- a/sci-chemistry/pointless/pointless-1.6.2.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-PYTHON_DEPEND="2"
-
-inherit eutils fortran-2 multilib python toolchain-funcs
-
-DESCRIPTION="Scores crystallographic Laue and space groups"
-HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html"
-SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="
-	sci-chemistry/ccp4-apps
-	>=sci-libs/ccp4-libs-6.1.3-r10
-	sci-libs/clipper
-	sci-libs/fftw:2.1
-	sci-libs/mmdb
-	>=sci-libs/cctbx-2010.03.29.2334-r3"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python_pkg_setup
-	python_set_active_version 2
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/1.5.1-gcc4.4.patch
-}
-
-src_compile() {
-	emake  \
-		-f Makefile.make \
-		CC=$(tc-getCC) \
-		CXX=$(tc-getCXX) \
-		CFLAGS="${CFLAGS}" \
-		CXXFLAGS="${CXXFLAGS}" \
-		LFLAGS="${LDFLAGS}" \
-		CLIB="${EPREFIX}/usr/$(get_libdir)" \
-		CCTBX_VERSION=2010 \
-		ICCP4=-I"${EPREFIX}/usr/include/ccp4" \
-		ITBX="-I${EPREFIX}/usr/include" \
-		ICLPR="-I${EPREFIX}/$(python_get_sitedir)/" \
-		LTBX="-L${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \
-		SLIB="-L${EPREFIX}/usr/$(get_libdir) -lgfortran"
-}
-
-src_install() {
-	dobin pointless othercell
-}
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
deleted file mode 100644
index ba3def103020..000000000000
--- a/sci-chemistry/refmac/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST refmac_5.5.0110.tar.gz 1326832 SHA256 1353fb1042586ec8fa37d0a90f274890d0ccc02377af5216200662338dfe08ca SHA512 7e7fd1a7d2d11ef5f2e08cae61da62ecfe6978730ce4ca80f8b00be9bdad5e7d0ad493e1b8d57d64f1393f2017a87b8342e2607b08bc4018def798038a111728 WHIRLPOOL 587260eebd2df3115ba01ee03c11ab773d7316100a09af1f259f7795a139f978d94c569b8e4ab85982c2eeda628e643376231bdca5311fc8c7d2de5b65a033ac
-DIST test-framework.tar.gz 130933173 SHA256 df050a2a29da80518cb0616a0bbeb82298ea0721549348d15353bf0f66240605 SHA512 3ef8253f472c5a481f836291afb80746ad73858e130130b848851b6b5dc53ada3b78c9f853af1c46fa22f469f2ce2f3248f5f760950e118610922c0429a7da16 WHIRLPOOL 022c1b493ecd35e769b44d1e52a351b4883682ef9759626bac36e26cc61078d95de0ec2531ed706897c683c38727139fa7a13d06b64c597026817ed79612d16d
diff --git a/sci-chemistry/refmac/files/5.5-test.log.patch b/sci-chemistry/refmac/files/5.5-test.log.patch
deleted file mode 100644
index 61858be357a0..000000000000
--- a/sci-chemistry/refmac/files/5.5-test.log.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- test-framework/refmac5/test_refmac5.py	2009-06-29 15:45:37.000000000 +0200
-+++ test-framework/refmac5/test_refmac5.py.new	2009-06-29 15:48:05.000000000 +0200
-@@ -88,7 +88,8 @@
-              'make hydr no',
-              'labin IP=IMEAN SIGIP=SIGIMEAN FREE=FreeR_flag',
-              'labout FC=FC PHIC=PHIC'],
--            working_directory = self.test_dir)
-+            working_directory = self.test_dir,
-+            log_file = 'test_twinned_refinement.log')
- 
-         self.assertEqual(status, 0)
- 
-@@ -123,7 +124,8 @@
-              'weight auto',
-              'ncyc 20',
-              'labout FC=FC PHIC=PHIC'],
--            working_directory = self.test_dir)
-+            working_directory = self.test_dir,
-+            log_file = 'test_4_domain_tls.log')
- 
-         self.assertEqual(status, 0)
- 
-@@ -156,7 +158,8 @@
-              'anomalous form SE -9.9 3.9',
-              'anomalous wavelength 0.97966',
-              'labout FC=FC PHIC=PHIC'],
--            working_directory = self.test_dir)
-+            working_directory = self.test_dir,
-+            log_file = 'test_sad_refinement.log')
- 
-         self.assertEqual(status, 0)
- 
diff --git a/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch
deleted file mode 100644
index 1efbaa04d9e6..000000000000
--- a/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,84 +0,0 @@
-diff --git a/makefile b/makefile
-index 66d4cee..5270677 100644
---- a/makefile
-+++ b/makefile
-@@ -9,7 +9,7 @@ XFFLAGS = -fno-second-underscore -static
- XCFLAGS = -DGFORTRAN -DPROTOTYPE
- FFLAGS = $(FOPTIM) $(XFFLAGS) 
- CFLAGS = $(COPTIM) $(XCFLAGS)
--CPPFLAGS = $(CFLAGS)
-+CPPFLAGS = $(CXXFLAGS) $(XCFLAGS)
- 
- LLIBCIF = 
- LLIBCCP = $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a 
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 371d84d..557077f 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -68,9 +68,7 @@ messy_pdb.o                 \
- bridge.o                    \
- i0.o                        \
- i1.o                        \
--chbevl.o                    \
--$(LLIBCIF)                  \
--$(LLIBLAPACK)
-+chbevl.o                    
- #$(LLIBCCP)                  \
- #crt0.o                      \
- #heavy.o                     \
-@@ -95,8 +93,7 @@ make_unix_ccp4.o            \
- emin.o                      \
- libcheck_min.o              \
- mol2_file.o                 \
--sdf_files.o                 \
--$(LLIBCCP)
-+sdf_files.o                 
- 
- SUBM =                      \
- main_makecif.o              \
-@@ -116,9 +113,7 @@ make_rst2.o                 \
- make_PDB.o                  \
- makecif.o                   \
- make_unix_ccp4.o            \
--make_vdw.o                  \
--$(LLIBCCP)                  \
--$(LLIBCIF)
-+make_vdw.o                  
- 
- SUBT =                      \
- tlsgroups.o                 \
-@@ -142,9 +137,7 @@ make_refmac_dummy.o         \
- inout_routines.o            \
- errwrt_1.o                  \
- linalgebra.o                \
--subnumrec.o                 \
--$(LLIBCCP)                  \
--$(LLIBCIF)
-+subnumrec.o                 
- #--------------------------------------------------------------------------------
- 
- ed = echo 'g/^CMDW-5.0/s//        /@w@q@' | tr "@" "\012" | ed -s
-@@ -154,18 +147,19 @@ ed = echo 'g/^CMDW-5.0/s//        /@w@q@' | tr "@" "\012" | ed -s
- all:	refmac libcheck makecif
- 
- refmac:	$(SUBR)
--	$(FC) $(FFLAGS) $(LDFLAGF)-o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
- 
- libcheck:	$(SUBL)
--	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP)
- 
- makecif:	$(SUBM)
--	$(FC) $(FFLAGS) -o makecif${VERSION} $(SUBM)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o makecif${VERSION} $(SUBM) $(LLIBCCP) $(LLIBCIF)
- 
- tlsgroups:	$(SUBT)
--	$(FC) $(FFLAGS) -o tlsgroups${VERSION} $(SUBT)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o tlsgroups${VERSION} $(SUBT) $(LLIBCCP) $(LLIBCIF)
- 
- clean:
- 	/bin/rm *.o
- 
- bridge.o:			bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h
-+	$(CXX) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch b/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch
deleted file mode 100644
index 3969cc9c8586..000000000000
--- a/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch
+++ /dev/null
@@ -1,17 +0,0 @@
- hkon_secder_tch.f |    3 ++-
- 1 files changed, 2 insertions(+), 1 deletions(-)
-
-diff --git a/hkon_secder_tch.f b/hkon_secder_tch.f
-index 31794b0..86d2cdf 100644
---- a/hkon_secder_tch.f
-+++ b/hkon_secder_tch.f
-@@ -3724,7 +3724,8 @@ c---External functions and subprutines
-       INTEGER NWORKSPACE
-       REAL*8 TOLER
-       REAL*8 WORKSPACE(300)
--      REAL LSTLSQ,D2DF_WEIGHT
-+      REAL*8 D2DF_WEIGHT
-+      REAL LSTLSQ
- C
-       INTEGER IBIN,IBIN_S
-       INTEGER I,J,K
diff --git a/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch
deleted file mode 100644
index 9998b759c664..000000000000
--- a/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,341 +0,0 @@
- makefile_refmac.inc1 |  215 ++++++++++++++++++++++++--------------------------
- 1 files changed, 104 insertions(+), 111 deletions(-)
-
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 0f8bd63..e59fbfb 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -96,9 +96,7 @@ bridge.o                    \
- i0.o                        \
- i1.o                        \
- chbevl.o                    \
--make_unix_ccp4.o            \
--$(LLIBCIF)                  \
--$(LLIBLAPACK)
-+make_unix_ccp4.o
- 
- 
- SUBL =                      \
-@@ -133,9 +131,7 @@ cell_symm_subrs.o           \
- iheap_sort.o                \
- linalgebra.o                \
- math_refmac.o               \
--subnumrec.o                 \
--$(LLIBLAPACK)               \
--$(LLIBCCP)
-+subnumrec.o
- 
- SUB_FREE  =                 \
- freer_twin.o                 \
-@@ -145,9 +141,7 @@ subnumrec.o                 \
- libT.o                      \
- iheap_sort.o                \
- cell_symm_subrs.o           \
--math_refmac.o               \
--$(LLIBLAPACK)               \
--$(LLIBCCP)
-+math_refmac.o
- 
- SUB_HEADER = header2matr.o
- #--------------------------------------------------------------------------------
-@@ -185,41 +179,41 @@ rharvest_mod.o:  rharvest_mod.f90
- twin77mod.o:  twin77mod.f
- 	$(FC) $(FFLAGS) -c twin77mod.f
- 
--gibbs_gm_sampler.o:  linalgebra_f90.f90 gibbs_gm_sampler.f90
--	$(FC) $(FFLAGS) -c linalgebra_f90.f90 gibbs_gm_sampler.f90
-+gibbs_gm_sampler.o:  linalgebra_f90.o gibbs_gm_sampler.f90
-+	$(FC) $(FFLAGS) -c gibbs_gm_sampler.f90
- 
--max_with_twins.o: restr_files.f90 max_with_twins.f weights.f90 agreem.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 max_with_twins.f
-+max_with_twins.o: restr_files.o max_with_twins.f weights.o agreem.o
-+	$(FC) $(FFLAGS) -c max_with_twins.f
- 
--merohedr_twin.o: restr_files.f90 merohedr_twin.f
--	$(FC) $(FFLAGS) -c restr_files.f90 merohedr_twin.f
-+merohedr_twin.o: restr_files.o merohedr_twin.f
-+	$(FC) $(FFLAGS) -c merohedr_twin.f
- 
--ls_scaling_twin_save.o: restr_files.f90 ls_scaling_twin_save.f weights.f90 agreem.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ls_scaling_twin_save.f
-+ls_scaling_twin_save.o: restr_files.o ls_scaling_twin_save.f weights.o agreem.o
-+	$(FC) $(FFLAGS) -c ls_scaling_twin_save.f
- 
--ml_params_refine.o: restr_files.f90 ml_params_refine.f weights.f90 agreem.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ml_params_refine.f
-+ml_params_refine.o: restr_files.o ml_params_refine.f weights.o agreem.o
-+	$(FC) $(FFLAGS) -c ml_params_refine.f
- 
--optimise_solvent_all.o: optimise_solvent_all.f90 agreem.f90
--	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 agreem.f90
-+optimise_solvent_all.o: optimise_solvent_all.f90 agreem.o
-+	$(FC) $(FFLAGS) -c optimise_solvent_all.f90
- 
--ncs_rest.o: ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f
-+ncs_rest.o: ncs_rest_mod.o restr_files.o ncs_ncs_generate.o ncs_rest.f weights.o
-+	$(FC) $(FFLAGS) -c ncs_rest.f
- 
--ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.f90
--	$(FC) $(FFLAGS) -c ncs_ncs_generate.f90 align_refmac.f90
-+ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.o
-+	$(FC) $(FFLAGS) -c ncs_ncs_generate.f90
- 
--lsq_exp2.o: ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90  lsq_exp2.f weights.f90 rharvest_mod.f90
-+lsq_exp2.o: ncs_rest_mod.o restr_files.o dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f weights.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c lsq_exp2.f
- 
--vdw_and_contacts.o: ncs_rest_mod.f90 vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f
-+vdw_and_contacts.o: ncs_rest_mod.o vdw_and_contacts.f local_tls.o ridge.o restr_files.o weights.o agreem.o
-+	$(FC) $(FFLAGS) -c vdw_and_contacts.f
- 
- dist_routines.o: dist_routines.f90
- 	$(FC) $(FFLAGS) -c dist_routines.f90
- 
--ncs_simil.o: ncs_rest_mod.f90 ncs_simil.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 ncs_simil.f90
-+ncs_simil.o: ncs_rest_mod.o ncs_simil.f90
-+	$(FC) $(FFLAGS) -c ncs_simil.f90
- 
- ridge.o: ridge.f90
- 	$(FC) $(FFLAGS) -c ridge.f90
-@@ -227,140 +221,138 @@ ridge.o: ridge.f90
- align_refmac.o: align_refmac.f90
- 	$(FC) $(FFLAGS) -c align_refmac.f90
- 
--rigid_allocate.o: restr_files.f90 rigid_allocate.f agreem.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 agreem.f90 rigid_allocate.f
-+rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o
-+	$(FC) $(FFLAGS) -c rigid_allocate.f
- 
--tls_allocate.o: restr_files.f90 tls_allocate.f weights.f90 agreem.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 tls_allocate.f
-+tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o
-+	$(FC) $(FFLAGS) -c tls_allocate.f
- 
--hkon_secder_tch.o: ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \
--                   restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \
--	                   hkon_secder_tch.f weights.f90 agreem.f90 rharvest_mod.f90
-+hkon_secder_tch.o: ridge.o gibbs_gm_sampler.o ncs_rest_mod.o hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \
-+                   restr_files.o weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c hkon_secder_tch.f
- 
--oppro_allocate.o: ncs_rest_mod.f90 oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f
-+oppro_allocate.o: ncs_rest_mod.o oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o
-+	$(FC) $(FFLAGS) -c oppro_allocate.f
- 
--read_extra_restraints.o: restr_files.f90 read_extra_restraints.f weights.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 read_extra_restraints.f
-+read_extra_restraints.o: restr_files.o read_extra_restraints.f weights.o
-+	$(FC) $(FFLAGS) -c read_extra_restraints.f
- 
--coords.o: coords.f90 atomf77mod.f
--	$(FC) $(FFLAGS) -c atomf77mod.f coords.f90
-+coords.o: coords.f90 atomf77mod.o
-+	$(FC) $(FFLAGS) -c coords.f90
- 
- 
--ls_scaling_double.o: ls_scaling_double.f weights.f90 agreem.f90
--	$(FC) $(FFLAGS) -c ls_scaling_double.f weights.f90 agreem.f90
-+ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o
-+	$(FC) $(FFLAGS) -c ls_scaling_double.f
- 
--fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90 
--	$(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90
-+fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o
-+	$(FC) $(FFLAGS) -c fast_hessian_tabulation.f
- 
--calc_stats_twin.o: calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90
-+calc_stats_twin.o: calc_stats_twin.f weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c calc_stats_twin.f
- 
--refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 weights.f90 agreem.f90 rharvest_mod.f90 refpre_twin.f
-+refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.o weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c refpre_twin.f
- 
- 
--decide_twin_opers_0.o: restr_files.f90 decide_twin_opers_0.f
--	$(FC) $(FFLAGS) -c restr_files.f90 decide_twin_opers_0.f
-+decide_twin_opers_0.o: restr_files.o decide_twin_opers_0.f
-+	$(FC) $(FFLAGS) -c decide_twin_opers_0.f
- 
- automorphism.o: automorphism.f90
- 	$(FC) $(FFLAGS) -c automorphism.f90
- 
--mtz_write_twin.o: mtz_write_twin.f filter_params.f90 restr_files.f90 weights.f90 agreem.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 weights.f90 agreem.f90 mtz_write_twin.f
-+mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.o weights.o agreem.o
-+	$(FC) $(FFLAGS) -c mtz_write_twin.f
- 
- filter_params.o: filter_params.f90
- 	$(FC) $(FFLAGS) -c filter_params.f90
- 
--rcard_tor1.o: ncs_rest_mod.f90 rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 \
--              agreem.f90 rharvest_mod.f90 ncs_constr.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 weights.f90 \
--	                   agreem.f90 rharvest_mod.f90 ncs_constr.f90 rcard_tor1.f
-+rcard_tor1.o: ncs_rest_mod.o rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o restr_files.o weights.o \
-+              agreem.o rharvest_mod.o ncs_constr.o
-+	$(FC) $(FFLAGS) -c rcard_tor1.f
- 
--inout_routines.o: restr_files.f90 inout_routines.f
--	$(FC) $(FFLAGS) -c restr_files.f90 inout_routines.f
-+inout_routines.o: restr_files.o inout_routines.f
-+	$(FC) $(FFLAGS) -c inout_routines.f
- 
--local_tls.o: local_tls.f90 linalgebra_f90.f90
--	$(FC) $(FFLAGS) -c linalgebra_f90.f90 local_tls.f90
-+local_tls.o: local_tls.f90 linalgebra_f90.o
-+	$(FC) $(FFLAGS) -c local_tls.f90
- 
- linalgebra_f90.o: linalgebra_f90.f90 
- 	$(FC) $(FFLAGS) -c linalgebra_f90.f90
- 
--make_refmac_dummy.o: restr_files.f90 ncs_rest_mod.f90 make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 ncs_rest_mod.f90 weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f
-+make_refmac_dummy.o: restr_files.o ncs_rest_mod.o make_refmac_dummy.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c make_refmac_dummy.f
- 
--ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ml_scaling_double.f
-+ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c ml_scaling_double.f
- 
--refall_twin.o: refall_twin.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90  weights.f90 agreem.f90 rharvest_mod.f90 refall_twin.f
-+refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.f90 weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c refall_twin.f
- 
--rharvest_subr.o: ncs_rest_mod.f90 rharvest_subr.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 optimise_solvent_all.f90  weights.f90 agreem.f90 rharvest_mod.f90 rharvest_subr.f
-+rharvest_subr.o: ncs_rest_mod.o rharvest_subr.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c rharvest_subr.f
- 
--solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90
--	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 solvent_contr_mask.f
-+solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ncs_constr.o
-+	$(FC) $(FFLAGS) -c solvent_contr_mask.f
- 
--subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 subag_scale_hessian.f
-+subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.o weights.o agreem.o rharvest_mod.o ncs_constr.o
-+	$(FC) $(FFLAGS) -c subag_scale_hessian.f
- 
--aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.f90
--	$(FC) $(FFLAGS) -c ncs_constr.f90 aniso_ref_eigen.f
-+aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.o
-+	$(FC) $(FFLAGS) -c aniso_ref_eigen.f
- 
--subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 subcf_scale1.f
-+subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c subcf_scale1.f
- 
--bvalue_routines.o: bvalue_routines.f90 restr_files.f90 atomf77mod.f
--	$(FC) $(FFLAGS) -c restr_files.f90 atomf77mod.f bvalue_routines.f90
-+bvalue_routines.o: bvalue_routines.f90 restr_files.o atomf77mod.o
-+	$(FC) $(FFLAGS) -c bvalue_routines.f90
- 
--newentry_idealise.o:: newentry_idealise.f weights.f90
--	$(FC) $(FFLAGS) -c newentry_idealise.f weights.f90
-+newentry_idealise.o:: newentry_idealise.f weights.o
-+	$(FC) $(FFLAGS) -c newentry_idealise.f
- 
--occupancy_only_refine.o: occupancy_only_refine.f agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c occupancy_only_refine.f agreem.f90 rharvest_mod.f90
-+occupancy_only_refine.o: occupancy_only_refine.f agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c occupancy_only_refine.f
- 
--refmac_completeness.o: weights.f90 agreem.f90 rharvest_mod.f90  refmac_completeness.f90
--	$(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90
-+refmac_completeness.o: weights.o agreem.o rharvest_mod.o refmac_completeness.f90
-+	$(FC) $(FFLAGS) -c refmac_completeness.f90
- 
--refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refmac_xml.f
-+refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c refmac_xml.f
- 
- hkl_pack.o:  hkl_pack.f90
- 	$(FC) $(FFLAGS) -c hkl_pack.f90
- 
--extra_eigen.o: extra_eigen.f agreem.f90 ncs_constr.f90
--	$(FC) $(FFLAGS) -c extra_eigen.f agreem.f90 ncs_constr.f90
-+extra_eigen.o: extra_eigen.f agreem.o ncs_constr.o
-+	$(FC) $(FFLAGS) -c extra_eigen.f
- 
--subvag.o: subvag.f hkl_pack.f90
--	$(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f
-+subvag.o: subvag.f hkl_pack.o
-+	$(FC) $(FFLAGS) -c subvag.f
- 
--make_PDB.o: make_PDB.f ncs_constr.f90
--	$(FC) $(FFLAGS) -c ncs_constr.f90 make_PDB.f
-+make_PDB.o: make_PDB.f ncs_constr.o
-+	$(FC) $(FFLAGS) -c make_PDB.f
- 
--make_CIF.o: make_CIF.f ncs_constr.f90
--	$(FC) $(FFLAGS) -c ncs_constr.f90 make_CIF.f
-+make_CIF.o: make_CIF.f ncs_constr.o
-+	$(FC) $(FFLAGS) -c make_CIF.f
- 
- refmac:	$(SUBR)
--	$(FC) $(FFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
- 
--mol2_file.o:	mol2_file.f odb_files.f90
--	$(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f
-+mol2_file.o:	mol2_file.f odb_files.o
-+	$(FC) $(FFLAGS) -c mol2_file.f
- 
--odb_files.o:	odb_files.f90 elements_module.f90 enerf77mod.f
--	$(FC) $(FFLAGS) -c elements_module.f90 enerf77mod.f odb_files.f90
-+odb_files.o:	odb_files.f90 elements_module.o enerf77mod.o
-+	$(FC) $(FFLAGS) -c odb_files.f90
- 
- elements_module.o:	elements_module.f90
- 	$(FC) $(FFLAGS) -c elements_module.f90
- 
--make_lib2.o:	make_lib2.f odb_files.f90 
--	$(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f
-+make_lib2.o:	make_lib2.f odb_files.o
-+	$(FC) $(FFLAGS) -c make_lib2.f
- 
- pdb2libcheck.o:	pdb2libcheck.f90
- 	$(FC) $(FFLAGS) -c pdb2libcheck.f90
- 
--libcheck.o:	libcheck.f elements_module.f90 pdb2libcheck.f90
--	$(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f
-+libcheck.o:	libcheck.f elements_module.o pdb2libcheck.o
-+	$(FC) $(FFLAGS) -c libcheck.f
- 
- header2matr.o:	header2matr.f90
- 	$(FC) $(FFLAGS) -c header2matr.f90
-@@ -369,16 +361,17 @@ freer_twin.o:	freer_twin.f90
- 	$(FC) $(FFLAGS) -c  freer_twin.f90
- 
- libcheck:	$(SUBL)
--	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
- 
- free_twin:	$(SUB_FREE)
--	$(FC) $(FFLAGS) -o FreeTwin${VERSION} $(SUB_FREE)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) $(LLIBCCP) $(LLIBLAPACK)
- 
- 
- header2matr:	$(SUB_HEADER)
--	$(FC) $(FFLAGS) -o header2matr${VERSION} $(SUB_HEADER)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o header2matr${VERSION} $(SUB_HEADER)
- 
- clean:
- 	/bin/rm *.o *.mod
- 
- bridge.o:			bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h
-+	$(CXX) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch
deleted file mode 100644
index 9998b759c664..000000000000
--- a/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,341 +0,0 @@
- makefile_refmac.inc1 |  215 ++++++++++++++++++++++++--------------------------
- 1 files changed, 104 insertions(+), 111 deletions(-)
-
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 0f8bd63..e59fbfb 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -96,9 +96,7 @@ bridge.o                    \
- i0.o                        \
- i1.o                        \
- chbevl.o                    \
--make_unix_ccp4.o            \
--$(LLIBCIF)                  \
--$(LLIBLAPACK)
-+make_unix_ccp4.o
- 
- 
- SUBL =                      \
-@@ -133,9 +131,7 @@ cell_symm_subrs.o           \
- iheap_sort.o                \
- linalgebra.o                \
- math_refmac.o               \
--subnumrec.o                 \
--$(LLIBLAPACK)               \
--$(LLIBCCP)
-+subnumrec.o
- 
- SUB_FREE  =                 \
- freer_twin.o                 \
-@@ -145,9 +141,7 @@ subnumrec.o                 \
- libT.o                      \
- iheap_sort.o                \
- cell_symm_subrs.o           \
--math_refmac.o               \
--$(LLIBLAPACK)               \
--$(LLIBCCP)
-+math_refmac.o
- 
- SUB_HEADER = header2matr.o
- #--------------------------------------------------------------------------------
-@@ -185,41 +179,41 @@ rharvest_mod.o:  rharvest_mod.f90
- twin77mod.o:  twin77mod.f
- 	$(FC) $(FFLAGS) -c twin77mod.f
- 
--gibbs_gm_sampler.o:  linalgebra_f90.f90 gibbs_gm_sampler.f90
--	$(FC) $(FFLAGS) -c linalgebra_f90.f90 gibbs_gm_sampler.f90
-+gibbs_gm_sampler.o:  linalgebra_f90.o gibbs_gm_sampler.f90
-+	$(FC) $(FFLAGS) -c gibbs_gm_sampler.f90
- 
--max_with_twins.o: restr_files.f90 max_with_twins.f weights.f90 agreem.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 max_with_twins.f
-+max_with_twins.o: restr_files.o max_with_twins.f weights.o agreem.o
-+	$(FC) $(FFLAGS) -c max_with_twins.f
- 
--merohedr_twin.o: restr_files.f90 merohedr_twin.f
--	$(FC) $(FFLAGS) -c restr_files.f90 merohedr_twin.f
-+merohedr_twin.o: restr_files.o merohedr_twin.f
-+	$(FC) $(FFLAGS) -c merohedr_twin.f
- 
--ls_scaling_twin_save.o: restr_files.f90 ls_scaling_twin_save.f weights.f90 agreem.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ls_scaling_twin_save.f
-+ls_scaling_twin_save.o: restr_files.o ls_scaling_twin_save.f weights.o agreem.o
-+	$(FC) $(FFLAGS) -c ls_scaling_twin_save.f
- 
--ml_params_refine.o: restr_files.f90 ml_params_refine.f weights.f90 agreem.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ml_params_refine.f
-+ml_params_refine.o: restr_files.o ml_params_refine.f weights.o agreem.o
-+	$(FC) $(FFLAGS) -c ml_params_refine.f
- 
--optimise_solvent_all.o: optimise_solvent_all.f90 agreem.f90
--	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 agreem.f90
-+optimise_solvent_all.o: optimise_solvent_all.f90 agreem.o
-+	$(FC) $(FFLAGS) -c optimise_solvent_all.f90
- 
--ncs_rest.o: ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f
-+ncs_rest.o: ncs_rest_mod.o restr_files.o ncs_ncs_generate.o ncs_rest.f weights.o
-+	$(FC) $(FFLAGS) -c ncs_rest.f
- 
--ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.f90
--	$(FC) $(FFLAGS) -c ncs_ncs_generate.f90 align_refmac.f90
-+ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.o
-+	$(FC) $(FFLAGS) -c ncs_ncs_generate.f90
- 
--lsq_exp2.o: ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90  lsq_exp2.f weights.f90 rharvest_mod.f90
-+lsq_exp2.o: ncs_rest_mod.o restr_files.o dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f weights.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c lsq_exp2.f
- 
--vdw_and_contacts.o: ncs_rest_mod.f90 vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f
-+vdw_and_contacts.o: ncs_rest_mod.o vdw_and_contacts.f local_tls.o ridge.o restr_files.o weights.o agreem.o
-+	$(FC) $(FFLAGS) -c vdw_and_contacts.f
- 
- dist_routines.o: dist_routines.f90
- 	$(FC) $(FFLAGS) -c dist_routines.f90
- 
--ncs_simil.o: ncs_rest_mod.f90 ncs_simil.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 ncs_simil.f90
-+ncs_simil.o: ncs_rest_mod.o ncs_simil.f90
-+	$(FC) $(FFLAGS) -c ncs_simil.f90
- 
- ridge.o: ridge.f90
- 	$(FC) $(FFLAGS) -c ridge.f90
-@@ -227,140 +221,138 @@ ridge.o: ridge.f90
- align_refmac.o: align_refmac.f90
- 	$(FC) $(FFLAGS) -c align_refmac.f90
- 
--rigid_allocate.o: restr_files.f90 rigid_allocate.f agreem.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 agreem.f90 rigid_allocate.f
-+rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o
-+	$(FC) $(FFLAGS) -c rigid_allocate.f
- 
--tls_allocate.o: restr_files.f90 tls_allocate.f weights.f90 agreem.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 tls_allocate.f
-+tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o
-+	$(FC) $(FFLAGS) -c tls_allocate.f
- 
--hkon_secder_tch.o: ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \
--                   restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \
--	                   hkon_secder_tch.f weights.f90 agreem.f90 rharvest_mod.f90
-+hkon_secder_tch.o: ridge.o gibbs_gm_sampler.o ncs_rest_mod.o hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \
-+                   restr_files.o weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c hkon_secder_tch.f
- 
--oppro_allocate.o: ncs_rest_mod.f90 oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f
-+oppro_allocate.o: ncs_rest_mod.o oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o
-+	$(FC) $(FFLAGS) -c oppro_allocate.f
- 
--read_extra_restraints.o: restr_files.f90 read_extra_restraints.f weights.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 read_extra_restraints.f
-+read_extra_restraints.o: restr_files.o read_extra_restraints.f weights.o
-+	$(FC) $(FFLAGS) -c read_extra_restraints.f
- 
--coords.o: coords.f90 atomf77mod.f
--	$(FC) $(FFLAGS) -c atomf77mod.f coords.f90
-+coords.o: coords.f90 atomf77mod.o
-+	$(FC) $(FFLAGS) -c coords.f90
- 
- 
--ls_scaling_double.o: ls_scaling_double.f weights.f90 agreem.f90
--	$(FC) $(FFLAGS) -c ls_scaling_double.f weights.f90 agreem.f90
-+ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o
-+	$(FC) $(FFLAGS) -c ls_scaling_double.f
- 
--fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90 
--	$(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90
-+fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o
-+	$(FC) $(FFLAGS) -c fast_hessian_tabulation.f
- 
--calc_stats_twin.o: calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90
-+calc_stats_twin.o: calc_stats_twin.f weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c calc_stats_twin.f
- 
--refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 weights.f90 agreem.f90 rharvest_mod.f90 refpre_twin.f
-+refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.o weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c refpre_twin.f
- 
- 
--decide_twin_opers_0.o: restr_files.f90 decide_twin_opers_0.f
--	$(FC) $(FFLAGS) -c restr_files.f90 decide_twin_opers_0.f
-+decide_twin_opers_0.o: restr_files.o decide_twin_opers_0.f
-+	$(FC) $(FFLAGS) -c decide_twin_opers_0.f
- 
- automorphism.o: automorphism.f90
- 	$(FC) $(FFLAGS) -c automorphism.f90
- 
--mtz_write_twin.o: mtz_write_twin.f filter_params.f90 restr_files.f90 weights.f90 agreem.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 weights.f90 agreem.f90 mtz_write_twin.f
-+mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.o weights.o agreem.o
-+	$(FC) $(FFLAGS) -c mtz_write_twin.f
- 
- filter_params.o: filter_params.f90
- 	$(FC) $(FFLAGS) -c filter_params.f90
- 
--rcard_tor1.o: ncs_rest_mod.f90 rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 \
--              agreem.f90 rharvest_mod.f90 ncs_constr.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 weights.f90 \
--	                   agreem.f90 rharvest_mod.f90 ncs_constr.f90 rcard_tor1.f
-+rcard_tor1.o: ncs_rest_mod.o rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o restr_files.o weights.o \
-+              agreem.o rharvest_mod.o ncs_constr.o
-+	$(FC) $(FFLAGS) -c rcard_tor1.f
- 
--inout_routines.o: restr_files.f90 inout_routines.f
--	$(FC) $(FFLAGS) -c restr_files.f90 inout_routines.f
-+inout_routines.o: restr_files.o inout_routines.f
-+	$(FC) $(FFLAGS) -c inout_routines.f
- 
--local_tls.o: local_tls.f90 linalgebra_f90.f90
--	$(FC) $(FFLAGS) -c linalgebra_f90.f90 local_tls.f90
-+local_tls.o: local_tls.f90 linalgebra_f90.o
-+	$(FC) $(FFLAGS) -c local_tls.f90
- 
- linalgebra_f90.o: linalgebra_f90.f90 
- 	$(FC) $(FFLAGS) -c linalgebra_f90.f90
- 
--make_refmac_dummy.o: restr_files.f90 ncs_rest_mod.f90 make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 ncs_rest_mod.f90 weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f
-+make_refmac_dummy.o: restr_files.o ncs_rest_mod.o make_refmac_dummy.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c make_refmac_dummy.f
- 
--ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ml_scaling_double.f
-+ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c ml_scaling_double.f
- 
--refall_twin.o: refall_twin.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90  weights.f90 agreem.f90 rharvest_mod.f90 refall_twin.f
-+refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.f90 weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c refall_twin.f
- 
--rharvest_subr.o: ncs_rest_mod.f90 rharvest_subr.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 optimise_solvent_all.f90  weights.f90 agreem.f90 rharvest_mod.f90 rharvest_subr.f
-+rharvest_subr.o: ncs_rest_mod.o rharvest_subr.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c rharvest_subr.f
- 
--solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90
--	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 solvent_contr_mask.f
-+solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ncs_constr.o
-+	$(FC) $(FFLAGS) -c solvent_contr_mask.f
- 
--subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 subag_scale_hessian.f
-+subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.o weights.o agreem.o rharvest_mod.o ncs_constr.o
-+	$(FC) $(FFLAGS) -c subag_scale_hessian.f
- 
--aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.f90
--	$(FC) $(FFLAGS) -c ncs_constr.f90 aniso_ref_eigen.f
-+aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.o
-+	$(FC) $(FFLAGS) -c aniso_ref_eigen.f
- 
--subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 subcf_scale1.f
-+subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c subcf_scale1.f
- 
--bvalue_routines.o: bvalue_routines.f90 restr_files.f90 atomf77mod.f
--	$(FC) $(FFLAGS) -c restr_files.f90 atomf77mod.f bvalue_routines.f90
-+bvalue_routines.o: bvalue_routines.f90 restr_files.o atomf77mod.o
-+	$(FC) $(FFLAGS) -c bvalue_routines.f90
- 
--newentry_idealise.o:: newentry_idealise.f weights.f90
--	$(FC) $(FFLAGS) -c newentry_idealise.f weights.f90
-+newentry_idealise.o:: newentry_idealise.f weights.o
-+	$(FC) $(FFLAGS) -c newentry_idealise.f
- 
--occupancy_only_refine.o: occupancy_only_refine.f agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c occupancy_only_refine.f agreem.f90 rharvest_mod.f90
-+occupancy_only_refine.o: occupancy_only_refine.f agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c occupancy_only_refine.f
- 
--refmac_completeness.o: weights.f90 agreem.f90 rharvest_mod.f90  refmac_completeness.f90
--	$(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90
-+refmac_completeness.o: weights.o agreem.o rharvest_mod.o refmac_completeness.f90
-+	$(FC) $(FFLAGS) -c refmac_completeness.f90
- 
--refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refmac_xml.f
-+refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o weights.o agreem.o rharvest_mod.o
-+	$(FC) $(FFLAGS) -c refmac_xml.f
- 
- hkl_pack.o:  hkl_pack.f90
- 	$(FC) $(FFLAGS) -c hkl_pack.f90
- 
--extra_eigen.o: extra_eigen.f agreem.f90 ncs_constr.f90
--	$(FC) $(FFLAGS) -c extra_eigen.f agreem.f90 ncs_constr.f90
-+extra_eigen.o: extra_eigen.f agreem.o ncs_constr.o
-+	$(FC) $(FFLAGS) -c extra_eigen.f
- 
--subvag.o: subvag.f hkl_pack.f90
--	$(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f
-+subvag.o: subvag.f hkl_pack.o
-+	$(FC) $(FFLAGS) -c subvag.f
- 
--make_PDB.o: make_PDB.f ncs_constr.f90
--	$(FC) $(FFLAGS) -c ncs_constr.f90 make_PDB.f
-+make_PDB.o: make_PDB.f ncs_constr.o
-+	$(FC) $(FFLAGS) -c make_PDB.f
- 
--make_CIF.o: make_CIF.f ncs_constr.f90
--	$(FC) $(FFLAGS) -c ncs_constr.f90 make_CIF.f
-+make_CIF.o: make_CIF.f ncs_constr.o
-+	$(FC) $(FFLAGS) -c make_CIF.f
- 
- refmac:	$(SUBR)
--	$(FC) $(FFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
- 
--mol2_file.o:	mol2_file.f odb_files.f90
--	$(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f
-+mol2_file.o:	mol2_file.f odb_files.o
-+	$(FC) $(FFLAGS) -c mol2_file.f
- 
--odb_files.o:	odb_files.f90 elements_module.f90 enerf77mod.f
--	$(FC) $(FFLAGS) -c elements_module.f90 enerf77mod.f odb_files.f90
-+odb_files.o:	odb_files.f90 elements_module.o enerf77mod.o
-+	$(FC) $(FFLAGS) -c odb_files.f90
- 
- elements_module.o:	elements_module.f90
- 	$(FC) $(FFLAGS) -c elements_module.f90
- 
--make_lib2.o:	make_lib2.f odb_files.f90 
--	$(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f
-+make_lib2.o:	make_lib2.f odb_files.o
-+	$(FC) $(FFLAGS) -c make_lib2.f
- 
- pdb2libcheck.o:	pdb2libcheck.f90
- 	$(FC) $(FFLAGS) -c pdb2libcheck.f90
- 
--libcheck.o:	libcheck.f elements_module.f90 pdb2libcheck.f90
--	$(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f
-+libcheck.o:	libcheck.f elements_module.o pdb2libcheck.o
-+	$(FC) $(FFLAGS) -c libcheck.f
- 
- header2matr.o:	header2matr.f90
- 	$(FC) $(FFLAGS) -c header2matr.f90
-@@ -369,16 +361,17 @@ freer_twin.o:	freer_twin.f90
- 	$(FC) $(FFLAGS) -c  freer_twin.f90
- 
- libcheck:	$(SUBL)
--	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
- 
- free_twin:	$(SUB_FREE)
--	$(FC) $(FFLAGS) -o FreeTwin${VERSION} $(SUB_FREE)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) $(LLIBCCP) $(LLIBLAPACK)
- 
- 
- header2matr:	$(SUB_HEADER)
--	$(FC) $(FFLAGS) -o header2matr${VERSION} $(SUB_HEADER)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o header2matr${VERSION} $(SUB_HEADER)
- 
- clean:
- 	/bin/rm *.o *.mod
- 
- bridge.o:			bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h
-+	$(CXX) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/metadata.xml b/sci-chemistry/refmac/metadata.xml
deleted file mode 100644
index c0432fefe855..000000000000
--- a/sci-chemistry/refmac/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-  <maintainer>
-    <email>jlec@gentoo.org</email>
-    <name>Justin Lecher (jlec)</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild b/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild
deleted file mode 100644
index eb8e87018219..000000000000
--- a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild
+++ /dev/null
@@ -1,85 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils fortran-2 flag-o-matic toolchain-funcs versionator
-
-DESCRIPTION="Macromolecular crystallographic refinement program"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac"
-SRC_URI="
-	${HOMEPAGE}/data/refmac_stable/refmac_${PV}.tar.gz
-	test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="
-	sci-chemistry/makecif
-	>=sci-libs/ccp4-libs-6.1.3-r7
-	sci-libs/mmdb
-	<sci-libs/monomer-db-1
-	virtual/blas
-	virtual/lapack"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-FORTRAN_STANDARD="77 90"
-
-S="${WORKDIR}"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-allow-dynamic-linking.patch
-	"${FILESDIR}"/${PV}-gcc4.6.patch
-	)
-
-src_prepare() {
-	epatch ${PATCHES[@]}
-
-	use test && epatch "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-test.log.patch
-	[[ ${FC} == *gfortran* ]] && \
-		append-fflags -fno-second-underscore && \
-		append-cflags -DGFORTRAN -DPROTOTYPE && \
-		append-libs -lgfortran -lgfortranbegin -lstdc++
-	[[ ${FC} == *ifort* ]] && \
-		append-libs -lstdc++
-}
-
-src_compile() {
-	emake \
-		FC=$(tc-getFC) \
-		CC=$(tc-getCC) \
-		CXX=$(tc-getCXX) \
-		COPTIM="${CFLAGS}" \
-		FOPTIM="${FFLAGS:- -O2}" \
-		VERSION="" \
-		XFFLAGS="" \
-		XCFLAGS="" \
-		LLIBCCP="-lccp4f -lccp4c -lccif $($(tc-getPKG_CONFIG) --libs mmdb)" \
-		LLIBLAPACK="$($(tc-getPKG_CONFIG) --libs lapack blas)" \
-		LLIBOTHERS="${LIBS}" \
-		${PN} libcheck
-}
-
-src_test() {
-	einfo "Starting tests ..."
-	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
-	export PATH="${WORKDIR}/test-framework/scripts:${S}:${PATH}"
-	export CCP4_TEST="${WORKDIR}"/test-framework
-	export CCP4_SCR="${T}"
-	ln -sf refmac "${S}"/refmac5
-	sed '/^ANISOU/d' -i ${CCP4_TEST}/data/pdb/1vr7.pdb
-	ccp4-run-thorough-tests -v test_refmac5 || die
-}
-
-src_install() {
-	exeinto /usr/libexec/ccp4/bin/
-	doexe ${PN}
-	dosym refmac /usr/libexec/ccp4/bin/refmac5
-	dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN}
-	dosym refmac /usr/bin/refmac5
-	dodoc refmac_keywords.pdf bugs_and_features.pdf
-}
diff --git a/sci-chemistry/scala/Manifest b/sci-chemistry/scala/Manifest
deleted file mode 100644
index e03416a28733..000000000000
--- a/sci-chemistry/scala/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST scala-3.3.20.tar.gz 368628 SHA256 0efb108923a4d21fdc75d7ee92567e4bac4ae409f8798fbabd8142b5b026e976 SHA512 9f9812527013d87c80101333baf7ee646f6b3c665cdb477bb4e633c0a1fa57b31b6327913cf712e961c4484a9d9edf1aab5f3cfc66e6834aca1e970a4e0ca898 WHIRLPOOL 7d6082872a9f2f992186a2626dbf7ccd9f827b1322d1399b41ebc1b07267a46cfed5f7ea085403415c01eba4fc44e9d51983080537db04b227469d6871f8f1f9
diff --git a/sci-chemistry/scala/files/3.3.18-gcc4.6.patch b/sci-chemistry/scala/files/3.3.18-gcc4.6.patch
deleted file mode 100644
index 0bb3d40d479a..000000000000
--- a/sci-chemistry/scala/files/3.3.18-gcc4.6.patch
+++ /dev/null
@@ -1,17 +0,0 @@
- scala.f |    3 ++-
- 1 files changed, 2 insertions(+), 1 deletions(-)
-
-diff --git a/scala.f b/scala.f
-index d7e1cbe..8ed6fd2 100644
---- a/scala.f
-+++ b/scala.f
-@@ -3955,7 +3955,8 @@ c line buffer
-       character*40 key, value
-       character*200 realfilename
- 
--      integer intfp, i2swap, lenstr
-+      integer intfp, lenstr
-+      integer*2 i2swap
-       external intfp, i2swap, lenstr
-       logical litend
-       external litend
diff --git a/sci-chemistry/scala/files/Makefile.am b/sci-chemistry/scala/files/Makefile.am
deleted file mode 100644
index 49fd61180ef0..000000000000
--- a/sci-chemistry/scala/files/Makefile.am
+++ /dev/null
@@ -1,7 +0,0 @@
-
-LIBS = -lccp4f $(LAPACK_LIBS)
-
-bin_PROGRAMS = scala
-
-scala_SOURCES = scala.f
-
diff --git a/sci-chemistry/scala/files/configure.ac b/sci-chemistry/scala/files/configure.ac
deleted file mode 100644
index 35c4c7fdd194..000000000000
--- a/sci-chemistry/scala/files/configure.ac
+++ /dev/null
@@ -1,14 +0,0 @@
-#                                               -*- Autoconf -*-
-# Process this file with autoconf to produce a configure script.
-
-AC_PREREQ(2.59)
-AC_INIT(scala, https://bugs.gentoo.org/)
-AC_CONFIG_SRCDIR([scala.f])
-AM_INIT_AUTOMAKE([foreign])
-
-PKG_CHECK_MODULES([LAPACK],[lapack])
-
-# Checks for programs.
-AC_PROG_FC
-AC_PROG_F77
-AC_OUTPUT([Makefile])
diff --git a/sci-chemistry/scala/metadata.xml b/sci-chemistry/scala/metadata.xml
deleted file mode 100644
index 2c9359ab3513..000000000000
--- a/sci-chemistry/scala/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-  <maintainer>
-    <email>jlec@gentoo.org</email>
-  </maintainer>
-  <longdescription>
-This program scales together multiple observations of reflections from
-Xray difraction experiments, and merges multiple observations into an 
-average intensity. 
-</longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/scala/scala-3.3.20.ebuild b/sci-chemistry/scala/scala-3.3.20.ebuild
deleted file mode 100644
index 3555cc29a9d1..000000000000
--- a/sci-chemistry/scala/scala-3.3.20.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit autotools fortran-2
-
-DESCRIPTION="Scale together multiple observations of reflections"
-HOMEPAGE="http://www.ccp4.ac.uk/dist/html/scala.html"
-SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz"
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	!<sci-chemistry/ccp4-6.1.2
-	!dev-lang/scala-bin
-	!dev-lang/scala
-	sci-libs/ccp4-libs
-	virtual/lapack"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_prepare() {
-	cp "${FILESDIR}"/{configure.ac,Makefile.am} "${S}"
-	eautoreconf
-}
-
-src_install() {
-	exeinto /usr/libexec/ccp4/bin/
-	doexe ${PN}
-	dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN}
-	dodoc ${PN}.doc
-	dohtml ${PN}.html
-}
diff --git a/sci-chemistry/sfcheck/Manifest b/sci-chemistry/sfcheck/Manifest
deleted file mode 100644
index 77615cec106b..000000000000
--- a/sci-chemistry/sfcheck/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST sfcheck-7.03.18.tar.gz 535707 SHA256 def9ceec86fc50f35b9a729e6f84b45a83560e2c6c20a5105647182e10313148 SHA512 256aa1690e0f5ca6aca0483a7d00c1deeb7b77701d950771a134532a658f7c3189bc6abec620ea6da2af200fc879ac9ff07ef7f4ba8614b6cd4e8455a11bed93 WHIRLPOOL 7b9f99f1a8387c5bc63bdab2078d3fcfab4146046429c56503760ca12a1898e944b5aa3c42b358d303206487e5d493bdcb77fe1795490779e7bd79b8b66a2d7a
diff --git a/sci-chemistry/sfcheck/files/7.03.17-ldflags.patch b/sci-chemistry/sfcheck/files/7.03.17-ldflags.patch
deleted file mode 100644
index 4163cb52ac1e..000000000000
--- a/sci-chemistry/sfcheck/files/7.03.17-ldflags.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/src/makefile b/src/makefile
-index ab43d7d..37e469f 100755
---- a/src/makefile
-+++ b/src/makefile
-@@ -60,6 +60,6 @@ main_sfcheck_ccp4.o: main_sfcheck_ccp4.f sfch_version.fh
- 	$(MR_FORT) -c  main_sfcheck_ccp4.f
- 
- sfcheck: $(OBJS)
--	$(MR_FORT) -o $(BIN)/sfcheck $(OBJSL) $(MR_LIBRARY)
-+	$(MR_FORT) $(LDFLAGS) -o $(BIN)/sfcheck $(OBJSL) $(MR_LIBRARY)
- 
- # ----------------------------------------
diff --git a/sci-chemistry/sfcheck/metadata.xml b/sci-chemistry/sfcheck/metadata.xml
deleted file mode 100644
index 9ac9ffdb3a41..000000000000
--- a/sci-chemistry/sfcheck/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci-chemistry</herd>
-</pkgmetadata>
diff --git a/sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild b/sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild
deleted file mode 100644
index e18673d0923e..000000000000
--- a/sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils fortran-2 toolchain-funcs
-
-DESCRIPTION="Program for assessing the agreement between the atomic model and X-ray data or EM map"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/sfcheck.html"
-#SRC_URI="http://www.ysbl.york.ac.uk/~alexei/downloads/sfcheck.tar.gz"
-SRC_URI="mirror://gentoo/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="sci-libs/ccp4-libs"
-DEPEND="${RDEPEND}
-	!<sci-chmistry/ccp4-apps-6.1.3"
-
-S="${WORKDIR}"/${PN}
-
-src_prepare() {
-	epatch "${FILESDIR}"/7.03.17-ldflags.patch
-
-	emake -C src clean
-}
-
-src_compile() {
-	MR_FORT="$(tc-getFC) ${FFLAGS}" \
-	MR_LIBRARY="-lccp4f" \
-	emake -C src all
-}
-
-src_install() {
-	exeinto /usr/libexec/ccp4/bin/
-	doexe bin/${PN}
-	dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN}
-	dodoc readme ${PN}.com.gz doc/${PN}*
-}
diff --git a/sci-chemistry/solve-resolve-bin/Manifest b/sci-chemistry/solve-resolve-bin/Manifest
deleted file mode 100644
index 43fcf716e995..000000000000
--- a/sci-chemistry/solve-resolve-bin/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST solve-2.13-linux-64.tar.gz 74444830 SHA256 e03250bb550686fc6e5f59d4e885b83b88cd342dfb4975eb31ddf95d9515650e SHA512 8f20715c3fb73940f03ba8a4bb3528f89ba01520cacead001796609bc15259ab7ab7f2d4960ea97efc43029863bc31e630c9e93f528a233652928220dafe0b4d WHIRLPOOL 125efe76024148656f3bb357ad1bc78d17f51eb8268c83241f4da9a94356170d0259fe48fadf6bf1ffe4b10b57bb27ed79199063dc95d0eef8d9e22de653c84a
-DIST solve-2.13-linux.tar.gz 71902534 SHA256 975466fe92d8f6256de20ea0b5101876f3e5a7e3093199946c9f4824236c79d3 SHA512 a3a779ada33bd189fc8c3e6fdc424ef9c032c5540138cce52e0c8dcf5a12847b1325402a2c1715ed4ab217f433169d3612c724f2d178ead576afc44ec4839c6a WHIRLPOOL 0fec411b795a107610e620586cba511a0cbf50400e0bdfef872b22ee05e3992fcc0a4b1cf1d84d450bbeb3838a7bc9633acd8f4cf97d5e4b7a01e6e7959ccd7c
diff --git a/sci-chemistry/solve-resolve-bin/metadata.xml b/sci-chemistry/solve-resolve-bin/metadata.xml
deleted file mode 100644
index ae9ec7c5f6a4..000000000000
--- a/sci-chemistry/solve-resolve-bin/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-  <maintainer>
-    <email>jlec@gentoo.org</email>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/solve-resolve-bin/solve-resolve-bin-2.13.ebuild b/sci-chemistry/solve-resolve-bin/solve-resolve-bin-2.13.ebuild
deleted file mode 100644
index 6deae178afdd..000000000000
--- a/sci-chemistry/solve-resolve-bin/solve-resolve-bin-2.13.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Automated crystallographic structure solution for MIR, SAD, and MAD"
-HOMEPAGE="http://www.solve.lanl.gov/index.html"
-SRC_URI="
-	x86? ( https://solve.lanl.gov/pub/solve/${PV}/solve-${PV}-linux.tar.gz )
-	amd64? ( https://solve.lanl.gov/pub/solve/${PV}/solve-${PV}-linux-64.tar.gz )"
-
-SLOT="0"
-LICENSE="solve"
-KEYWORDS="-* x86 amd64"
-IUSE="examples"
-
-RDEPEND="sci-libs/ccp4-libs"
-DEPEND=""
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/solve-${PV}
-
-QA_PREBUILT="opt/solve-resolve/bin/*"
-
-src_install(){
-	local IN_PATH="/opt/solve-resolve/"
-
-	exeinto ${IN_PATH}bin/
-	doexe bin/*
-
-	insinto ${IN_PATH}lib/
-	doins -r lib/{*sym,sym*,hist*,*dat,segments,patterns}
-
-	docinto html
-	dodoc -r lib/html/*
-
-	sed \
-		-e 's:/usr/local/lib/solve/:${EPREFIX}/opt/solve-resolve/lib/:' \
-		-i lib/examples_solve/p9/solve* || die
-	if use examples; then
-		sed \
-			-e 's:/usr/local/lib/resolve/:${EPREFIX}/opt/solve-resolve/lib/:' \
-			-i lib/examples_resolve/{resolve.csh,prime_and_switch.csh} || die
-		insinto /usr/share/${PF}/
-		doins -r lib/examples_*solve
-	fi
-
-	cat >> "${T}"/20solve-resolve <<- EOF
-	CCP4_OPEN="UNKNOWN"
-	SYMOP="${EPREFIX}/usr/share/ccp4/data/symop.lib"
-	SYMINFO="${EPREFIX}/usr/share/ccp4/data/syminfo.lib"
-	SOLVEDIR="${EPREFIX}/${IN_PATH}lib/"
-	PATH="${EPREFIX}/${IN_PATH}bin"
-	EOF
-
-	doenvd "${T}"/20solve-resolve
-}
-
-pkg_postinst(){
-	einfo "Get a valid license key from"
-	einfo "http://solve.lanl.gov/license.html"
-	einfo "and place it in"
-	einfo "${EPREFIX}${IN_PATH}lib/"
-}
diff --git a/sci-chemistry/xdsi/Manifest b/sci-chemistry/xdsi/Manifest
deleted file mode 100644
index e33598d79364..000000000000
--- a/sci-chemistry/xdsi/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST xdsi_0.92.tar.gz 886028 SHA256 416403f167d26b56965283b407783ea80927ace533df76e330b51ca37c9bb9e4
diff --git a/sci-chemistry/xdsi/files/0.92-gentoo.patch b/sci-chemistry/xdsi/files/0.92-gentoo.patch
deleted file mode 100644
index f4a37ff1838d..000000000000
--- a/sci-chemistry/xdsi/files/0.92-gentoo.patch
+++ /dev/null
@@ -1,27 +0,0 @@
- xdsi |    6 +++---
- 1 files changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/xdsi b/xdsi
-index cbedee8..1037913 100755
---- a/xdsi
-+++ b/xdsi
-@@ -20,8 +20,8 @@
- ####################################################################
- # These are the only two things you should change#
- 
--set Templates "/mydir/templates"
--set initial "/mydir/SLS-2009"
-+set Templates "GENTOOTEMPLATE"
-+set initial "./"
- 
- 
- ####################################################################
-@@ -121,7 +121,7 @@ your system administrator."
- }
- 
- 
--CheckExecutables "kpdf gnuplot xds_par xdsstat xds-viewer-0.6 convert pointless ipmosflm VIEW"
-+CheckExecutables "kpdf gnuplot xds_par xds-viewer convert pointless ipmosflm"
- 
- #wm resizable . 0 0
- 
diff --git a/sci-chemistry/xdsi/metadata.xml b/sci-chemistry/xdsi/metadata.xml
deleted file mode 100644
index 431fb2be13b4..000000000000
--- a/sci-chemistry/xdsi/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-  <maintainer>
-    <email>jlec@gentoo.org</email>
-  </maintainer>
-  <longdescription>
-XDSi offers you the possibility to process all your datasets in a given directory with minimum effort.
-* You just have to provide it with a resultdirectory and the directory where your frames are stored.
-* All datasets consisting of more than 100 frames within the given directory and all its subdirectories will be processed.
-* For each dataset a space group assignment is done using POINTLESS of the CCP4 software package
-* Plots of the most informative statistics of INTEGRATE.LP, CORRECT.LP and XDSSTAT.LP are generated for each dataset
-* A plot comparing Rmeas, I/sig and Completeness of all the processed datasets is generated
-* You can also generate plots for datasets that have been processed using XDS without XDSi 
-</longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/xdsi/xdsi-0.92-r1.ebuild b/sci-chemistry/xdsi/xdsi-0.92-r1.ebuild
deleted file mode 100644
index 6a6c9bb7ec8b..000000000000
--- a/sci-chemistry/xdsi/xdsi-0.92-r1.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="A crude interface for running the XDS"
-HOMEPAGE="http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsi"
-SRC_URI="ftp://turn5.biologie.uni-konstanz.de/pub/${PN}_${PV}.tar.gz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	app-text/mupdf
-	dev-lang/tk
-	|| ( media-gfx/imagemagick media-gfx/graphicsmagick[imagemagick] )
-	sci-chemistry/mosflm
-	sci-chemistry/pointless
-	sci-chemistry/xds-bin[smp]
-	sci-visualization/gnuplot
-	sci-visualization/xds-viewer"
-# Need to clarified for licensing
-# sci-chemistry/xdsstat-bin
-DEPEND=""
-
-RESTRICT="mirror bindist"
-
-S="${WORKDIR}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
-	sed \
-		-e "s:GENTOOTEMPLATE:${EPREFIX}/usr/share/${PN}/templates:g" \
-		-e "s:kpdf:mupdf:g" \
-		-e "s:xds-viewer-0.6:xds-viewer:g" \
-		-i ${PN} || die
-}
-
-src_install() {
-	dobin ${PN}
-	insinto /usr/share/${PN}/templates
-	doins templates/{*.INP,bohr*,fortran,pauli,info.png,*.pck,tablesf_xdsi}
-	dodoc templates/*.pdf
-}
-
-pkg_postinst() {
-	elog "Documentation can be found here:"
-	elog "ftp://turn14.biologie.uni-konstanz.de/pub/xdsi/xdsi_doc_print.pdf"
-}
diff --git a/sci-chemistry/xia2/Manifest b/sci-chemistry/xia2/Manifest
deleted file mode 100644
index 52cb6c13f104..000000000000
--- a/sci-chemistry/xia2/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-DIST xia2-0.3.1.0.tar.bz2 3389906 SHA256 32f1866bc17b093cbf157ec7bc217e47d059957104b20c88ed1b5c3706fc7e28 SHA512 cd595147164e4a281431a1d5a7298588001bb11662b517a5f95366e7b0ba4fdb33adf88dd2672c8c2ee84f48356fccb7cbd07667d5f04417a1564c7ea9f878c5 WHIRLPOOL e5493526d3075a5c61ce582a3bf42e2b4a2a73d7a28b1c8df786f0bdf5c8b1eaee986a60f379559ba556f256057794211a6c1e812b785aa9fe3179357b24b0da
-DIST xia2-0.3.1.6.tar.bz2 3464982 SHA256 fde814a763e6666a1618d01569c19d574f1bf71d754dc3960beeb13c35dd201f SHA512 d00ba2c42c88d01522859839cbee6a93662ed7f89fb146babffa1dd5d6af12ca72cc146157e0dc88bba1d6543f8509fc9027e1c42ed3ae15dd3e168ca18e1858 WHIRLPOOL ccedcbf910ec5bed637739f7519e14eb249b89ae6ccd83a632ab8571a3af62f1f168f8dfd88287fed9fe927b98230e083a0d2d4525f47bc49c4074375a46a796
-DIST xia2-0.3.1.7.tar.bz2 3650285 SHA256 54beb26396c4b6ecb343544c777c2505238385f2127482d035d2c47b24a7fcf1 SHA512 d25788e6564b0f8f4c8e6723347b7691277b01192ead8f37bc7e6d1cdfbee5b22a1329f4ff82d9287875df2de1358e738de08c6a4d19353ccb40c31343dce7bd WHIRLPOOL 1c7306a54a5262632e0319a289f57610badea3945b61653039c78772399557f895ea57e02bbff6804704df8a08f4aa35fce7746e9e03807143d0e395bcd93c75
-DIST xia2-0.3.3.1.tar.bz2 3074989 SHA256 f1bf94cd9305f768fea1b541ac53d66917126e92620263a96f9c23923ec829c4 SHA512 656abd51dc6764dee16423e2ea75f590e7a04046c5ac60ce013615c91b3fd41c0089351ceb948203643bff442753773aa639b036efc089ce26592b52b187f656 WHIRLPOOL f11a6bba359ce9f3095d2993fb331a8c70a44bc1ef31dc08663ee63372db995047d5e1b4693808a347eedeb487a1b799c4e080c05416786209f62e7b619ddec8
-DIST xia2-0.3.3.3.tar.bz2 2919316 SHA256 3cf09fcf9d2c0ea6d6cb8cf66a3c5af752b4345af6a882e2d398424cf3b4b0d3 SHA512 913b5a6e24c3c070cc36b404b987331d8de99756d0f598ef485ba5fef3b4bc42d17bf4b4e648d5c99f014872d554b94880a7542dfb9ab6969e272ec986127561 WHIRLPOOL 5f19e3b06df7d5a83d75296fe9c9956f5c0b995cd5d10f1adb66e519d9dbcdd73edcbec53acb90aede6f2955bbd88991d6283af9a3578ad26a686e8530bfdffa
-DIST xia2-0.3.4.0.tar.bz2 21404771 SHA256 20afe3d24c35446ef8c8944974d684229f053d3916e96e46766d8eefa4c5fabf SHA512 7d2444cb2acfcd2d7ca4c37d5714e7c249ffc419e9d7e1dbb33ccf18adc07f05a2b043af5aee721c64639b991dbbfd356181630229e91e0f871489870f9a8d51 WHIRLPOOL 14759e436d42e4b5ae558616d297f41eb9a345b19df4a4d02d2cb3c61937320d9161343b126b393049319ab6e37dc3890566b1bd3f2bff1a29cd108931640a90
diff --git a/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch
deleted file mode 100644
index 9d92af7e33ce..000000000000
--- a/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff --git a/xia2-0.3.1.0/Applications/xia2find.py b/xia2-0.3.1.0/Applications/xia2find.py
-index 1a3b0e2..e0b8a1e 100755
---- a/xia2-0.3.1.0/Applications/xia2find.py
-+++ b/xia2-0.3.1.0/Applications/xia2find.py
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory
- from Experts.FindImages import image2template_directory
- 
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450',
--                          'osc', 'cbf', 'mar2000']]
-+                          'osc', 'cbf', 'mar2000']
- known_sweeps = { }
- 
- def is_image_name(file):
-diff --git a/xia2-0.3.1.0/Experts/DRStrategyExpert.py b/xia2-0.3.1.0/Experts/DRStrategyExpert.py
-index 28b1dc3..dba3ef7 100644
---- a/xia2-0.3.1.0/Experts/DRStrategyExpert.py
-+++ b/xia2-0.3.1.0/Experts/DRStrategyExpert.py
-@@ -48,24 +48,24 @@ strategy_dict = {
-     'default':{
-     'score':1,
-     'pipeline':{
--    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
-+    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
-     'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
-                   'pointless-1.1.0.4']},
-     'default':{
-     'score':2,
-     'pipeline':{
--    'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}
-+    'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'},
-     'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex',
-                   'pointless-1.1.0.4']},
-     'mosaic':{
-     'score':1,
-     'pipeline':{
--    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
-+    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
-     'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
-                   'pointless-1.1.0.4']},
-     'mosaic':{
-     'score':2,
-     'pipeline':{
--    'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}
-+    'indexer':'xds', 'integrater':'xds', 'scaler':'xds'},
-     'depends-on':['xds', 'xscale']}
-     }
-diff --git a/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py
-index 88f9218..5fb6f2a 100644
---- a/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py
-+++ b/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py
-@@ -49,8 +49,8 @@ def Cad(DriverType = None):
-             self.add_command_line(hklin)
- 
-             self.set_task('Rewriting reflections %s => %s' % 
--                      `   (os.path.split(hklin)[-1],
--                       `   os.path.split(self.getHklout())[-1]))
-+                         (os.path.split(hklin)[-1],
-+                          os.path.split(self.getHklout())[-1]))
- 
-             self.start()
- 
diff --git a/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch
deleted file mode 100644
index 7770a53c4451..000000000000
--- a/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff --git a/xia2-0.3.1.6/Applications/xia2find.py b/xia2-0.3.1.6/Applications/xia2find.py
-index 1a3b0e2..e0b8a1e 100755
---- a/xia2-0.3.1.6/Applications/xia2find.py
-+++ b/xia2-0.3.1.6/Applications/xia2find.py
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory
- from Experts.FindImages import image2template_directory
- 
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450',
--                          'osc', 'cbf', 'mar2000']]
-+                          'osc', 'cbf', 'mar2000']
- known_sweeps = { }
- 
- def is_image_name(file):
-diff --git a/xia2-0.3.1.6/Experts/DRStrategyExpert.py b/xia2-0.3.1.6/Experts/DRStrategyExpert.py
-index 28b1dc3..dba3ef7 100644
---- a/xia2-0.3.1.6/Experts/DRStrategyExpert.py
-+++ b/xia2-0.3.1.6/Experts/DRStrategyExpert.py
-@@ -48,24 +48,24 @@ strategy_dict = {
-     'default':{
-     'score':1,
-     'pipeline':{
--    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
-+    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
-     'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
-                   'pointless-1.1.0.4']},
-     'default':{
-     'score':2,
-     'pipeline':{
--    'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}
-+    'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'},
-     'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex',
-                   'pointless-1.1.0.4']},
-     'mosaic':{
-     'score':1,
-     'pipeline':{
--    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
-+    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
-     'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
-                   'pointless-1.1.0.4']},
-     'mosaic':{
-     'score':2,
-     'pipeline':{
--    'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}
-+    'indexer':'xds', 'integrater':'xds', 'scaler':'xds'},
-     'depends-on':['xds', 'xscale']}
-     }
-diff --git a/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py
-index 88f9218..5fb6f2a 100644
---- a/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py
-+++ b/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py
-@@ -49,8 +49,8 @@ def Cad(DriverType = None):
-             self.add_command_line(hklin)
- 
-             self.set_task('Rewriting reflections %s => %s' % 
--                      `   (os.path.split(hklin)[-1],
--                       `   os.path.split(self.getHklout())[-1]))
-+                         (os.path.split(hklin)[-1],
-+                          os.path.split(self.getHklout())[-1]))
- 
-             self.start()
- 
diff --git a/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch
deleted file mode 100644
index ec8ada48aad1..000000000000
--- a/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff --git a/xia2-0.3.1.7/Applications/xia2find.py b/xia2-0.3.1.7/Applications/xia2find.py
-index 1a3b0e2..e0b8a1e 100755
---- a/xia2-0.3.1.7/Applications/xia2find.py
-+++ b/xia2-0.3.1.7/Applications/xia2find.py
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory
- from Experts.FindImages import image2template_directory
- 
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450',
--                          'osc', 'cbf', 'mar2000']]
-+                          'osc', 'cbf', 'mar2000']
- known_sweeps = { }
- 
- def is_image_name(file):
-diff --git a/xia2-0.3.1.7/Experts/DRStrategyExpert.py b/xia2-0.3.1.7/Experts/DRStrategyExpert.py
-index 28b1dc3..dba3ef7 100644
---- a/xia2-0.3.1.7/Experts/DRStrategyExpert.py
-+++ b/xia2-0.3.1.7/Experts/DRStrategyExpert.py
-@@ -48,24 +48,24 @@ strategy_dict = {
-     'default':{
-     'score':1,
-     'pipeline':{
--    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
-+    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
-     'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
-                   'pointless-1.1.0.4']},
-     'default':{
-     'score':2,
-     'pipeline':{
--    'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}
-+    'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'},
-     'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex',
-                   'pointless-1.1.0.4']},
-     'mosaic':{
-     'score':1,
-     'pipeline':{
--    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
-+    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
-     'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
-                   'pointless-1.1.0.4']},
-     'mosaic':{
-     'score':2,
-     'pipeline':{
--    'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}
-+    'indexer':'xds', 'integrater':'xds', 'scaler':'xds'},
-     'depends-on':['xds', 'xscale']}
-     }
-diff --git a/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py
-index 88f9218..5fb6f2a 100644
---- a/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py
-+++ b/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py
-@@ -49,8 +49,8 @@ def Cad(DriverType = None):
-             self.add_command_line(hklin)
- 
-             self.set_task('Rewriting reflections %s => %s' % 
--                      `   (os.path.split(hklin)[-1],
--                       `   os.path.split(self.getHklout())[-1]))
-+                         (os.path.split(hklin)[-1],
-+                          os.path.split(self.getHklout())[-1]))
- 
-             self.start()
- 
diff --git a/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch
deleted file mode 100644
index 36cf6bb60d1d..000000000000
--- a/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py
-index 1a3b0e2..e0b8a1e 100755
---- a/xia2-0.3.3.1/Applications/xia2find.py
-+++ b/xia2-0.3.3.1/Applications/xia2find.py
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory
- from Experts.FindImages import image2template_directory
- 
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450',
--                          'osc', 'cbf', 'mar2000']]
-+                          'osc', 'cbf', 'mar2000']
- known_sweeps = { }
- 
- def is_image_name(file):
-diff --git a/xia2-0.3.3.0/Experts/DRStrategyExpert.py b/xia2-0.3.3.0/Experts/DRStrategyExpert.py
-index 28b1dc3..dba3ef7 100644
---- a/xia2-0.3.3.1/Experts/DRStrategyExpert.py
-+++ b/xia2-0.3.3.1/Experts/DRStrategyExpert.py
-@@ -48,24 +48,24 @@ strategy_dict = {
-     'default':{
-     'score':1,
-     'pipeline':{
--    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
-+    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
-     'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
-                   'pointless-1.1.0.4']},
-     'default':{
-     'score':2,
-     'pipeline':{
--    'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}
-+    'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'},
-     'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex',
-                   'pointless-1.1.0.4']},
-     'mosaic':{
-     'score':1,
-     'pipeline':{
--    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
-+    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
-     'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
-                   'pointless-1.1.0.4']},
-     'mosaic':{
-     'score':2,
-     'pipeline':{
--    'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}
-+    'indexer':'xds', 'integrater':'xds', 'scaler':'xds'},
-     'depends-on':['xds', 'xscale']}
-     }
-diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py
-index 88f9218..5fb6f2a 100644
---- a/xia2core-0.3.3.1/Python/Examples/CCP4/Cad.py
-+++ b/xia2core-0.3.3.1/Python/Examples/CCP4/Cad.py
-@@ -49,8 +49,8 @@ def Cad(DriverType = None):
-             self.add_command_line(hklin)
- 
-             self.set_task('Rewriting reflections %s => %s' % 
--                      `   (os.path.split(hklin)[-1],
--                       `   os.path.split(self.getHklout())[-1]))
-+                         (os.path.split(hklin)[-1],
-+                          os.path.split(self.getHklout())[-1]))
- 
-             self.start()
- 
diff --git a/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch
deleted file mode 100644
index 53cacbb5c681..000000000000
--- a/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py
-index 1a3b0e2..e0b8a1e 100755
---- a/xia2-0.3.3.3/Applications/xia2find.py
-+++ b/xia2-0.3.3.3/Applications/xia2find.py
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory
- from Experts.FindImages import image2template_directory
- 
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450',
--                          'osc', 'cbf', 'mar2000']]
-+                          'osc', 'cbf', 'mar2000']
- known_sweeps = { }
- 
- def is_image_name(file):
-diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py
-index 88f9218..5fb6f2a 100644
---- a/xia2core-0.3.3.3/Python/Examples/CCP4/Cad.py
-+++ b/xia2core-0.3.3.3/Python/Examples/CCP4/Cad.py
-@@ -49,8 +49,8 @@ def Cad(DriverType = None):
-             self.add_command_line(hklin)
- 
-             self.set_task('Rewriting reflections %s => %s' % 
--                      `   (os.path.split(hklin)[-1],
--                       `   os.path.split(self.getHklout())[-1]))
-+                         (os.path.split(hklin)[-1],
-+                          os.path.split(self.getHklout())[-1]))
- 
-             self.start()
- 
diff --git a/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch
deleted file mode 100644
index 9ba4c94495ea..000000000000
--- a/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py
-index 1a3b0e2..e0b8a1e 100755
---- a/xia2-0.3.4.0/Applications/xia2find.py
-+++ b/xia2-0.3.4.0/Applications/xia2find.py
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory
- from Experts.FindImages import image2template_directory
- 
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450',
--                          'osc', 'cbf', 'mar2000']]
-+                          'osc', 'cbf', 'mar2000']
- known_sweeps = { }
- 
- def is_image_name(file):
-diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py
-index 88f9218..5fb6f2a 100644
---- a/xia2core-0.3.4.0/Python/Examples/CCP4/Cad.py
-+++ b/xia2core-0.3.4.0/Python/Examples/CCP4/Cad.py
-@@ -49,8 +49,8 @@ def Cad(DriverType = None):
-             self.add_command_line(hklin)
- 
-             self.set_task('Rewriting reflections %s => %s' % 
--                      `   (os.path.split(hklin)[-1],
--                       `   os.path.split(self.getHklout())[-1]))
-+                         (os.path.split(hklin)[-1],
-+                          os.path.split(self.getHklout())[-1]))
- 
-             self.start()
- 
diff --git a/sci-chemistry/xia2/metadata.xml b/sci-chemistry/xia2/metadata.xml
deleted file mode 100644
index 9ac9ffdb3a41..000000000000
--- a/sci-chemistry/xia2/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci-chemistry</herd>
-</pkgmetadata>
diff --git a/sci-chemistry/xia2/xia2-0.3.1.0.ebuild b/sci-chemistry/xia2/xia2-0.3.1.0.ebuild
deleted file mode 100644
index 33b3d841acfa..000000000000
--- a/sci-chemistry/xia2/xia2-0.3.1.0.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="3"
-
-inherit eutils python
-
-DESCRIPTION="An automated data reduction system for crystallography"
-HOMEPAGE="http://www.ccp4.ac.uk/xia/"
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	>=sci-chemistry/ccp4-apps-6.1.2
-	sci-chemistry/mosflm
-	sci-chemistry/pointless
-	>=sci-libs/ccp4-libs-6.1.2
-	sci-libs/cctbx"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	find . -name '*.bat' | xargs rm || die
-
-	epatch "${FILESDIR}"/${PV}-fix-syntax.patch
-}
-
-src_install() {
-	rm -rf ${P}/binaries ${PN}core-${PV}/Test || die
-
-	insinto /usr/share/ccp4/XIAROOT/
-	doins -r * || die
-
-	# Set programs executable
-# fperms cannot handle wildcards
-	chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
-	chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
-
-	cat >> "${T}"/23XIA <<- EOF
-	XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT
-	XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV}
-	XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}
-	PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications
-	EOF
-
-	doenvd "${T}"/23XIA
-}
-
-pkg_postinst() {
-	python_mod_optimize /usr/share/ccp4/XIAROOT
-}
-
-pkg_postrm() {
-	python_mod_cleanup /usr/share/ccp4/XIAROOT
-}
diff --git a/sci-chemistry/xia2/xia2-0.3.1.6.ebuild b/sci-chemistry/xia2/xia2-0.3.1.6.ebuild
deleted file mode 100644
index 537735e1351f..000000000000
--- a/sci-chemistry/xia2/xia2-0.3.1.6.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="3"
-
-PYTHON_DEPEND="2"
-
-inherit eutils python
-
-DESCRIPTION="An automated data reduction system for crystallography"
-HOMEPAGE="http://www.ccp4.ac.uk/xia/"
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	>=sci-chemistry/ccp4-apps-6.1.2
-	sci-chemistry/mosflm
-	sci-chemistry/pointless
-	>=sci-libs/ccp4-libs-6.1.2
-	sci-libs/cctbx"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
-	python_set_active_version 2
-}
-
-src_prepare() {
-	find . -name '*.bat' -delete || die
-
-	epatch "${FILESDIR}"/${PV}-fix-syntax.patch
-	python_convert_shebangs -r $(python_get_version) .
-}
-
-src_install() {
-	rm -rf ${P}/binaries ${PN}core-${PV}/Test || die
-
-	insinto /usr/share/ccp4/XIAROOT/
-	doins -r * || die
-
-	# Set programs executable
-# fperms cannot handle wildcards
-	chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
-	chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
-
-	cat >> "${T}"/23XIA <<- EOF
-	XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT
-	XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV}
-	XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}
-	PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications
-	EOF
-
-	doenvd "${T}"/23XIA
-}
-
-pkg_postinst() {
-	python_mod_optimize /usr/share/ccp4/XIAROOT
-}
-
-pkg_postrm() {
-	python_mod_cleanup /usr/share/ccp4/XIAROOT
-}
diff --git a/sci-chemistry/xia2/xia2-0.3.1.7.ebuild b/sci-chemistry/xia2/xia2-0.3.1.7.ebuild
deleted file mode 100644
index 16fbf797d1b4..000000000000
--- a/sci-chemistry/xia2/xia2-0.3.1.7.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="3"
-
-PYTHON_DEPEND="2"
-
-inherit eutils python
-
-DESCRIPTION="An automated data reduction system for crystallography"
-HOMEPAGE="http://www.ccp4.ac.uk/xia/"
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	>=sci-chemistry/ccp4-apps-6.1.2
-	sci-chemistry/mosflm
-	sci-chemistry/pointless
-	>=sci-libs/ccp4-libs-6.1.2
-	sci-libs/cctbx"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
-	python_set_active_version 2
-}
-
-src_prepare() {
-	find . -name '*.bat' -delete || die
-
-	epatch "${FILESDIR}"/${PV}-fix-syntax.patch
-	python_convert_shebangs -r $(python_get_version) .
-}
-
-src_install() {
-	rm -rf ${P}/binaries ${PN}core-${PV}/Test || die
-
-	insinto /usr/share/ccp4/XIAROOT/
-	doins -r * || die
-
-	# Set programs executable
-# fperms cannot handle wildcards
-	chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
-	chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
-
-	cat >> "${T}"/23XIA <<- EOF
-	XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT
-	XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV}
-	XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}
-	PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications
-	EOF
-
-	doenvd "${T}"/23XIA
-}
-
-pkg_postinst() {
-	python_mod_optimize /usr/share/ccp4/XIAROOT
-}
-
-pkg_postrm() {
-	python_mod_cleanup /usr/share/ccp4/XIAROOT
-}
diff --git a/sci-chemistry/xia2/xia2-0.3.3.1.ebuild b/sci-chemistry/xia2/xia2-0.3.3.1.ebuild
deleted file mode 100644
index 26fb7d0d4c83..000000000000
--- a/sci-chemistry/xia2/xia2-0.3.3.1.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-PYTHON_DEPEND="2"
-
-inherit eutils python
-
-DESCRIPTION="An automated data reduction system for crystallography"
-HOMEPAGE="http://www.ccp4.ac.uk/xia/"
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	>=sci-chemistry/ccp4-apps-6.1.2
-	sci-chemistry/mosflm
-	sci-chemistry/pointless
-	>=sci-libs/ccp4-libs-6.1.2
-	sci-libs/cctbx"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
-	python_set_active_version 2
-}
-
-src_prepare() {
-	find . -name '*.bat' -delete || die
-
-	epatch "${FILESDIR}"/${PV}-fix-syntax.patch
-	python_convert_shebangs -r $(python_get_version) .
-}
-
-src_install() {
-	rm -rf ${P}/binaries ${PN}core-${PV}/Test || die
-
-	insinto /usr/share/ccp4/XIAROOT/
-	doins -r * || die
-
-	# Set programs executable
-# fperms cannot handle wildcards
-	chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
-	chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
-
-	cat >> "${T}"/23XIA <<- EOF
-	XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT"
-	XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}"
-	XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}"
-	PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications"
-	EOF
-
-	doenvd "${T}"/23XIA
-}
-
-pkg_postinst() {
-	python_mod_optimize /usr/share/ccp4/XIAROOT
-	echo ""
-	elog "In order to use the package, you need to"
-	elog "\t source ${EPREFIX}/etc/profile"
-	echo ""
-}
-
-pkg_postrm() {
-	python_mod_cleanup /usr/share/ccp4/XIAROOT
-}
diff --git a/sci-chemistry/xia2/xia2-0.3.3.3.ebuild b/sci-chemistry/xia2/xia2-0.3.3.3.ebuild
deleted file mode 100644
index 60778aa75fb9..000000000000
--- a/sci-chemistry/xia2/xia2-0.3.3.3.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-PYTHON_DEPEND="2"
-
-inherit eutils python
-
-DESCRIPTION="An automated data reduction system for crystallography"
-HOMEPAGE="http://www.ccp4.ac.uk/xia/"
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	>=sci-chemistry/ccp4-apps-6.1.2
-	sci-chemistry/mosflm
-	sci-chemistry/pointless
-	>=sci-libs/ccp4-libs-6.1.2
-	sci-libs/cctbx"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
-	python_set_active_version 2
-}
-
-src_prepare() {
-	find . -name '*.bat' -delete || die
-
-	epatch "${FILESDIR}"/${PV}-fix-syntax.patch
-	python_convert_shebangs -r $(python_get_version) .
-}
-
-src_install() {
-	rm -rf ${P}/binaries ${PN}core-${PV}/Test || die
-
-	insinto /usr/share/ccp4/XIAROOT/
-	doins -r * || die
-
-	# Set programs executable
-# fperms cannot handle wildcards
-	chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
-	chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
-
-	cat >> "${T}"/23XIA <<- EOF
-	XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT"
-	XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}"
-	XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}"
-	PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications"
-	EOF
-
-	doenvd "${T}"/23XIA
-}
-
-pkg_postinst() {
-	python_mod_optimize /usr/share/ccp4/XIAROOT
-	echo ""
-	elog "In order to use the package, you need to"
-	elog "\t source ${EPREFIX}/etc/profile"
-	echo ""
-}
-
-pkg_postrm() {
-	python_mod_cleanup /usr/share/ccp4/XIAROOT
-}
diff --git a/sci-chemistry/xia2/xia2-0.3.4.0.ebuild b/sci-chemistry/xia2/xia2-0.3.4.0.ebuild
deleted file mode 100644
index 1d27abd355dc..000000000000
--- a/sci-chemistry/xia2/xia2-0.3.4.0.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-PYTHON_DEPEND="2"
-
-inherit eutils python
-
-DESCRIPTION="An automated data reduction system for crystallography"
-HOMEPAGE="http://www.ccp4.ac.uk/xia/"
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	>=sci-chemistry/ccp4-apps-6.1.2
-	sci-chemistry/mosflm
-	sci-chemistry/pointless
-	>=sci-libs/ccp4-libs-6.1.2
-	sci-libs/cctbx"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
-	python_set_active_version 2
-}
-
-src_prepare() {
-	find . -name '*.bat' -delete || die
-
-	epatch "${FILESDIR}"/${PV}-fix-syntax.patch
-	python_convert_shebangs -r $(python_get_version) .
-}
-
-src_install() {
-	rm -rf ${P}/binaries ${PN}core-${PV}/Test || die
-
-	insinto /usr/share/ccp4/XIAROOT/
-	doins -r * || die
-
-	# Set programs executable
-# fperms cannot handle wildcards
-	chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
-	chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
-
-	cat >> "${T}"/23XIA <<- EOF
-	XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT"
-	XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}"
-	XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}"
-	PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications"
-	EOF
-
-	doenvd "${T}"/23XIA
-}
-
-pkg_postinst() {
-	python_mod_optimize /usr/share/ccp4/XIAROOT
-	echo ""
-	elog "In order to use the package, you need to"
-	elog "\t source ${EPREFIX}/etc/profile"
-	echo ""
-}
-
-pkg_postrm() {
-	python_mod_cleanup /usr/share/ccp4/XIAROOT
-}
author	Justin Lecher <jlec@gentoo.org>	2015-10-26 08:29:56 +0100
committer	Justin Lecher <jlec@gentoo.org>	2015-10-26 08:32:25 +0100
commit	7d62034735e700ca67e977470d79f5571b15b221 (patch)
tree	78d45bafd1284caf0c06b4b98131677301303cbb /sci-chemistry
parent	add co-maintainer Coacher to metadata (diff)
download	gentoo-7d62034735e700ca67e977470d79f5571b15b221.tar.gz gentoo-7d62034735e700ca67e977470d79f5571b15b221.tar.bz2 gentoo-7d62034735e700ca67e977470d79f5571b15b221.zip