ccp4 cleanup and transmission to ccp4-6.1.2

17 files changed, 22 insertions, 2382 deletions

diff --git a/sci-chemistry/ccp4/ChangeLog b/sci-chemistry/ccp4/ChangeLog
index 5d239ff57..1320943e6 100644
--- a/sci-chemistry/ccp4/ChangeLog
+++ b/sci-chemistry/ccp4/ChangeLog
@@ -4,6 +4,17 @@
 
 *ccp4-6.1.1-r6 (07 Jul 2009)
 
+  03 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +ccp4-6.1.2.ebuild:
+  transmission ccp4 --> ccp4-apps and ccp4 as meta package
+
+  03 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> -ccp4-6.1.1.ebuild,
+  -ccp4-6.1.1-r1.ebuild, -ccp4-6.1.1-r3.ebuild, -ccp4-6.1.1-r4.ebuild,
+  -ccp4-6.1.1-r5.ebuild:
+  Cleanup old versions
+
+*ccp4-6.1.1-r6 (07 Jul 2009)
+
   07 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
   +ccp4-6.1.1-r6.ebuild:
   resort DEPENDENCIES
diff --git a/sci-chemistry/ccp4/Manifest b/sci-chemistry/ccp4/Manifest
index b21ae3e08..3e5bfc89f 100644
--- a/sci-chemistry/ccp4/Manifest
+++ b/sci-chemistry/ccp4/Manifest
@@ -7,24 +7,11 @@ AUX 6.1.1-nomolref.patch 559 RMD160 93a81aec6548fa909c67546958878fc27632b392 SHA
 AUX 6.1.1-noxia.patch 712 RMD160 dd3f8bcf309b7d84c31bf4cf829d1d9f95618d4a SHA1 b4e32e245bd8f5fde6a9573777592b3787f5becd SHA256 931bf9027e503d19d1d4446ea3ada2c20044b355d8071756ae58e88159eab75f
 AUX 6.1.1-rename-rapper.patch 2856 RMD160 37504bed3cb4e1858d88331305deef6564616b02 SHA1 31f513c987e1408b868f8c9de4aaa9f2c35cb378 SHA256 d9fed1ec65089c4130358aeed771b32c1253e48a73e90f0ce7b92bd0abbb0c2b
 AUX 6.1.1-rename-truncate.patch 1515 RMD160 eff332faa67a1732e0f99cc6cdcb846932eadc87 SHA1 b504542cf710e1b54a684b0fa0e8d73d967c96ac SHA256 50a59a1856867daa3de1f8f53e92bcfe74dea3a6d3c4ba238a9ea83dbcdfbf07
-AUX 6.1.2-clipper-mmdbold-ggc-4.3.patch 656 RMD160 6b302779b48217a14f5ac9110bc307db3a3b51eb SHA1 f5813d6769fa9dc11605425cdbda85691d3016bc SHA256 982eff0336a6dfaf4e280d51a59cf722fc063ca89d15ca0af46ce83727fb9a8a
-AUX 6.1.2-dont-build-double-and-make-bindir.patch 688 RMD160 f5f93cbec122ce81a1ddb1cf57a852d51fa5e5d6 SHA1 4c924554c5c1991ed691fe3474eeffbd108493a9 SHA256 037a3d9042c784c895083fe5348ed3bde74620c1b6b3b2cd4eea53bdbfe77d53
-AUX 6.1.2-dont-build-libs.patch 1255 RMD160 6454c2f61a13dbb8238b5ceed69c233fcf336ed4 SHA1 ff23480016731940279b8742707024f5a6e10bf3 SHA256 0d4a083d6c6bce38db0b84f9dccf0f339d746f9c0dd316eeb745f8427401be75
-AUX 6.1.2-dont-make-dirs-in-configure.patch 2866 RMD160 ba49e45ab609a42a2d93b96f55af913bf9625610 SHA1 36c9329c3768c08687ef062c9ab649d32833b422 SHA256 1b5997f17526a4fd60ffa9eccf4b765aadf3a78c9394657000e0454f364240ca
-AUX 6.1.2-fix-setup-bash-incompatibility.patch 422 RMD160 e7e886ab030cf3324302c8fd0c866b48eeb34f8c SHA1 4e549abcd3ced1e6ecf9d3f2bddfed70425d61aa SHA256 109a0e806f9c0e1b8bf5e5f0c58be6f1dae06396b62ee4dae9f579ff7dcb5a01
-AUX 6.1.2-nomolref.patch 559 RMD160 93a81aec6548fa909c67546958878fc27632b392 SHA1 e16dafd552839128f81bc2e8e8f9953258e1c398 SHA256 1ba59db41f93c02494beb7a5d816dea966341009344805df4dfb873ab4e98eca
-AUX 6.1.2-rename-rapper.patch 2856 RMD160 37504bed3cb4e1858d88331305deef6564616b02 SHA1 31f513c987e1408b868f8c9de4aaa9f2c35cb378 SHA256 d9fed1ec65089c4130358aeed771b32c1253e48a73e90f0ce7b92bd0abbb0c2b
-AUX 6.1.2-rename-truncate.patch 1515 RMD160 eff332faa67a1732e0f99cc6cdcb846932eadc87 SHA1 b504542cf710e1b54a684b0fa0e8d73d967c96ac SHA256 50a59a1856867daa3de1f8f53e92bcfe74dea3a6d3c4ba238a9ea83dbcdfbf07
 DIST 6.1.1-090511-updates.patch.bz2 8915 RMD160 58114b0ba6d225078044a8a6f9245aab66c6b572 SHA1 15c327c0b218b542b0c3955a9e63d2c6de299f7e SHA256 c0dbbde05b72f2460ada22f556d4cfe1f286a448ceb1181fd48b758468e509ac
 DIST ccp4-6.1.1-core-src.tar.gz 246661086 RMD160 6722367727e4b6b1f8456f1458c9aac124923a89 SHA1 9141801e021f8a5107ed1e3989840e4de849b39c SHA256 56f971e05fe4543173451e48600813492fd0081b25d4a659cb0fed1fd2529407
 DIST ccp4-6.1.1-src-patch-04_03_09.tar.gz 279642 RMD160 1a7c3b6cc846d315fc577e78b4aa00ab85a3d3d2 SHA1 29dbb84f3d63fc860694473ca99cf8bb71dae18a SHA256 eb806168235b55fbafdd72591ba94d35b78cc715a56a8b90979644d420ad672a
 DIST ctruncate.cpp-r1.13.2.5-r1.13.2.7.diff 4993 RMD160 06deba4ffc19292d3c1b9136e380c8bf273d8311 SHA1 ce91a917547f03b699504b325aadfc4af1b3b51d SHA256 5eb6d6bfbc0197761864fa69062065639adfa8507c3ced99164afc0b5105132d
-EBUILD ccp4-6.1.1-r1.ebuild 11281 RMD160 523a351ef16aaa5a599ca081a9fa1a0f9d50319c SHA1 ab186ddc879f443fe8bf0db7b14001fe5e6dd3a0 SHA256 e92b2d21f1332f808b14f7cc9bcc04648d93983c5a50014e40b27b55b2578189
-EBUILD ccp4-6.1.1-r3.ebuild 11533 RMD160 75cf324436d1264af8cee88d7acdc3d61d1a1163 SHA1 034966380384691a05f60547b294b21167c04424 SHA256 2f195a63886488f0e1c7eedbd35c513805f9da224cb1272b82a61442e7027f9c
-EBUILD ccp4-6.1.1-r4.ebuild 11487 RMD160 73c05354efb4e32495f8abda001354199939b5fa SHA1 a3e4db5ca08657e83da1411af68a00f6ad5dc218 SHA256 9b494f31162b28a061fb6f3d5be322ee7733b767fce9e6199026e2622334e63a
-EBUILD ccp4-6.1.1-r5.ebuild 11541 RMD160 baa8f0063fe798506c543fbed6c14557fa4a9b96 SHA1 19dfb2c04b8e335ddd073459724aadc0e55169b9 SHA256 f482d3f3680416b5d5287c024ecac89993c62f93b74a990784e0e03563f458d1
-EBUILD ccp4-6.1.1-r6.ebuild 11643 RMD160 41ec2ac76ddd724fedb4a850e0fad750f9856f17 SHA1 61a411ad26bcf50cd766318559e7b52f583a8515 SHA256 2e898b66a09e38aa26f2651ac25b053da075ee5be442c613ebf26c31d4d5c1ea
-EBUILD ccp4-6.1.1.ebuild 11078 RMD160 bdda0b25af939be1d59f1d25a3f5d1b603f8b17c SHA1 ceb05f4916197ca661660510e7eec70924032a1e SHA256 33214b5ca84c710112fb286de06073a843400fa2331715db1672713b33032024
-EBUILD ccp4-6.1.2.ebuild 535 RMD160 6d151ead41bc0b309432688768031eab35d0b0ce SHA1 9faa74ed9dd01dbbfd8180af3ab52ca70c8ab144 SHA256 a506584eecf45ba2adc7c9ff8ea426f2993c5397f4401a88bab57d0a58278988
-MISC ChangeLog 5725 RMD160 a561282ea9bd67da0b6e17eaaf47d559c711b055 SHA1 23ba90946cda15225ebabf48309e41267d30f22e SHA256 0b9ab8e5fe091a7a79a394c355e7d253711b08f7f0ce4fbb65e4860d30229308
+EBUILD ccp4-6.1.1-r6.ebuild 11637 RMD160 9c731cc601a6972c692719e0647f6fbda5a106c2 SHA1 d0d34f6830d311da0fc9d866e5ac140d61b6c523 SHA256 48d5a285b33f2cc57e5c4aaa4697d4865a14b5b5248b36951d1a170371f7bd88
+EBUILD ccp4-6.1.2.ebuild 557 RMD160 ef938d986aa591db0deb86f7ee15ae260b8ba935 SHA1 69e01064d89a1f479609b0f7f6a66040959c0c13 SHA256 483fbd66482d898e9741d49c3cc8f99e1a1c4287062ef630a604887aef1c5d3b
+MISC ChangeLog 6091 RMD160 1d470631021d9c305350e1e97d1a1f8d534e9e93 SHA1 430a28f7339f961e07b3009aeb6c4e339721410f SHA256 cd62881632080f3574a2e4282ef5c155ff94dc83f8437c3713681b0d22e0ed9e
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-chemistry/ccp4/ccp4-6.1.1-r1.ebuild b/sci-chemistry/ccp4/ccp4-6.1.1-r1.ebuild
deleted file mode 100644
index b53210874..000000000
--- a/sci-chemistry/ccp4/ccp4-6.1.1-r1.ebuild
+++ /dev/null
@@ -1,406 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit fortran eutils gnuconfig toolchain-funcs autotools
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-UPDATE="04_03_09"
-PATCHDATE="090511"
-
-PATCH_TOT="0"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-#PATCH1=( src/topp_
-#topp.f-r1.16.2.5-r1.16.2.6.diff )
-#PATCH2=( .
-#configure-r1.372.2.18-r1.372.2.19.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
-#SRC_URI="${SRC}/${PV}/source/${P}-core-src.tar.gz"
-SRC_URI="${SRC}/6.1.1/${P}-core-src.tar.gz
-	${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz
-	http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
-#	${SRC}/6.1/${P}-phaser-src.tar.gz"
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="X"
-# app-office/sc overlaps sc binary and man page
-# We can't rename ours since the automated ccp4i interface expects it there,
-# as do many scripts. app-office/sc can't rename its because that's the name
-# of the package.
-RDEPEND="X? (
-			x11-libs/libX11
-			x11-libs/libXt
-			x11-libs/libXaw
-			x11-libs/libxdl_view
-			x11-libs/libjwc_c
-			x11-libs/libjwc_f
-		)
-		>=dev-lang/tk-8.3
-		>=dev-tcltk/blt-2.4
-		virtual/lapack
-		virtual/blas
-		=sci-libs/fftw-2*
-		sci-chemistry/pdb-extract
-		sci-chemistry/rasmol
-		sci-libs/clipper
-		app-shells/tcsh
-		dev-python/pyxml
-		dev-libs/libxml2
-		dev-libs/boehm-gc
-		dev-tcltk/iwidgets
-		>=dev-tcltk/tdom-0.8
-		dev-tcltk/tkimg
-		dev-tcltk/tktreectrl
-		dev-tcltk/itcl
-		dev-tcltk/itk
-		sci-libs/ccp4-libs
-		!app-office/sc"
-DEPEND="${RDEPEND}
-		=sys-devel/automake-1.6*
-		X? (
-				x11-misc/imake
-				x11-proto/inputproto
-				x11-proto/xextproto
-		)"
-PDEPEND="sci-chemistry/mosflm
-	 sci-chemistry/imosflm
-	 sci-chemistry/molrep
-	 sci-chemistry/refmac
-	 sci-chemistry/xia2
-	 sci-chemistry/ccp4i
-	 sci-libs/balbes-db"
-
-S="${WORKDIR}/${PN}-${PV}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	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
-
-	epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	einfo "Applying Gentoo patches ..."
-	# These two only needed when attempting to install outside build dir via
-	# --bindir and --libdir instead of straight copying after build
-
-	# it attempts to install some libraries during the build
-	#ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch
-	# hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
-	# without this patch when --libdir is set
-	# Rotgen still needs more patching to find it
-	#ccp_patch "${FILESDIR}"/add-xdl-libdir.patch
-
-	# 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
-
-	# We already have sci-chemistry/pdb-extract
-# Use configure option instead
-#	ccp_patch "${FILESDIR}"/dont-build-pdb-extract.patch
-
-# Don't use these when we aren't building phaser
-#	ccp_patch "${FILESDIR}"/make-phaser-bindir.patch
-#	ccp_patch "${FILESDIR}"/no-phaser-ld-assume-kernel.patch
-#	# scons config.py tries to chmod python on live system
-#	ccp_patch "${FILESDIR}"/dont-chmod-python-binary.patch
-
-# Upstream fixed it
-	# csh syntax doesn't work in a bash script
-#	ccp_patch "${FILESDIR}"/${PV}-fix-setup-bash-incompatibility.patch
-
-	# libraries come from sci-libs/ccp4-libs
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch
-
-	# coreutils installs a binary called truncate
-	ccp_patch "${FILESDIR}"/${PV}-rename-truncate.patch
-	mv ./doc/truncate.doc ./doc/ftruncate.doc || die
-	mv ./html/truncate.html ./html/ftruncate.html || die
-
-	# conflicts with media-libs/raptor
-	ccp_patch "${FILESDIR}"/${PV}-rename-rapper.patch
-	mv ./doc/rapper.doc ./doc/rappermc.doc || die
-	mv ./html/rapper.html ./html/rappermc.html || die
-
-	# mosflm has its own ebuild
-#	ccp_patch "${FILESDIR}"/${PV}-dont-build-mosflm.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# Don't build refmac binaries available from the standalone version
-	sed -i -e "/^REFMACTARGETS/s:refmac5 libcheck makecif molrep::g" configure
-
-	# Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
-	pushd src/rapper 2>/dev/null
-	sed -i \
-		-e '/^AC_CONFIG_SUBDIRS(\[gc7.0 libxml2\])/d' \
-		configure.ac
-	sed -i \
-		-e '/^SUBDIRS/s:libxml2 gc7.0::g' \
-		Makefile.am
-	sed -i \
-		-e '/^rappermc_LDADD/s:../gc7.0/libgc.la ../libxml2/libxml2.la:-lgc -lxml2:g' \
-		LOOP/Makefile.am
-	sed -i \
-		-e '/^INCLUDES/s:-I../gc7.0/include -I../libxml2/include:-I/usr/include/gc -I/usr/include/libxml2:g' \
-		LOOP/Makefile.am
-	eautoreconf
-	popd 2>/dev/null
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# Build system is broken if we set LDFLAGS
-	unset LDFLAGS
-
-	# 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 [[ "${FORTRANC}" = "ifc" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${S}"/include/ccp4.setup
-
-	# We agree to the license by emerging this, set in LICENSE
-	sed -i \
-		-e "s~^\(^agreed=\).*~\1yes~g" \
-		"${S}"/configure
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
-		"${S}"/include/ccp4.setup*
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-	export CC=$(tc-getCC)
-	export CXX=$(tc-getCXX)
-	export COPTIM=${CFLAGS}
-	export CXXOPTIM=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=${FORTRANC}
-	export FOPTIM=${FFLAGS:- -O2}
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		$(use_enable X x) \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-pdb_extract \
-		--disable-cctbx \
-		--disable-phaser \
-		--disable-clipper \
-		--disable-mrbump \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-
-	# fsplit is required for the programs
-	pushd lib/src 2>/dev/null
-	emake fsplit -j1 || die
-	popd 2>/dev/null
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd src/clipper_progs 2>/dev/null
-	econf \
-		--prefix="${S}" \
-		--with-ccp4="${S}" \
-		--with-clipper=/usr \
-		--with-fftw=/usr \
-		--with-mmdb=/usr \
-		CXX=$(tc-getCXX) \
-		|| die
-	emake || die
-	popd 2>/dev/null
-
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-# Only needed when using --bindir and --libdir
-	# Needed to avoid errors. Originally tried to make lib and bin
-	# in configure script, now patched out by dont-make-dirs-in-configure.patch
-#	dodir /usr/include /usr/$(get_libdir) /usr/bin
-
-#	make install || die "install failed"
-
-	# 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"
-
-	# Fix env
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \
-		-e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
-		-e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
-		-e "s~^\(setenv DBCCP4I_TOP\).*~\1 \$CCP4/share/ccp4/dbccp4i~g" \
-		-e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
-		-e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \
-		-e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
-		-e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
-		-e "s~^\(.*setenv PYTHONPATH .*\)\$CCP4.*~\1\$CCP4/share/ccp4/python~g" \
-		-e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Don't check for updates on every sourcing of /etc/profile
-	sed -i \
-		-e "s:\(eval python.*\):#\1:g"
-		"${S}"/include/ccp4.setup*
-
-	# Get rid of S instances
-	# Also the main clipper library is built as libclipper-core, not libclipper
-#	sed -i \
-#		-e "s:${S}:$usr:g" \
-#		-e "s:lclipper :lclipper-core :g" \
-#		"${S}"/bin/clipper-config || die
-#	sed -i \
-#		-e "s:${S}:usr:g" \
-#		"${S}"/$(get_libdir)/cctbx/cctbx_build/setpaths*
-
-	# Bins
-	dobin "${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 ${file} || die
-		fi
-	done
-
-	# Setup scripts
-	insinto /etc/profile.d
-	newins "${S}"/include/ccp4.setup-bash ccp4.setup.sh || die
-	newins "${S}"/include/ccp4.setup-dist ccp4.setup.csh || die
-	rm -f "${S}"/include/ccp4.setup-bash
-	rm -f "${S}"/include/ccp4.setup-dist
-
-	# Environment files, setup scripts, etc.
-	insinto /usr/share/ccp4/include
-	doins "${S}"/include/* || die
-
-	# balbes
-#	insinto /usr/share/ccp4
-#	doins -r "${S}"/share/balbes || die
-
-	# smartie -- log parsing
-	insinto /usr/share/ccp4
-	doins -r "${S}"/share/smartie || die
-
-	# Install docs and examples
-
-	doman "${S}"/man/cat1/*
-
-	mv "${S}"/manual/README "${S}"/manual/README-manual
-	dodoc "${S}"/manual/*
-
-	dodoc "${S}"/README "${S}"/CHANGES
-
-	dodoc "${S}"/doc/*
-	rm "${D}"/usr/share/doc/${PF}/GNUmakefile.*
-	rm "${D}"/usr/share/doc/${PF}/COPYING.*
-
-	dohtml -r "${S}"/html/*
-	dodoc "${S}"/examples/README
-
-	# Fix wrongly installed HTML pages from clipper
-	dohtml "${D}"/usr/html/*
-	rm -rf "${D}"/usr/html
-
-	for i in data rnase toxd; do
-		docinto examples/${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/${i}/*
-	done
-
-	# Needed for ccp4i docs to work
-	dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html
-
-	# Fix overlaps with other packages
-	rm -f "${D}"/usr/share/man/man1/rasmol.1* "${D}"/usr/lib/font84.dat || die
-}
-
-pkg_postinst() {
-	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
-	einfo "in /etc/profile.d/ccp4.setup* to modify this."
-}
-
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-chemistry/ccp4/ccp4-6.1.1-r3.ebuild b/sci-chemistry/ccp4/ccp4-6.1.1-r3.ebuild
deleted file mode 100644
index 664712441..000000000
--- a/sci-chemistry/ccp4/ccp4-6.1.1-r3.ebuild
+++ /dev/null
@@ -1,413 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit fortran eutils gnuconfig toolchain-funcs autotools
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-UPDATE="04_03_09"
-PATCHDATE="090511"
-
-PATCH_TOT="0"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-#PATCH1=( src/topp_
-#topp.f-r1.16.2.5-r1.16.2.6.diff )
-#PATCH2=( .
-#configure-r1.372.2.18-r1.372.2.19.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
-#SRC_URI="${SRC}/${PV}/source/${P}-core-src.tar.gz"
-SRC_URI="${SRC}/6.1.1/${P}-core-src.tar.gz
-	${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz
-	http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
-#	${SRC}/6.1/${P}-phaser-src.tar.gz"
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="X examples"
-# app-office/sc overlaps sc binary and man page
-# We can't rename ours since the automated ccp4i interface expects it there,
-# as do many scripts. app-office/sc can't rename its because that's the name
-# of the package.
-RDEPEND="X? (
-			x11-libs/libX11
-			x11-libs/libXt
-			x11-libs/libXaw
-			x11-libs/libxdl_view
-			x11-libs/libjwc_c
-			x11-libs/libjwc_f
-		)
-		>=dev-lang/tk-8.3
-		>=dev-tcltk/blt-2.4
-		virtual/lapack
-		virtual/blas
-		=sci-libs/fftw-2*
-		sci-chemistry/pdb-extract
-		sci-chemistry/rasmol
-		sci-libs/clipper
-		app-shells/tcsh
-		dev-python/pyxml
-		dev-libs/libxml2
-		dev-libs/boehm-gc
-		dev-tcltk/iwidgets
-		>=dev-tcltk/tdom-0.8
-		dev-tcltk/tkimg
-		dev-tcltk/tktreectrl
-		dev-tcltk/itcl
-		dev-tcltk/itk
-		sci-libs/ccp4-libs
-		!app-office/sc"
-DEPEND="${RDEPEND}
-		=sys-devel/automake-1.6*
-		X? (
-				x11-misc/imake
-				x11-proto/inputproto
-				x11-proto/xextproto
-		)"
-PDEPEND="sci-chemistry/mosflm
-	 sci-chemistry/imosflm
-	 sci-chemistry/molrep
-	 sci-chemistry/refmac
-	 sci-chemistry/xia2
-	 sci-chemistry/ccp4i
-	 sci-libs/balbes-db"
-
-S="${WORKDIR}/${PN}-${PV}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	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
-
-	epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	einfo "Applying Gentoo patches ..."
-	# These two only needed when attempting to install outside build dir via
-	# --bindir and --libdir instead of straight copying after build
-
-	# it attempts to install some libraries during the build
-	#ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch
-	# hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
-	# without this patch when --libdir is set
-	# Rotgen still needs more patching to find it
-	#ccp_patch "${FILESDIR}"/add-xdl-libdir.patch
-
-	# 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
-
-	# We already have sci-chemistry/pdb-extract
-# Use configure option instead
-#	ccp_patch "${FILESDIR}"/dont-build-pdb-extract.patch
-
-# Don't use these when we aren't building phaser
-#	ccp_patch "${FILESDIR}"/make-phaser-bindir.patch
-#	ccp_patch "${FILESDIR}"/no-phaser-ld-assume-kernel.patch
-#	# scons config.py tries to chmod python on live system
-#	ccp_patch "${FILESDIR}"/dont-chmod-python-binary.patch
-
-# Upstream fixed it
-	# csh syntax doesn't work in a bash script
-#	ccp_patch "${FILESDIR}"/${PV}-fix-setup-bash-incompatibility.patch
-
-	# libraries come from sci-libs/ccp4-libs
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch
-
-	# coreutils installs a binary called truncate
-	ccp_patch "${FILESDIR}"/${PV}-rename-truncate.patch
-	mv ./doc/truncate.doc ./doc/ftruncate.doc || die
-	mv ./html/truncate.html ./html/ftruncate.html || die
-
-	# conflicts with media-libs/raptor
-	ccp_patch "${FILESDIR}"/${PV}-rename-rapper.patch
-	mv ./doc/rapper.doc ./doc/rappermc.doc || die
-	mv ./html/rapper.html ./html/rappermc.html || die
-
-	# molref is provided as binary and dynamically linked against icc
-	ccp_patch "${FILESDIR}"/${PV}-nomolref.patch
-
-	# mosflm has its own ebuild
-#	ccp_patch "${FILESDIR}"/${PV}-dont-build-mosflm.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# glibc-2.10 getline fix
-	sed -e "s:getline:${PN}getline:g" -i lib/src/fsplit.c
-
-	# Don't build refmac binaries available from the standalone version
-	sed -i -e "/^REFMACTARGETS/s:refmac5 libcheck makecif molrep::g" configure
-
-	# Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
-	pushd src/rapper 2>/dev/null
-	sed -i \
-		-e '/^AC_CONFIG_SUBDIRS(\[gc7.0 libxml2\])/d' \
-		configure.ac
-	sed -i \
-		-e '/^SUBDIRS/s:libxml2 gc7.0::g' \
-		Makefile.am
-	sed -i \
-		-e '/^rappermc_LDADD/s:../gc7.0/libgc.la ../libxml2/libxml2.la:-lgc -lxml2:g' \
-		LOOP/Makefile.am
-	sed -i \
-		-e '/^INCLUDES/s:-I../gc7.0/include -I../libxml2/include:-I/usr/include/gc -I/usr/include/libxml2:g' \
-		LOOP/Makefile.am
-	eautoreconf
-	popd 2>/dev/null
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# Build system is broken if we set LDFLAGS
-	unset LDFLAGS
-
-	# 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 [[ "${FORTRANC}" = "ifc" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${S}"/include/ccp4.setup
-
-	# We agree to the license by emerging this, set in LICENSE
-	sed -i \
-		-e "s~^\(^agreed=\).*~\1yes~g" \
-		"${S}"/configure
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
-		"${S}"/include/ccp4.setup*
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-	export CC=$(tc-getCC)
-	export CXX=$(tc-getCXX)
-	export COPTIM=${CFLAGS}
-	export CXXOPTIM=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=${FORTRANC}
-	export FOPTIM=${FFLAGS:- -O2}
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		$(use_enable X x) \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-pdb_extract \
-		--disable-cctbx \
-		--disable-phaser \
-		--disable-clipper \
-		--disable-mrbump \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-
-	# fsplit is required for the programs
-	pushd lib/src 2>/dev/null
-	emake fsplit -j1 || die
-	popd 2>/dev/null
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd src/clipper_progs 2>/dev/null
-	econf \
-		--prefix="${S}" \
-		--with-ccp4="${S}" \
-		--with-clipper=/usr \
-		--with-fftw=/usr \
-		--with-mmdb=/usr \
-		CXX=$(tc-getCXX) \
-		|| die
-	emake || die
-	popd 2>/dev/null
-
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-# Only needed when using --bindir and --libdir
-	# Needed to avoid errors. Originally tried to make lib and bin
-	# in configure script, now patched out by dont-make-dirs-in-configure.patch
-#	dodir /usr/include /usr/$(get_libdir) /usr/bin
-
-#	make install || die "install failed"
-
-	# 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"
-
-	# Fix env
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \
-		-e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
-		-e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
-		-e "s~^\(setenv DBCCP4I_TOP\).*~\1 \$CCP4/share/ccp4/dbccp4i~g" \
-		-e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
-		-e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \
-		-e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
-		-e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
-		-e "s~^\(.*setenv PYTHONPATH .*\)\$CCP4.*~\1\$CCP4/share/ccp4/python~g" \
-		-e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Don't check for updates on every sourcing of /etc/profile
-	sed -i \
-		-e "s:\(eval python.*\):#\1:g"
-		"${S}"/include/ccp4.setup* || die
-
-	# Get rid of S instances
-	# Also the main clipper library is built as libclipper-core, not libclipper
-#	sed -i \
-#		-e "s:${S}:$usr:g" \
-#		-e "s:lclipper :lclipper-core :g" \
-#		"${S}"/bin/clipper-config || die
-#	sed -i \
-#		-e "s:${S}:usr:g" \
-#		"${S}"/$(get_libdir)/cctbx/cctbx_build/setpaths*
-
-	# Bins
-	dobin "${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 ${file} || die
-		fi
-	done
-
-	# Setup scripts
-	insinto /etc/profile.d
-	newins "${S}"/include/ccp4.setup-bash ccp4.setup.sh || die
-	newins "${S}"/include/ccp4.setup-dist ccp4.setup.csh || die
-	rm -f "${S}"/include/ccp4.setup-bash
-	rm -f "${S}"/include/ccp4.setup-dist
-
-	# Environment files, setup scripts, etc.
-	insinto /usr/share/ccp4/include
-	doins "${S}"/include/* || die
-
-	# balbes
-#	insinto /usr/share/ccp4
-#	doins -r "${S}"/share/balbes || die
-
-	# smartie -- log parsing
-	insinto /usr/share/ccp4
-	doins -r "${S}"/share/smartie || die
-
-	# Install docs and examples
-
-	doman "${S}"/man/cat1/*
-
-	mv "${S}"/manual/README "${S}"/manual/README-manual
-	dodoc "${S}"/manual/*
-
-	dodoc "${S}"/README "${S}"/CHANGES
-
-	dodoc "${S}"/doc/*
-	rm "${D}"/usr/share/doc/${PF}/GNUmakefile.*
-	rm "${D}"/usr/share/doc/${PF}/COPYING.*
-
-	dohtml -r "${S}"/html/*
-	dodoc "${S}"/examples/README
-
-	# Fix wrongly installed HTML pages from clipper
-	dohtml "${D}"/usr/html/*
-	rm -rf "${D}"/usr/html
-
-	if use examples; then
-		for i in data rnase toxd; do
-			docinto examples/${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/$(get_libdir)/ccp4/examples
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html
-
-	# Fix overlaps with other packages
-	rm -f "${D}"/usr/share/man/man1/rasmol.1* "${D}"/usr/lib/font84.dat || die
-}
-
-pkg_postinst() {
-	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
-	einfo "in /etc/profile.d/ccp4.setup* to modify this."
-}
-
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-chemistry/ccp4/ccp4-6.1.1-r4.ebuild b/sci-chemistry/ccp4/ccp4-6.1.1-r4.ebuild
deleted file mode 100644
index 12f838f69..000000000
--- a/sci-chemistry/ccp4/ccp4-6.1.1-r4.ebuild
+++ /dev/null
@@ -1,411 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit fortran eutils gnuconfig toolchain-funcs autotools
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-UPDATE="04_03_09"
-PATCHDATE="090511"
-
-PATCH_TOT="1"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-PATCH1=( src/clipper_progs/src/
-ctruncate.cpp-r1.13.2.5-r1.13.2.7.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
-#SRC_URI="${SRC}/${PV}/source/${P}-core-src.tar.gz"
-SRC_URI="${SRC}/6.1.1/${P}-core-src.tar.gz
-	${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz
-	http://dev.gentooexperimental.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/${!NAME}"
-done
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="X examples"
-# app-office/sc overlaps sc binary and man page
-# We can't rename ours since the automated ccp4i interface expects it there,
-# as do many scripts. app-office/sc can't rename its because that's the name
-# of the package.
-RDEPEND="X? (
-			x11-libs/libX11
-			x11-libs/libXt
-			x11-libs/libXaw
-			x11-libs/libxdl_view
-			x11-libs/libjwc_c
-			x11-libs/libjwc_f
-		)
-		>=dev-lang/tk-8.3
-		>=dev-tcltk/blt-2.4
-		virtual/lapack
-		virtual/blas
-		=sci-libs/fftw-2*
-		sci-chemistry/pdb-extract
-		sci-chemistry/rasmol
-		sci-libs/clipper
-		app-shells/tcsh
-		dev-python/pyxml
-		dev-libs/libxml2
-		dev-libs/boehm-gc
-		dev-tcltk/iwidgets
-		>=dev-tcltk/tdom-0.8
-		dev-tcltk/tkimg
-		dev-tcltk/tktreectrl
-		dev-tcltk/itcl
-		dev-tcltk/itk
-		sci-libs/ccp4-libs
-		!app-office/sc"
-DEPEND="${RDEPEND}
-		=sys-devel/automake-1.6*
-		X? (
-				x11-misc/imake
-				x11-proto/inputproto
-				x11-proto/xextproto
-		)"
-PDEPEND="sci-chemistry/mosflm
-	 sci-chemistry/imosflm
-	 sci-chemistry/molrep
-	 sci-chemistry/refmac
-	 sci-chemistry/xia2
-	 sci-chemistry/ccp4i
-	 sci-libs/balbes-db"
-
-S="${WORKDIR}/${PN}-${PV}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	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
-
-	epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	einfo "Applying Gentoo patches ..."
-	# These two only needed when attempting to install outside build dir via
-	# --bindir and --libdir instead of straight copying after build
-
-	# it attempts to install some libraries during the build
-	#ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch
-	# hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
-	# without this patch when --libdir is set
-	# Rotgen still needs more patching to find it
-	#ccp_patch "${FILESDIR}"/add-xdl-libdir.patch
-
-	# 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
-
-	# We already have sci-chemistry/pdb-extract
-# Use configure option instead
-#	ccp_patch "${FILESDIR}"/dont-build-pdb-extract.patch
-
-# Don't use these when we aren't building phaser
-#	ccp_patch "${FILESDIR}"/make-phaser-bindir.patch
-#	ccp_patch "${FILESDIR}"/no-phaser-ld-assume-kernel.patch
-#	# scons config.py tries to chmod python on live system
-#	ccp_patch "${FILESDIR}"/dont-chmod-python-binary.patch
-
-# Upstream fixed it
-	# csh syntax doesn't work in a bash script
-#	ccp_patch "${FILESDIR}"/${PV}-fix-setup-bash-incompatibility.patch
-
-	# libraries come from sci-libs/ccp4-libs
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch
-
-	# coreutils installs a binary called truncate
-	ccp_patch "${FILESDIR}"/${PV}-rename-truncate.patch
-	mv ./doc/truncate.doc ./doc/ftruncate.doc || die
-	mv ./html/truncate.html ./html/ftruncate.html || die
-
-	# conflicts with media-libs/raptor
-	ccp_patch "${FILESDIR}"/${PV}-rename-rapper.patch
-	mv ./doc/rapper.doc ./doc/rappermc.doc || die
-	mv ./html/rapper.html ./html/rappermc.html || die
-
-	# molref is provided as binary and dynamically linked against icc
-	ccp_patch "${FILESDIR}"/${PV}-nomolref.patch
-
-	# mosflm has its own ebuild
-#	ccp_patch "${FILESDIR}"/${PV}-dont-build-mosflm.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# glibc-2.10 getline fix
-	sed -e "s:getline:${PN}getline:g" -i lib/src/fsplit.c
-
-	# Don't build refmac binaries available from the standalone version
-	sed -i -e "/^REFMACTARGETS/s:refmac5 libcheck makecif molrep::g" configure
-
-	# Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
-	pushd src/rapper 2>/dev/null
-	sed -i \
-		-e '/^AC_CONFIG_SUBDIRS(\[gc7.0 libxml2\])/d' \
-		configure.ac
-	sed -i \
-		-e '/^SUBDIRS/s:libxml2 gc7.0::g' \
-		Makefile.am
-	sed -i \
-		-e '/^rappermc_LDADD/s:../gc7.0/libgc.la ../libxml2/libxml2.la:-lgc -lxml2:g' \
-		LOOP/Makefile.am
-	sed -i \
-		-e '/^INCLUDES/s:-I../gc7.0/include -I../libxml2/include:-I/usr/include/gc -I/usr/include/libxml2:g' \
-		LOOP/Makefile.am
-	eautoreconf
-	popd 2>/dev/null
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# Build system is broken if we set LDFLAGS
-	unset LDFLAGS
-
-	# 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 [[ "${FORTRANC}" = "ifc" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${S}"/include/ccp4.setup
-
-	# We agree to the license by emerging this, set in LICENSE
-	sed -i \
-		-e "s~^\(^agreed=\).*~\1yes~g" \
-		"${S}"/configure
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
-		"${S}"/include/ccp4.setup*
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-	export CC=$(tc-getCC)
-	export CXX=$(tc-getCXX)
-	export COPTIM=${CFLAGS}
-	export CXXOPTIM=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=${FORTRANC}
-	export FOPTIM=${FFLAGS:- -O2}
-	export BINSORT_SCR="${T}"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		$(use_enable X x) \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-pdb_extract \
-		--disable-cctbx \
-		--disable-phaser \
-		--disable-clipper \
-		--disable-mrbump \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-
-	# fsplit is required for the programs
-	pushd lib/src 2>/dev/null
-	emake fsplit -j1 || die
-	popd 2>/dev/null
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd src/clipper_progs 2>/dev/null
-	econf \
-		--prefix="${S}" \
-		--with-ccp4="${S}" \
-		--with-clipper=/usr \
-		--with-fftw=/usr \
-		--with-mmdb=/usr \
-		CXX=$(tc-getCXX) \
-		|| die
-	emake || die
-	popd 2>/dev/null
-
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-# Only needed when using --bindir and --libdir
-	# Needed to avoid errors. Originally tried to make lib and bin
-	# in configure script, now patched out by dont-make-dirs-in-configure.patch
-#	dodir /usr/include /usr/$(get_libdir) /usr/bin
-
-#	make install || die "install failed"
-
-	# 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"
-
-	# Fix env
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \
-		-e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
-		-e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
-		-e "s~^\(setenv DBCCP4I_TOP\).*~\1 \$CCP4/share/ccp4/dbccp4i~g" \
-		-e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
-		-e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \
-		-e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
-		-e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
-		-e "s~^\(.*setenv PYTHONPATH .*\)\$CCP4.*~\1\$CCP4/share/ccp4/python~g" \
-		-e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Don't check for updates on every sourcing of /etc/profile
-	sed -i \
-		-e "s:\(eval python.*\):#\1:g"
-		"${S}"/include/ccp4.setup* || die
-
-	# Get rid of S instances
-	# Also the main clipper library is built as libclipper-core, not libclipper
-#	sed -i \
-#		-e "s:${S}:$usr:g" \
-#		-e "s:lclipper :lclipper-core :g" \
-#		"${S}"/bin/clipper-config || die
-#	sed -i \
-#		-e "s:${S}:usr:g" \
-#		"${S}"/$(get_libdir)/cctbx/cctbx_build/setpaths*
-
-	# Bins
-	dobin "${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 ${file} || die
-		fi
-	done
-
-	# Setup scripts
-	insinto /etc/profile.d
-	newins "${S}"/include/ccp4.setup-bash ccp4.setup.sh || die
-	newins "${S}"/include/ccp4.setup-dist ccp4.setup.csh || die
-	rm -f "${S}"/include/ccp4.setup-bash
-	rm -f "${S}"/include/ccp4.setup-dist
-
-	# Environment files, setup scripts, etc.
-	insinto /usr/share/ccp4/include
-	doins "${S}"/include/* || die
-
-	# balbes
-#	insinto /usr/share/ccp4
-#	doins -r "${S}"/share/balbes || die
-
-	# smartie -- log parsing
-	insinto /usr/share/ccp4
-	doins -r "${S}"/share/smartie || die
-
-	# Install docs and examples
-
-	doman "${S}"/man/cat1/*
-
-	mv "${S}"/manual/README "${S}"/manual/README-manual
-	dodoc "${S}"/manual/*
-
-	dodoc "${S}"/README "${S}"/CHANGES
-
-	dodoc "${S}"/doc/*
-	rm "${D}"/usr/share/doc/${PF}/GNUmakefile.*
-	rm "${D}"/usr/share/doc/${PF}/COPYING.*
-
-	dohtml -r "${S}"/html/*
-	dodoc "${S}"/examples/README
-
-	# Fix wrongly installed HTML pages from clipper
-	dohtml "${D}"/usr/html/*
-	rm -rf "${D}"/usr/html
-
-	if use examples; then
-		for i in data rnase toxd; do
-			docinto examples/${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/$(get_libdir)/ccp4/examples
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html
-
-	# Fix overlaps with other packages
-	rm -f "${D}"/usr/share/man/man1/rasmol.1* "${D}"/usr/lib/font84.dat || die
-}
-
-pkg_postinst() {
-	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
-	einfo "in /etc/profile.d/ccp4.setup* to modify this."
-}
-
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-chemistry/ccp4/ccp4-6.1.1-r5.ebuild b/sci-chemistry/ccp4/ccp4-6.1.1-r5.ebuild
deleted file mode 100644
index e36b96d52..000000000
--- a/sci-chemistry/ccp4/ccp4-6.1.1-r5.ebuild
+++ /dev/null
@@ -1,414 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit fortran eutils gnuconfig toolchain-funcs autotools
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-UPDATE="04_03_09"
-PATCHDATE="090511"
-
-PATCH_TOT="1"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-PATCH1=( src/clipper_progs/src/
-ctruncate.cpp-r1.13.2.5-r1.13.2.7.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
-#SRC_URI="${SRC}/${PV}/source/${P}-core-src.tar.gz"
-SRC_URI="${SRC}/6.1.1/${P}-core-src.tar.gz
-	${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz
-	http://dev.gentooexperimental.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/${!NAME}"
-done
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="X examples"
-# app-office/sc overlaps sc binary and man page
-# We can't rename ours since the automated ccp4i interface expects it there,
-# as do many scripts. app-office/sc can't rename its because that's the name
-# of the package.
-RDEPEND="X? (
-			x11-libs/libX11
-			x11-libs/libXt
-			x11-libs/libXaw
-			x11-libs/libxdl_view
-			x11-libs/libjwc_c
-			x11-libs/libjwc_f
-		)
-		>=dev-lang/tk-8.3
-		>=dev-tcltk/blt-2.4
-		virtual/lapack
-		virtual/blas
-		=sci-libs/fftw-2*
-		sci-chemistry/pdb-extract
-		sci-chemistry/rasmol
-		sci-libs/clipper
-		app-shells/tcsh
-		dev-python/pyxml
-		dev-libs/libxml2
-		dev-libs/boehm-gc
-		dev-tcltk/iwidgets
-		>=dev-tcltk/tdom-0.8
-		dev-tcltk/tkimg
-		dev-tcltk/tktreectrl
-		dev-tcltk/itcl
-		dev-tcltk/itk
-		sci-libs/ccp4-libs
-		!app-office/sc"
-DEPEND="${RDEPEND}
-		=sys-devel/automake-1.6*
-		X? (
-				x11-misc/imake
-				x11-proto/inputproto
-				x11-proto/xextproto
-		)"
-PDEPEND="sci-chemistry/mosflm
-	 sci-chemistry/imosflm
-	 sci-chemistry/molrep
-	 sci-chemistry/refmac
-	 sci-chemistry/xia2
-	 sci-chemistry/ccp4i
-	 sci-libs/balbes-db"
-
-S="${WORKDIR}/${PN}-${PV}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	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
-
-	epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	einfo "Applying Gentoo patches ..."
-	# These two only needed when attempting to install outside build dir via
-	# --bindir and --libdir instead of straight copying after build
-
-	# it attempts to install some libraries during the build
-	#ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch
-	# hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
-	# without this patch when --libdir is set
-	# Rotgen still needs more patching to find it
-	#ccp_patch "${FILESDIR}"/add-xdl-libdir.patch
-
-	# 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
-
-	# We already have sci-chemistry/pdb-extract
-# Use configure option instead
-#	ccp_patch "${FILESDIR}"/dont-build-pdb-extract.patch
-
-# Don't use these when we aren't building phaser
-#	ccp_patch "${FILESDIR}"/make-phaser-bindir.patch
-#	ccp_patch "${FILESDIR}"/no-phaser-ld-assume-kernel.patch
-#	# scons config.py tries to chmod python on live system
-#	ccp_patch "${FILESDIR}"/dont-chmod-python-binary.patch
-
-# Upstream fixed it
-	# csh syntax doesn't work in a bash script
-#	ccp_patch "${FILESDIR}"/${PV}-fix-setup-bash-incompatibility.patch
-
-	# libraries come from sci-libs/ccp4-libs
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch
-
-	# coreutils installs a binary called truncate
-	ccp_patch "${FILESDIR}"/${PV}-rename-truncate.patch
-	mv ./doc/truncate.doc ./doc/ftruncate.doc || die
-	mv ./html/truncate.html ./html/ftruncate.html || die
-
-	# conflicts with media-libs/raptor
-	ccp_patch "${FILESDIR}"/${PV}-rename-rapper.patch
-	mv ./doc/rapper.doc ./doc/rappermc.doc || die
-	mv ./html/rapper.html ./html/rappermc.html || die
-
-	# molref is provided as binary and dynamically linked against icc
-	ccp_patch "${FILESDIR}"/${PV}-nomolref.patch
-
-	# mosflm has its own ebuild
-#	ccp_patch "${FILESDIR}"/${PV}-dont-build-mosflm.patch
-
-	# no xia
-	ccp_patch "${FILESDIR}"/${PV}-noxia.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# glibc-2.10 getline fix
-	sed -e "s:getline:${PN}getline:g" -i lib/src/fsplit.c
-
-	# Don't build refmac binaries available from the standalone version
-	sed -i -e "/^REFMACTARGETS/s:refmac5 libcheck makecif molrep::g" configure
-
-	# Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
-	pushd src/rapper 2>/dev/null
-	sed -i \
-		-e '/^AC_CONFIG_SUBDIRS(\[gc7.0 libxml2\])/d' \
-		configure.ac
-	sed -i \
-		-e '/^SUBDIRS/s:libxml2 gc7.0::g' \
-		Makefile.am
-	sed -i \
-		-e '/^rappermc_LDADD/s:../gc7.0/libgc.la ../libxml2/libxml2.la:-lgc -lxml2:g' \
-		LOOP/Makefile.am
-	sed -i \
-		-e '/^INCLUDES/s:-I../gc7.0/include -I../libxml2/include:-I/usr/include/gc -I/usr/include/libxml2:g' \
-		LOOP/Makefile.am
-	eautoreconf
-	popd 2>/dev/null
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# Build system is broken if we set LDFLAGS
-	unset LDFLAGS
-
-	# 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 [[ "${FORTRANC}" = "ifc" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${S}"/include/ccp4.setup
-
-	# We agree to the license by emerging this, set in LICENSE
-	sed -i \
-		-e "s~^\(^agreed=\).*~\1yes~g" \
-		"${S}"/configure
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
-		"${S}"/include/ccp4.setup*
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-	export CC=$(tc-getCC)
-	export CXX=$(tc-getCXX)
-	export COPTIM=${CFLAGS}
-	export CXXOPTIM=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=${FORTRANC}
-	export FOPTIM=${FFLAGS:- -O2}
-	export BINSORT_SCR="${T}"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		$(use_enable X x) \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-pdb_extract \
-		--disable-cctbx \
-		--disable-phaser \
-		--disable-clipper \
-		--disable-mrbump \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-
-	# fsplit is required for the programs
-	pushd lib/src 2>/dev/null
-	emake fsplit -j1 || die
-	popd 2>/dev/null
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd src/clipper_progs 2>/dev/null
-	econf \
-		--prefix="${S}" \
-		--with-ccp4="${S}" \
-		--with-clipper=/usr \
-		--with-fftw=/usr \
-		--with-mmdb=/usr \
-		CXX=$(tc-getCXX) \
-		|| die
-	emake || die
-	popd 2>/dev/null
-
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-# Only needed when using --bindir and --libdir
-	# Needed to avoid errors. Originally tried to make lib and bin
-	# in configure script, now patched out by dont-make-dirs-in-configure.patch
-#	dodir /usr/include /usr/$(get_libdir) /usr/bin
-
-#	make install || die "install failed"
-
-	# 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"
-
-	# Fix env
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \
-		-e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
-		-e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
-		-e "s~^\(setenv DBCCP4I_TOP\).*~\1 \$CCP4/share/ccp4/dbccp4i~g" \
-		-e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
-		-e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \
-		-e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
-		-e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
-		-e "s~^\(.*setenv PYTHONPATH .*\)\$CCP4.*~\1\$CCP4/share/ccp4/python~g" \
-		-e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Don't check for updates on every sourcing of /etc/profile
-	sed -i \
-		-e "s:\(eval python.*\):#\1:g"
-		"${S}"/include/ccp4.setup* || die
-
-	# Get rid of S instances
-	# Also the main clipper library is built as libclipper-core, not libclipper
-#	sed -i \
-#		-e "s:${S}:$usr:g" \
-#		-e "s:lclipper :lclipper-core :g" \
-#		"${S}"/bin/clipper-config || die
-#	sed -i \
-#		-e "s:${S}:usr:g" \
-#		"${S}"/$(get_libdir)/cctbx/cctbx_build/setpaths*
-
-	# Bins
-	dobin "${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 ${file} || die
-		fi
-	done
-
-	# Setup scripts
-	insinto /etc/profile.d
-	newins "${S}"/include/ccp4.setup-bash ccp4.setup.sh || die
-	newins "${S}"/include/ccp4.setup-dist ccp4.setup.csh || die
-	rm -f "${S}"/include/ccp4.setup-bash
-	rm -f "${S}"/include/ccp4.setup-dist
-
-	# Environment files, setup scripts, etc.
-	insinto /usr/share/ccp4/include
-	doins "${S}"/include/* || die
-
-	# balbes
-#	insinto /usr/share/ccp4
-#	doins -r "${S}"/share/balbes || die
-
-	# smartie -- log parsing
-	insinto /usr/share/ccp4
-	doins -r "${S}"/share/smartie || die
-
-	# Install docs and examples
-
-	doman "${S}"/man/cat1/*
-
-	mv "${S}"/manual/README "${S}"/manual/README-manual
-	dodoc "${S}"/manual/*
-
-	dodoc "${S}"/README "${S}"/CHANGES
-
-	dodoc "${S}"/doc/*
-	rm "${D}"/usr/share/doc/${PF}/GNUmakefile.*
-	rm "${D}"/usr/share/doc/${PF}/COPYING.*
-
-	dohtml -r "${S}"/html/*
-	dodoc "${S}"/examples/README
-
-	# Fix wrongly installed HTML pages from clipper
-	dohtml "${D}"/usr/html/*
-	rm -rf "${D}"/usr/html
-
-	if use examples; then
-		for i in data rnase toxd; do
-			docinto examples/${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/$(get_libdir)/ccp4/examples
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html
-
-	# Fix overlaps with other packages
-	rm -f "${D}"/usr/share/man/man1/rasmol.1* "${D}"/usr/lib/font84.dat || die
-}
-
-pkg_postinst() {
-	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
-	einfo "in /etc/profile.d/ccp4.setup* to modify this."
-}
-
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-chemistry/ccp4/ccp4-6.1.1-r6.ebuild b/sci-chemistry/ccp4/ccp4-6.1.1-r6.ebuild
index 9d10dfd5b..7ef6a07d3 100644
--- a/sci-chemistry/ccp4/ccp4-6.1.1-r6.ebuild
+++ b/sci-chemistry/ccp4/ccp4-6.1.1-r6.ebuild
@@ -94,7 +94,7 @@ PDEPEND="sci-chemistry/mosflm
 	 sci-chemistry/ccp4i
 	 sci-libs/balbes-db"
 
-S="${WORKDIR}/${PN}-${PV}"
+S="${WORKDIR}/${P}"
 
 src_unpack() {
 	unpack ${A}
@@ -423,3 +423,4 @@ pkg_postinst() {
 ccp_patch() {
 	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
 }
+
diff --git a/sci-chemistry/ccp4/ccp4-6.1.1.ebuild b/sci-chemistry/ccp4/ccp4-6.1.1.ebuild
deleted file mode 100644
index 8f5d7c72e..000000000
--- a/sci-chemistry/ccp4/ccp4-6.1.1.ebuild
+++ /dev/null
@@ -1,400 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit fortran eutils gnuconfig toolchain-funcs autotools
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-PATCH_TOT="0"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-#PATCH1=( src/topp_
-#topp.f-r1.16.2.5-r1.16.2.6.diff )
-#PATCH2=( .
-#configure-r1.372.2.18-r1.372.2.19.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
-#SRC_URI="${SRC}/${PV}/source/${P}-core-src.tar.gz"
-SRC_URI="${SRC}/6.1.1/${P}-core-src.tar.gz"
-#	${SRC}/6.1/${P}-phaser-src.tar.gz
-#	${SRC}/6.1/${P}-balbes_db.tar.gz"
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="X"
-# app-office/sc overlaps sc binary and man page
-# We can't rename ours since the automated ccp4i interface expects it there,
-# as do many scripts. app-office/sc can't rename its because that's the name
-# of the package.
-RDEPEND="X? (
-			x11-libs/libX11
-			x11-libs/libXt
-			x11-libs/libXaw
-			x11-libs/libxdl_view
-			x11-libs/libjwc_c
-			x11-libs/libjwc_f
-		)
-		>=dev-lang/tk-8.3
-		>=dev-tcltk/blt-2.4
-		virtual/lapack
-		virtual/blas
-		=sci-libs/fftw-2*
-		sci-chemistry/pdb-extract
-		sci-chemistry/rasmol
-		sci-libs/clipper
-		app-shells/tcsh
-		dev-python/pyxml
-		dev-libs/libxml2
-		dev-libs/boehm-gc
-		dev-tcltk/iwidgets
-		>=dev-tcltk/tdom-0.8
-		dev-tcltk/tkimg
-		dev-tcltk/tktreectrl
-		dev-tcltk/itcl
-		dev-tcltk/itk
-		sci-libs/ccp4-libs
-		!app-office/sc"
-DEPEND="${RDEPEND}
-		=sys-devel/automake-1.6*
-		X? (
-				x11-misc/imake
-				x11-proto/inputproto
-				x11-proto/xextproto
-		)"
-PDEPEND="sci-chemistry/mosflm
-	 sci-chemistry/imosflm
-	 sci-chemistry/molrep
-	 sci-chemistry/refmac
-	 sci-chemistry/xia2
-	 sci-chemistry/ccp4i
-	 sci-libs/balbes-db"
-
-S="${WORKDIR}/${PN}-${PV}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	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
-
-	einfo "Applying Gentoo patches ..."
-	# These two only needed when attempting to install outside build dir via
-	# --bindir and --libdir instead of straight copying after build
-
-	# it attempts to install some libraries during the build
-	#ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch
-	# hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
-	# without this patch when --libdir is set
-	# Rotgen still needs more patching to find it
-	#ccp_patch "${FILESDIR}"/add-xdl-libdir.patch
-
-	# it tries to create libdir, bindir etc on live system in configure
-	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
-	# We already have sci-chemistry/rasmol
-	# Also remember to create the bindir.
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch
-
-	# We already have sci-chemistry/pdb-extract
-# Use configure option instead
-#	ccp_patch "${FILESDIR}"/dont-build-pdb-extract.patch
-
-# Don't use these when we aren't building phaser
-#	ccp_patch "${FILESDIR}"/make-phaser-bindir.patch
-#	ccp_patch "${FILESDIR}"/no-phaser-ld-assume-kernel.patch
-#	# scons config.py tries to chmod python on live system
-#	ccp_patch "${FILESDIR}"/dont-chmod-python-binary.patch
-
-# Upstream fixed it
-	# csh syntax doesn't work in a bash script
-#	ccp_patch "${FILESDIR}"/${PV}-fix-setup-bash-incompatibility.patch
-
-	# libraries come from sci-libs/ccp4-libs
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch
-
-	# coreutils installs a binary called truncate
-	ccp_patch "${FILESDIR}"/${PV}-rename-truncate.patch
-	mv ./doc/truncate.doc ./doc/ftruncate.doc || die
-	mv ./html/truncate.html ./html/ftruncate.html || die
-
-	# conflicts with media-libs/raptor
-	ccp_patch "${FILESDIR}"/${PV}-rename-rapper.patch
-	mv ./doc/rapper.doc ./doc/rappermc.doc || die
-	mv ./html/rapper.html ./html/rappermc.html || die
-
-	# mosflm has its own ebuild
-#	ccp_patch "${FILESDIR}"/${PV}-dont-build-mosflm.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# Don't build refmac binaries available from the standalone version
-	sed -i -e "/^REFMACTARGETS/s:refmac5 libcheck makecif molrep::g" configure
-
-	# Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
-	pushd src/rapper 2>/dev/null
-	sed -i \
-		-e '/^AC_CONFIG_SUBDIRS(\[gc7.0 libxml2\])/d' \
-		configure.ac
-	sed -i \
-		-e '/^SUBDIRS/s:libxml2 gc7.0::g' \
-		Makefile.am
-	sed -i \
-		-e '/^rappermc_LDADD/s:../gc7.0/libgc.la ../libxml2/libxml2.la:-lgc -lxml2:g' \
-		LOOP/Makefile.am
-	sed -i \
-		-e '/^INCLUDES/s:-I../gc7.0/include -I../libxml2/include:-I/usr/include/gc -I/usr/include/libxml2:g' \
-		LOOP/Makefile.am
-	eautoreconf
-	popd 2>/dev/null
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# Build system is broken if we set LDFLAGS
-	unset LDFLAGS
-
-	# 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 [[ "${FORTRANC}" = "ifc" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${S}"/include/ccp4.setup
-
-	# We agree to the license by emerging this, set in LICENSE
-	sed -i \
-		-e "s~^\(^agreed=\).*~\1yes~g" \
-		"${S}"/configure
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
-		"${S}"/include/ccp4.setup*
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-	export CC=$(tc-getCC)
-	export CXX=$(tc-getCXX)
-	export COPTIM=${CFLAGS}
-	export CXXOPTIM=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=${FORTRANC}
-	export FOPTIM=${FFLAGS:- -O2}
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		$(use_enable X x) \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-pdb_extract \
-		--disable-cctbx \
-		--disable-phaser \
-		--disable-clipper \
-		--disable-mrbump \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-
-	# fsplit is required for the programs
-	pushd lib/src 2>/dev/null
-	emake fsplit -j1 || die
-	popd 2>/dev/null
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd src/clipper_progs 2>/dev/null
-	econf \
-		--prefix="${S}" \
-		--with-ccp4="${S}" \
-		--with-clipper=/usr \
-		--with-fftw=/usr \
-		--with-mmdb=/usr \
-		CXX=$(tc-getCXX) \
-		|| die
-	emake || die
-	popd 2>/dev/null
-
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-# Only needed when using --bindir and --libdir
-	# Needed to avoid errors. Originally tried to make lib and bin
-	# in configure script, now patched out by dont-make-dirs-in-configure.patch
-#	dodir /usr/include /usr/$(get_libdir) /usr/bin
-
-#	make install || die "install failed"
-
-	# 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"
-
-	# Fix env
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \
-		-e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
-		-e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
-		-e "s~^\(setenv DBCCP4I_TOP\).*~\1 \$CCP4/share/ccp4/dbccp4i~g" \
-		-e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
-		-e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \
-		-e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
-		-e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
-		-e "s~^\(.*setenv PYTHONPATH .*\)\$CCP4.*~\1\$CCP4/share/ccp4/python~g" \
-		-e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Don't check for updates on every sourcing of /etc/profile
-	sed -i \
-		-e "s:\(eval python.*\):#\1:g"
-		"${S}"/include/ccp4.setup*
-
-	# Get rid of S instances
-	# Also the main clipper library is built as libclipper-core, not libclipper
-#	sed -i \
-#		-e "s:${S}:$usr:g" \
-#		-e "s:lclipper :lclipper-core :g" \
-#		"${S}"/bin/clipper-config || die
-#	sed -i \
-#		-e "s:${S}:usr:g" \
-#		"${S}"/$(get_libdir)/cctbx/cctbx_build/setpaths*
-
-	# Bins
-	dobin "${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 ${file} || die
-		fi
-	done
-
-	# Setup scripts
-	insinto /etc/profile.d
-	newins "${S}"/include/ccp4.setup-bash ccp4.setup.sh || die
-	newins "${S}"/include/ccp4.setup-dist ccp4.setup.csh || die
-	rm -f "${S}"/include/ccp4.setup-bash
-	rm -f "${S}"/include/ccp4.setup-dist
-
-	# Environment files, setup scripts, etc.
-	insinto /usr/share/ccp4/include
-	doins "${S}"/include/* || die
-
-	# balbes
-#	insinto /usr/share/ccp4
-#	doins -r "${S}"/share/balbes || die
-
-	# smartie -- log parsing
-	insinto /usr/share/ccp4
-	doins -r "${S}"/share/smartie || die
-
-	# Install docs and examples
-
-	doman "${S}"/man/cat1/*
-
-	mv "${S}"/manual/README "${S}"/manual/README-manual
-	dodoc "${S}"/manual/*
-
-	dodoc "${S}"/README "${S}"/CHANGES
-
-	dodoc "${S}"/doc/*
-	rm "${D}"/usr/share/doc/${PF}/GNUmakefile.*
-	rm "${D}"/usr/share/doc/${PF}/COPYING.*
-
-	dohtml -r "${S}"/html/*
-	dodoc "${S}"/examples/README
-
-	# Fix wrongly installed HTML pages from clipper
-	dohtml "${D}"/usr/html/*
-	rm -rf "${D}"/usr/html
-
-	for i in data rnase toxd; do
-		docinto examples/${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/${i}/*
-	done
-
-	# Needed for ccp4i docs to work
-	dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html
-
-	# Fix overlaps with other packages
-	rm -f "${D}"/usr/share/man/man1/rasmol.1* "${D}"/usr/lib/font84.dat || die
-}
-
-pkg_postinst() {
-	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
-	einfo "in /etc/profile.d/ccp4.setup* to modify this."
-}
-
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-chemistry/ccp4/ccp4-6.1.2.ebuild b/sci-chemistry/ccp4/ccp4-6.1.2.ebuild
index bb0962522..b2ed81be0 100644
--- a/sci-chemistry/ccp4/ccp4-6.1.2.ebuild
+++ b/sci-chemistry/ccp4/ccp4-6.1.2.ebuild
@@ -2,6 +2,8 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
+EAPI="2"
+
 DESCRIPTION="Protein X-ray crystallography toolkit -- meta package"
 HOMEPAGE="http://www.ccp4.ac.uk/"
 SRC_URI=""
@@ -9,15 +11,15 @@ SRC_URI=""
 LICENSE="ccp4"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
+IUSE="X"
 
-RDEPEND="sci-chemistry/ccp4-apps
-	sci-chemistry/ccp4i
+RDEPEND="sci-chemistry/ccp4-apps[X?]
+	X? ( sci-chemistry/ccp4i
 	sci-chemistry/imosflm
+	sci-chemistry/rasmol )
 	sci-chemistry/molrep
 	sci-chemistry/mosflm
 	sci-chemistry/pdb-extract
-	sci-chemistry/rasmol
 	sci-chemistry/refmac
 	sci-chemistry/scala
 	sci-chemistry/xia2"
diff --git a/sci-chemistry/ccp4/files/6.1.2-clipper-mmdbold-ggc-4.3.patch b/sci-chemistry/ccp4/files/6.1.2-clipper-mmdbold-ggc-4.3.patch
deleted file mode 100644
index 66186609a..000000000
--- a/sci-chemistry/ccp4/files/6.1.2-clipper-mmdbold-ggc-4.3.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- ccp4-6.0.99e.orig/lib/clipper/clipper/mmdbold/clipper_mmdb.cpp	2008-07-31 13:23:13.000000000 -0700
-+++ ccp4-6.0.99e/lib/clipper/clipper/mmdbold/clipper_mmdb.cpp	2008-07-31 13:47:35.000000000 -0700
-@@ -43,7 +43,7 @@
- 
- #include <set>
- #include <algorithm>
--
-+#include <string.h>
- 
- namespace clipper {
- 
---- ccp4-6.0.99e.orig/lib/clipper/clipper/mmdbold/clipper_mmdb_wrapper.cpp.orig	2008-07-31 13:49:53.000000000 -0700
-+++ ccp4-6.0.99e/lib/clipper/clipper/mmdbold/clipper_mmdb_wrapper.cpp	2008-07-31 13:50:25.000000000 -0700
-@@ -40,7 +40,7 @@
- //L  MA 02111-1307 USA
- 
- #include "clipper_mmdb_wrapper.h"
--
-+#include <string.h>
- 
- namespace clipper {
- 
diff --git a/sci-chemistry/ccp4/files/6.1.2-dont-build-double-and-make-bindir.patch b/sci-chemistry/ccp4/files/6.1.2-dont-build-double-and-make-bindir.patch
deleted file mode 100644
index e62ae12ad..000000000
--- a/sci-chemistry/ccp4/files/6.1.2-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/files/6.1.2-dont-build-libs.patch b/sci-chemistry/ccp4/files/6.1.2-dont-build-libs.patch
deleted file mode 100644
index 5859093e7..000000000
--- a/sci-chemistry/ccp4/files/6.1.2-dont-build-libs.patch
+++ /dev/null
@@ -1,35 +0,0 @@
---- ./Makefile.in.orig	2008-08-01 10:27:23.000000000 -0700
-+++ ./Makefile.in	2008-08-01 14:30:22.000000000 -0700
-@@ -3,7 +3,7 @@
- # $Header: /nfs/ccpdisk/xtal/CVSROOT/ccp4/Makefile.in,v 1.57 2008/04/09 10:41:58 fr45 Exp $
- 
- SHELL = /bin/sh
--DIRS = $(fftwdir) $(clipperdir) $(diffimdir) $(lapackdir) $(ccifdir) lib/src $(ssmdir) src lib/data unsupported/src x-windows share $(prereleasedir)
-+DIRS = src lib/data unsupported/src x-windows share $(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
-@@ -67,19 +67,19 @@
- 	$(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/files/6.1.2-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/6.1.2-dont-make-dirs-in-configure.patch
deleted file mode 100644
index 583697cea..000000000
--- a/sci-chemistry/ccp4/files/6.1.2-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 $i/Makefile.in
-+#       fi
-+#     fi
-+#   done
-+#fi
- 
- ### sanity checks
- 
diff --git a/sci-chemistry/ccp4/files/6.1.2-fix-setup-bash-incompatibility.patch b/sci-chemistry/ccp4/files/6.1.2-fix-setup-bash-incompatibility.patch
deleted file mode 100644
index d98f54cdb..000000000
--- a/sci-chemistry/ccp4/files/6.1.2-fix-setup-bash-incompatibility.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4-6.0.99e.orig/include/ccp4.setup-bash	2008-07-31 10:37:22.000000000 -0700
-+++ ccp4-6.0.99e/include/ccp4.setup-bash	2008-07-31 12:47:14.000000000 -0700
-@@ -181,7 +181,7 @@
- 
- #Python path for the subprocess fixed module
- 
--if ($ccp4_first_in_path) then
-+if [ $ccp4_first_in_path -eq 1 ]; then
-     setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
- else
-     setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
diff --git a/sci-chemistry/ccp4/files/6.1.2-nomolref.patch b/sci-chemistry/ccp4/files/6.1.2-nomolref.patch
deleted file mode 100644
index f16b0ecb9..000000000
--- a/sci-chemistry/ccp4/files/6.1.2-nomolref.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 = $(datadir)/pisa
- 
---- src/pisa/Makefile.in	2009-06-12 21:12:08.000000000 +0200
-+++ src/pisa/Makefile.in.new	2009-06-12 21:41:52.000000000 +0200
-@@ -82,7 +82,7 @@
- am__quote = @am__quote@
- install_sh = @install_sh@
- pisa_LDFLAGS = @pisa_LDFLAGS@
--SUBDIRS = molref pisastore sbase
-+SUBDIRS = pisastore sbase
- 
- dist_pkgdata_DATA = pisa.cfg
- 
diff --git a/sci-chemistry/ccp4/files/6.1.2-rename-rapper.patch b/sci-chemistry/ccp4/files/6.1.2-rename-rapper.patch
deleted file mode 100644
index a71c13544..000000000
--- a/sci-chemistry/ccp4/files/6.1.2-rename-rapper.patch
+++ /dev/null
@@ -1,77 +0,0 @@
---- src/rapper/LOOP/Makefile.in	2008-05-29 16:39:40.000000000 +0200
-+++ src/rapper/LOOP/Makefile.in.new	2009-03-12 20:40:03.157602172 +0100
-@@ -111,9 +111,9 @@
- pyexecdir = @pyexecdir@
- pythondir = @pythondir@
- rapper_LDFLAGS = @rapper_LDFLAGS@
--bin_PROGRAMS = rapper
-+bin_PROGRAMS = rappermc
- 
--rapper_SOURCES = \
-+rappermc_SOURCES = \
- kip.h aaconv.cpp atomconv.cpp kip_snake.cpp \
- kip_pdb.cpp measure.cpp lib_frags.cpp ran2.cpp \
- heap.cpp queue.cpp 3Dgeom.cpp space_grid.cpp list.cpp search_residue.cpp bitfield.cpp \
-@@ -129,7 +129,7 @@
- residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp
- 
- 
--rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la
-+rappermc_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la
- dist_pkgdata_DATA = params.xml
- 
- INCLUDES = -I. -I../gc7.0/include -I../libxml2/include
-@@ -139,7 +139,7 @@
- bin_PROGRAMS = rapper$(EXEEXT)
- PROGRAMS = $(bin_PROGRAMS)
- 
--am_rapper_OBJECTS = aaconv.$(OBJEXT) atomconv.$(OBJEXT) \
-+am_rappermc_OBJECTS = aaconv.$(OBJEXT) atomconv.$(OBJEXT) \
- 	kip_snake.$(OBJEXT) kip_pdb.$(OBJEXT) measure.$(OBJEXT) \
- 	lib_frags.$(OBJEXT) ran2.$(OBJEXT) heap.$(OBJEXT) \
- 	queue.$(OBJEXT) 3Dgeom.$(OBJEXT) space_grid.$(OBJEXT) \
-@@ -164,8 +164,8 @@
- 	iterator.$(OBJEXT) residue_range.$(OBJEXT) \
- 	pop_search_frags.$(OBJEXT) saxs.$(OBJEXT) lib_choral.$(OBJEXT) \
- 	pdf.$(OBJEXT) WeightedDistribMean.$(OBJEXT)
--rapper_OBJECTS = $(am_rapper_OBJECTS)
--rapper_DEPENDENCIES = ../gc7.0/libgc.la ../libxml2/libxml2.la
-+rappermc_OBJECTS = $(am_rapper_OBJECTS)
-+rappermc_DEPENDENCIES = ../gc7.0/libgc.la ../libxml2/libxml2.la
- 
- DEFS = @DEFS@
- DEFAULT_INCLUDES =  -I. -I$(srcdir)
-@@ -233,11 +233,11 @@
- CCLD = $(CC)
- LINK = $(LIBTOOL) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
- 	$(AM_LDFLAGS) $(LDFLAGS) -o $@
--DIST_SOURCES = $(rapper_SOURCES)
-+DIST_SOURCES = $(rappermc_SOURCES)
- DATA = $(dist_pkgdata_DATA)
- 
- DIST_COMMON = $(dist_pkgdata_DATA) Makefile.am Makefile.in
--SOURCES = $(rapper_SOURCES)
-+SOURCES = $(rappermc_SOURCES)
- 
- all: all-am
- 
---- src/rapper/LOOP/Makefile.am 2008-01-24 15:08:17.000000000 +0100
-+++ src/rapper/LOOP/Makefile.am.new     2009-03-12 23:01:56.697533874 +0100
-@@ -1,6 +1,6 @@
--bin_PROGRAMS = rapper
-+bin_PROGRAMS = rappermc
- 
--rapper_SOURCES = \
-+rappermc_SOURCES = \
- kip.h aaconv.cpp atomconv.cpp kip_snake.cpp \
- kip_pdb.cpp measure.cpp lib_frags.cpp ran2.cpp \
- heap.cpp queue.cpp 3Dgeom.cpp space_grid.cpp list.cpp search_residue.cpp bitfield.cpp \
-@@ -15,7 +15,7 @@
- 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
-+rappermc_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la
- 
- pkgdatadir = $(datadir)/rapper
- dist_pkgdata_DATA = params.xml
diff --git a/sci-chemistry/ccp4/files/6.1.2-rename-truncate.patch b/sci-chemistry/ccp4/files/6.1.2-rename-truncate.patch
deleted file mode 100644
index 43bfcf7c7..000000000
--- a/sci-chemistry/ccp4/files/6.1.2-rename-truncate.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-coreutils now installs a binary called truncate.
-
---- src/Makefile.in.orig	2009-03-02 23:25:45.000000000 -0800
-+++ src/Makefile.in	2009-03-02 23:25:53.000000000 -0800
-@@ -41,7 +41,7 @@
- professs r500 rantan rebatch reindex revise rfcorr rotamer rotmat \
- rstats rwcontents sapi scaleit scalepack2mtz seqwt sfall sigmaa sortmtz sortwater \
- stgrid stnet surface tffc tracer \
--truncate unique vecref vectors volume watertidy watncs watpeak \
-+ftruncate unique vecref vectors volume watertidy watncs watpeak \
- wilson $(CIFTARGETS)
- 
- BALBESTARGETS = search_DB get_structure_DB f2cif check_file_DB check_cell_sg \
-@@ -982,7 +982,7 @@
- surface:	$(srcdir)/surface.f
- tffc:		$(srcdir)/tffc.f
- tracer:		$(srcdir)/tracer.f
--truncate:	$(srcdir)/truncate.f
-+ftruncate:	$(srcdir)/truncate.f
- unique:		$(srcdir)/unique.f
- vecref:		$(srcdir)/vecref.f
- vectors:	$(srcdir)/vectors.f
---- examples/unix/runnable/truncate.exam.orig	2009-03-02 23:35:04.000000000 -0800
-+++ examples/unix/runnable/truncate.exam	2009-03-02 23:35:11.000000000 -0800
-@@ -15,7 +15,7 @@
-   exit 1
- fi
- #
--truncate hklin $CCP4_SCR/aucn_mrg.mtz \
-+ftruncate hklin $CCP4_SCR/aucn_mrg.mtz \
-    hklout $CCP4_SCR/aucn_trn.mtz <<EOF-trunc
- title DMSO red aucn2 Data - mosflm
- truncate yes
-@@ -28,7 +28,7 @@
- # do this if you already have Fs but want to look at the
- # output graphs of TRUNCATE
- 
--truncate hklin $CEXAM/rnase/rnase18.mtz <<EOF
-+ftruncate hklin $CEXAM/rnase/rnase18.mtz <<EOF
- title Analysis of rnase data
- labin F=FNAT SIGF=SIGFNAT
- nresidue 192