Bump. Reads CNS maps, handles anisotropy better, other bugfixes and features.

Package-Manager: portage-2.1.3.5

6 files changed, 630 insertions, 5 deletions

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 280aac46b74d..77b6dba82e9c 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/coot
 # Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.13 2007/06/22 22:33:19 dberkholz Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.14 2007/08/16 06:05:12 dberkholz Exp $
+
+*coot-0.3.3 (16 Aug 2007)
+
+  16 Aug 2007; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/0.3.3-as-needed.patch,
+  +files/0.3.3-link-against-guile-gtk-properly.patch, +coot-0.3.3.ebuild:
+  Bump. Reads CNS maps, handles anisotropy better, other bugfixes and features.
 
   22 Jun 2007; Donnie Berkholz <dberkholz@gentoo.org>;
   +files/0.3.1-link-against-guile-gtk-properly.patch,
diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index a050bc0f6dea..fe571b45450f 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -10,8 +10,17 @@ AUX 0.3.1-link-against-guile-gtk-properly.patch 785 RMD160 56900791f5800cfee9157
 MD5 8adcd042736352fd280032e9a1173dc1 files/0.3.1-link-against-guile-gtk-properly.patch 785
 RMD160 56900791f5800cfee9157697914318d35828b791 files/0.3.1-link-against-guile-gtk-properly.patch 785
 SHA256 8e267168766be09fbda929d19c0a440ed7306320da1918e8d0ecfc55b27f827e files/0.3.1-link-against-guile-gtk-properly.patch 785
+AUX 0.3.3-as-needed.patch 19288 RMD160 0c6e09f8eed01e4e2b9c228cb9806ec23f5498f0 SHA1 1448e9b9ef8b17f347bb804c28ec60d82b1a9df7 SHA256 99665ff2815f144ac4dc0149e1a3c54a2862cd56ceba9a9c85e06a035629b619
+MD5 b6fc62a9733a0a51bd55291950152e33 files/0.3.3-as-needed.patch 19288
+RMD160 0c6e09f8eed01e4e2b9c228cb9806ec23f5498f0 files/0.3.3-as-needed.patch 19288
+SHA256 99665ff2815f144ac4dc0149e1a3c54a2862cd56ceba9a9c85e06a035629b619 files/0.3.3-as-needed.patch 19288
+AUX 0.3.3-link-against-guile-gtk-properly.patch 785 RMD160 7c98e6510b484baa6a47cd12e219d6c45ce3344a SHA1 d4f9bd96b6fc356d875f121b890073847296f39f SHA256 b92ca0f392b9ad7d6afe89fd69be91506e494651492544e9e8eb92cd3878ba81
+MD5 b7801512f56bd0fe6f40a34c8488a493 files/0.3.3-link-against-guile-gtk-properly.patch 785
+RMD160 7c98e6510b484baa6a47cd12e219d6c45ce3344a files/0.3.3-link-against-guile-gtk-properly.patch 785
+SHA256 b92ca0f392b9ad7d6afe89fd69be91506e494651492544e9e8eb92cd3878ba81 files/0.3.3-link-against-guile-gtk-properly.patch 785
 DIST coot-0.1.2.tar.gz 2704638 RMD160 bb0ff46297fc7135b1bf31159bf41b18462b916c SHA1 66f4b13f37cab6537b454a0ad23050044eb4a95f SHA256 fcd2e5862ef57baffc19aa30b1bb48b5271baf0667cc72bf5ecd8a02911fe22a
 DIST coot-0.3.1.tar.gz 3708033 RMD160 8fefe5498171563d0ee660c87175b9af419f07ca SHA1 d612fde00e538682f64c4d204b27556fa742de5e SHA256 f13142b478a1bc9c94a242dd0bf18ac074707f7bd80bf72c8f0f906675099a34
+DIST coot-0.3.3.tar.gz 3870046 RMD160 b23ca227894a469456c5af0284d0bb8530c855b5 SHA1 63755615b05572b43e8f0768a5c0315191f698bf SHA256 f3a7d6f789846b1f7670d4dc3e61a430cbab811f2f22349b84f49e10aaa4a41c
 EBUILD coot-0.1.2.ebuild 2308 RMD160 b59de80ec0ab129eb3d739710d9f07388e6582e0 SHA1 d534ac54efd5b2a8be66b5e23e6992d49419d625 SHA256 6ce0825594abf6d21ac17cdc715cb2c9d522b809f798a7f1d70cc6cd8c392717
 MD5 d61e130fcb36e9fbc37937d6fce495c7 coot-0.1.2.ebuild 2308
 RMD160 b59de80ec0ab129eb3d739710d9f07388e6582e0 coot-0.1.2.ebuild 2308
@@ -20,10 +29,14 @@ EBUILD coot-0.3.1.ebuild 2865 RMD160 0f87fd416dad57a889caacb1670f903a16225aef SH
 MD5 2a5479616096a380adf0fe1323545531 coot-0.3.1.ebuild 2865
 RMD160 0f87fd416dad57a889caacb1670f903a16225aef coot-0.3.1.ebuild 2865
 SHA256 a08fd746af8e1856b388214db33680326a1e4fd11075d3bff15bb84e42eabd25 coot-0.3.1.ebuild 2865
-MISC ChangeLog 2346 RMD160 73512214a6b668b68bb24fbc7b9d573c71e48d96 SHA1 e87438c3755ec6c7e5e5ca8f60e0545c14a7dff3 SHA256 102d55e4906b353c49786f513ef13476cddae23dc4f148f47d733c10d4788d7f
-MD5 ad070bdf78aea8afc9edfdef917882d9 ChangeLog 2346
-RMD160 73512214a6b668b68bb24fbc7b9d573c71e48d96 ChangeLog 2346
-SHA256 102d55e4906b353c49786f513ef13476cddae23dc4f148f47d733c10d4788d7f ChangeLog 2346
+EBUILD coot-0.3.3.ebuild 3156 RMD160 8e0eafaee723edcac57a246e96e8bdfb473ff8d6 SHA1 dedeb0f43ff6e424efb72e99ffb9e937ca783405 SHA256 f7b72e46e5294c70601a1de7cd4b5f6fca44608e21df4bb0ecc61c7981b0712b
+MD5 b6d771a431db0f7f1ea348891697aab4 coot-0.3.3.ebuild 3156
+RMD160 8e0eafaee723edcac57a246e96e8bdfb473ff8d6 coot-0.3.3.ebuild 3156
+SHA256 f7b72e46e5294c70601a1de7cd4b5f6fca44608e21df4bb0ecc61c7981b0712b coot-0.3.3.ebuild 3156
+MISC ChangeLog 2615 RMD160 33a67e92960400c04d0a94d231c98411d50e90b6 SHA1 6e48a8d2559843c5e389a51413e0e935e50210ad SHA256 7ca40221006727ac6893b49d6173f08cdeb58df5314943eef032e26502171d2a
+MD5 34447bee5df5f87d055742c5a5b96df6 ChangeLog 2615
+RMD160 33a67e92960400c04d0a94d231c98411d50e90b6 ChangeLog 2615
+SHA256 7ca40221006727ac6893b49d6173f08cdeb58df5314943eef032e26502171d2a ChangeLog 2615
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166
 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166
@@ -34,3 +47,6 @@ SHA256 19a197b638681d05d7847a3563ef6cea23606b94a6f3056043ea775fcb88d515 files/di
 MD5 563b4d4eead620811ec06a632ba3d435 files/digest-coot-0.3.1 235
 RMD160 d27b3e1c98f29bb401f14e77cb16f7e9c109d0fe files/digest-coot-0.3.1 235
 SHA256 2a6628adb6460117d951325f2e7bfc3ecaf3123ad537352b1f3d8f55df3fc1ce files/digest-coot-0.3.1 235
+MD5 c9c3622fb7c8a17578cfa47243a1a425 files/digest-coot-0.3.3 235
+RMD160 5ddddb6896b9284ecdf848e1cb423c25d9f6b2ad files/digest-coot-0.3.3 235
+SHA256 b2f9df048652f39fd7e4e147cc12ce41ce468a25677b5426990d772ceb7588c6 files/digest-coot-0.3.3 235
diff --git a/sci-chemistry/coot/coot-0.3.3.ebuild b/sci-chemistry/coot/coot-0.3.3.ebuild
new file mode 100644
index 000000000000..d67c09da7b4b
--- /dev/null
+++ b/sci-chemistry/coot/coot-0.3.3.ebuild
@@ -0,0 +1,120 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/coot-0.3.3.ebuild,v 1.1 2007/08/16 06:05:12 dberkholz Exp $
+
+inherit autotools eutils
+
+MY_PV=${PV/_pre/-pre-}
+MY_P="${PN}-${MY_PV}"
+
+DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~emsley/coot/"
+if [[ ${MY_PV} = *pre* ]]; then
+	SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/pre-release/${MY_P}.tar.gz"
+else
+	SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/${MY_P}.tar.gz"
+fi
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~ppc ~x86"
+IUSE="new-interface"
+RDEPEND=">=sci-libs/gsl-1.3
+	new-interface? (
+		>=x11-libs/gtk+-2.2
+		gnome-base/libgnomecanvas
+		=x11-libs/guile-gtk-2*
+	)
+	!new-interface? (
+		=dev-libs/glib-1.2*
+		=x11-libs/gtkglarea-1.2*
+		=x11-libs/guile-gtk-1*
+	)
+	x11-libs/gtkglext
+	virtual/glut
+	virtual/opengl
+	sci-chemistry/ccp4
+	dev-lang/python
+	>=x11-libs/gtk-canvas-0.1.1-r2
+	dev-lang/python
+	dev-scheme/guile-gui
+	dev-scheme/net-http
+	dev-scheme/goosh
+	dev-scheme/guile-www
+	sci-libs/coot-data
+	sci-chemistry/reduce
+	sci-chemistry/probe
+	sci-libs/clipper"
+DEPEND="${RDEPEND}
+	dev-lang/swig"
+S="${WORKDIR}/${MY_P}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	epatch "${FILESDIR}"/${PV}-as-needed.patch
+	epatch "${FILESDIR}"/${PV}-link-against-guile-gtk-properly.patch
+
+	# Link against single-precision fftw
+	sed -i \
+		-e "s:lfttw:lsfttw:g" \
+		-e "s:lrfttw:lsrfttw:g" \
+		"${S}"/macros/clipper.m4
+
+	# Fix where it looks for some binaries
+	sed -i \
+		-e "s:/y/people/emsley/coot/Linux/bin/probe.2.11.050121.linux.RH9:/usr/bin/probe:g" \
+		-e "s:/y/people/emsley/coot/Linux/bin/reduce.2.21.030604:/usr/bin/reduce:g" \
+		"${S}"/scheme/group-settings.scm
+
+	# Look for clipper slotted with '-2' suffix
+	sed -i \
+		-e "s~\(-lclipper[[:alnum:]-]*\)~\1-2~g" \
+		"${S}"/macros/clipper.m4 \
+		|| die "sed to find -2 slotted libraries failed"
+	grep 'include.*clipper' -rl . \
+		| xargs sed -i \
+			-e "s~\(include.*clipper\)/~\1-2/~g" \
+			|| die "sed to find -2 slotted headers failed"
+
+	cd "${S}"
+	AT_M4DIR="macros" eautoreconf
+}
+
+src_compile() {
+	# All the --with's are used to activate various parts.
+	# Yes, this is broken behavior.
+	econf \
+		--includedir='${prefix}/include/coot' \
+		--with-gtkcanvas-prefix=/usr \
+		--with-clipper-prefix=/usr \
+		--with-mmdb-prefix=/usr \
+		--with-ssmlib-prefix=/usr \
+		--with-guile=/usr \
+		--with-python=/usr \
+		--with-guile-gtk \
+		$(use_with new-interface gtk2) \
+		|| die "econf failed"
+
+	# Regenerate wrappers, otherwise at least gtk-2 build fails
+	pushd src
+	rm -f coot_wrap_python.cc coot_wrap_python_pre.cc \
+		&& emake coot_wrap_python.cc \
+		|| die "failed to regenerate python wrapper"
+
+	rm -f coot_wrap_guile.cc coot_wrap_guile_pre.cc \
+		&& emake coot_wrap_guile.cc \
+		||die "failed to regenerate guile wrapper"
+	popd
+
+	# Parallel build's broken
+	emake -j1 || die "emake failed"
+}
+
+src_install() {
+	emake -j1 DESTDIR="${D}" install || die "install failed"
+
+	# Install misses this
+	insinto /usr/share/coot/python
+	doins "${S}"/src/coot.py
+}
diff --git a/sci-chemistry/coot/files/0.3.3-as-needed.patch b/sci-chemistry/coot/files/0.3.3-as-needed.patch
new file mode 100644
index 000000000000..6dec443dd231
--- /dev/null
+++ b/sci-chemistry/coot/files/0.3.3-as-needed.patch
@@ -0,0 +1,464 @@
+diff -urN coot-0.3.3.orig/analysis/Makefile.am coot-0.3.3/analysis/Makefile.am
+--- coot-0.3.3.orig/analysis/Makefile.am	2007-08-15 12:20:04.000000000 -0700
++++ coot-0.3.3/analysis/Makefile.am	2007-08-15 12:21:22.000000000 -0700
+@@ -9,6 +9,7 @@
+ 	$(MMDB_CXXFLAGS)
+ 
+ libcoot_analysis_la_SOURCES = bfkurt.cc
++libcoot_analysis_la_LIBADD = $(top_builddir)/coot-utils/libcoot-coord-utils.la
+ 
+ bin_PROGRAMS = bfactan
+ 
+@@ -16,7 +17,6 @@
+ 
+ bfactan_LDADD = \
+ 	libcoot-analysis.la 					\
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la 	\
+ 	$(top_builddir)/coot-utils/libcoot-utils.la 		\
+ 	$(top_builddir)/geometry/libcoot-geometry.la    	\
+ 	$(CLIPPER_LIBS) 	\
+diff -urN coot-0.3.3.orig/coords/Makefile.am coot-0.3.3/coords/Makefile.am
+--- coot-0.3.3.orig/coords/Makefile.am	2007-08-15 12:20:04.000000000 -0700
++++ coot-0.3.3/coords/Makefile.am	2007-08-15 12:21:22.000000000 -0700
+@@ -37,4 +37,6 @@
+ libcoot_coords_la_SOURCES =  Bond_lines.cc Cartesian.cc cos-sin.cc \
+ 		 mmdb-extras.cc utils.cc mmdb.cc mmdb-crystal.cc \
+ 		 Bond_lines_ext.cc coot-close.cc
+-
++libcoot_coords_la_LIBADD = \
++	$(top_builddir)/coot-utils/libcoot-shelx.la \
++	$(top_builddir)/mini-mol/libcoot-mini-mol.la
+diff -urN coot-0.3.3.orig/coot-surface/Makefile.am coot-0.3.3/coot-surface/Makefile.am
+--- coot-0.3.3.orig/coot-surface/Makefile.am	2007-08-15 12:20:04.000000000 -0700
++++ coot-0.3.3/coot-surface/Makefile.am	2007-08-15 12:21:22.000000000 -0700
+@@ -25,3 +25,4 @@
+ 
+ libcoot_surface_la_SOURCES = \
+ 	 coot-surface.cc coot-surface.hh rgbreps.cc rgbreps.h
++libcoot_surface_la_LIBADD = $(top_builddir)/surface/libccp4mg-surface.la
+diff -urN coot-0.3.3.orig/coot-utils/Makefile.am coot-0.3.3/coot-utils/Makefile.am
+--- coot-0.3.3.orig/coot-utils/Makefile.am	2007-08-15 12:20:04.000000000 -0700
++++ coot-0.3.3/coot-utils/Makefile.am	2007-08-15 12:21:22.000000000 -0700
+@@ -39,9 +39,11 @@
+ 
+ # for pure coordinates (mmdb) things
+ libcoot_coord_utils_la_SOURCES = coot-coord-utils.cc 
++libcoot_coord_utils_la_LIBADD = $(CLIPPER_LIBS) libcoot-utils.la
+ 
+ # shelx
+ libcoot_shelx_la_SOURCES = coot-shelx-ins.cc
++libcoot_shelx_la_LIBADD = $(MMDB_LIBS) libcoot-coord-utils.la
+ 
+ # for non-simple coordinates things
+ libcoot_coord_extras_la_SOURCES = coot-coord-extras.cc coot-coord-lsq.cc
+@@ -51,21 +53,20 @@
+ 
+ # for map things that need mmdb, clipper, gsl and other things
+ libcoot_map_heavy_la_SOURCES = coot-map-heavy.cc coot-fffear.cc
++libcoot_map_heavy_la_LIBADD = $(GSL_LIBS)
+ 
+ noinst_PROGRAMS = testshelxreader testcootutils
+ 
+ testshelxreader_SOURCES = test-shelx-reader.cc
+ testshelxreader_LDADD = \
+ 	./libcoot-shelx.la \
+-	./libcoot-coord-utils.la \
+-	./libcoot-utils.la \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS)
++	./libcoot-utils.la
+ 
+ testcootutils_SOURCES = test-utils.cc
+ testcootutils_LDADD = \
+ 	./libcoot-shelx.la \
+ 	./libcoot-coord-utils.la \
+ 	./libcoot-utils.la \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS)
++	$(MMDB_LIBS)
+ 
+ 
+diff -urN coot-0.3.3.orig/geometry/Makefile.am coot-0.3.3/geometry/Makefile.am
+--- coot-0.3.3.orig/geometry/Makefile.am	2007-08-15 12:20:04.000000000 -0700
++++ coot-0.3.3/geometry/Makefile.am	2007-08-15 12:21:22.000000000 -0700
+@@ -34,6 +34,9 @@
+ libcoot_geometry_a_sources = protein-geometry.cc protein-geometry-mmdb.cc
+ 
+ libcoot_geometry_la_SOURCES = $(libcoot_geometry_a_sources)
++libcoot_geometry_la_LIBADD = \
++	$(top_builddir)/coot-utils/libcoot-utils.la \
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+ # libcoot_geometry_la_CXXFLAGS = -g -O1
+ 
+@@ -41,6 +44,4 @@
+ 
+ test_geometry_SOURCES = test-geometry.cc
+ 
+-test_geometry_LDADD = ./libcoot-geometry.la         \
+-        $(top_builddir)/coot-utils/libcoot-utils.la \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS)
++test_geometry_LDADD = ./libcoot-geometry.la
+diff -urN coot-0.3.3.orig/high-res/Makefile.am coot-0.3.3/high-res/Makefile.am
+--- coot-0.3.3.orig/high-res/Makefile.am	2007-08-15 12:20:04.000000000 -0700
++++ coot-0.3.3/high-res/Makefile.am	2007-08-15 12:21:22.000000000 -0700
+@@ -39,13 +39,16 @@
+ 
+ libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \
+ 	sequence-assignment.cc
++libcoot_high_res_la_LIBADD = \
++	$(top_builddir)/ligand/libcoot-ligand.la \
++	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+ noinst_PROGRAMS = testatomgraph tracehighres testseqalign testseqassignment globularize_protein
+ 
+ testatomgraph_SOURCES = test-atom-graph.cc
+ 
+ testatomgraph_LDADD =  libcoot-high-res.la                \
+-	$(top_builddir)/ligand/libcoot-ligand.la          \
+ 	$(top_builddir)/db-main/libcoot-db-main.la        \
+ 	$(top_builddir)/ideal/libcoot-ideal.la            \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+@@ -53,90 +56,73 @@
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+ 	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+-	$(GSL_LIBS)			                  \
+-	$(CLIPPER_LIBS)
++	$(GSL_LIBS)
+ 
+ testseqassignment_SOURCES = testseqassignment.cc
+ testseqassignment_LDADD = libcoot-high-res.la             \
+-	$(top_builddir)/ligand/libcoot-ligand.la          \
+ 	$(top_builddir)/db-main/libcoot-db-main.la        \
+ 	$(top_builddir)/ideal/libcoot-ideal.la            \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+ 	$(top_builddir)/coords/libcoot-coords.la          \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+-	$(GSL_LIBS)				          \
+-	$(CLIPPER_LIBS)
++	$(GSL_LIBS)
+ 
+ # tracehighres_LDFLAGS = -static 
+ tracehighres_SOURCES = trace-high-res.cc
+ tracehighres_LDADD = libcoot-high-res.la                  \
+-	$(top_builddir)/ligand/libcoot-ligand.la          \
+ 	$(top_builddir)/ideal/libcoot-ideal.la            \
+ 	$(top_builddir)/db-main/libcoot-db-main.la        \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+ 	$(top_builddir)/coords/libcoot-coords.la          \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+-	$(GSL_LIBS)				          \
+-	$(CLIPPER_LIBS)
+-
++	$(GSL_LIBS)
+ 
+ testseqalign_SOURCES = testseqalign.cc
+ 
+ # why do we need to link with all this (junk)?
+ testseqalign_LDADD = libcoot-high-res.la                  \
+-	$(top_builddir)/ligand/libcoot-ligand.la          \
+ 	$(top_builddir)/ideal/libcoot-ideal.la            \
+ 	$(top_builddir)/db-main/libcoot-db-main.la        \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+ 	$(top_builddir)/coords/libcoot-coords.la          \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+-	$(GSL_LIBS)				          \
+-	$(CLIPPER_LIBS)
+-
++	$(GSL_LIBS)
+ 
+ globularize_protein_SOURCES = globularize.cc
+ 
+ globularize_protein_LDADD = libcoot-high-res.la           \
+-	$(top_builddir)/ligand/libcoot-ligand.la          \
+ 	$(top_builddir)/db-main/libcoot-db-main.la        \
+ 	$(top_builddir)/ideal/libcoot-ideal.la            \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+ 	$(top_builddir)/coords/libcoot-coords.la          \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+-	$(GSL_LIBS)				          \
+-	$(CLIPPER_LIBS)
+-
++	$(GSL_LIBS)
+ 
+diff -urN coot-0.3.3.orig/ideal/Makefile.am coot-0.3.3/ideal/Makefile.am
+--- coot-0.3.3.orig/ideal/Makefile.am	2007-08-15 12:20:04.000000000 -0700
++++ coot-0.3.3/ideal/Makefile.am	2007-08-15 12:21:22.000000000 -0700
+@@ -43,6 +43,12 @@
+ AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS)
+ 
+ libcoot_ideal_la_SOURCES = simple-restraint.cc  pepflip.cc regularize-minimol.cc
++libcoot_ideal_la_LIBADD = \
++	$(top_builddir)/coot-utils/libcoot-utils.la       \
++	$(top_builddir)/mini-mol/libcoot-mini-mol.la       \
++	$(top_builddir)/coot-utils/libcoot-shelx.la       \
++	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
++	$(GSL_LIBS)
+ 
+ noinst_PROGRAMS = test-indexing with-geometry with-map
+ # bin_PROGRAMS = 
+@@ -60,31 +66,20 @@
+ with_geometry_LDADD = \
+         ./libcoot-ideal.la                                \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+-	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coords/libcoot-coords.la          \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+-	$(top_builddir)/coot-utils/libcoot-utils.la       \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+ with_map_LDADD =  \
+         ./libcoot-ideal.la                                 \
+ 	$(top_builddir)/geometry/libcoot-geometry.la       \
+-	$(top_builddir)/mini-mol/libcoot-mini-mol.la       \
+ 	$(top_builddir)/coords/libcoot-coords.la           \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la        \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la  \
+-	$(top_builddir)/coot-utils/libcoot-utils.la        \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
++	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+ test_indexing_LDADD = \
+         ./libcoot-ideal.la                                \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+-	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+-	$(top_builddir)/coot-utils/libcoot-utils.la       \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+diff -urN coot-0.3.3.orig/ligand/Makefile.am coot-0.3.3/ligand/Makefile.am
+--- coot-0.3.3.orig/ligand/Makefile.am	2007-08-15 12:20:04.000000000 -0700
++++ coot-0.3.3/ligand/Makefile.am	2007-08-15 12:21:22.000000000 -0700
+@@ -42,6 +42,16 @@
+ libcoot_ligand_la_SOURCES = ligand.cc ligand-extras.cc  residue_by_phi_psi.cc \
+ 	wiggly-ligand.cc monomer-utils.cc dunbrack.cc chi-angles-autogen.cc   \
+ 	chi-angles.cc helix-placement.cc rigid-body.cc ideal-rna.cc
++libcoot_ligand_la_LIBADD = \
++	$(top_builddir)/ideal/libcoot-ideal.la       \
++	$(top_builddir)/coords/libcoot-coords.la           \
++	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
++	$(top_builddir)/coot-utils/libcoot-map-utils.la    \
++	$(top_builddir)/db-main/libcoot-db-main.la         \
++	$(top_builddir)/coot-utils/libcoot-shelx.la        \
++	$(top_builddir)/geometry/libcoot-geometry.la       \
++	$(top_builddir)/coot-utils/libcoot-coord-utils.la  \
++	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la
+ 
+ AM_CXXFLAGS = \
+ 	-DPKGDATADIR='"$(pkgdatadir)"' \
+@@ -59,35 +69,17 @@
+ test_random_SOURCES = test-random.cc
+ test_random_LDADD = \
+ 	./libcoot-ligand.la \
+-	$(top_builddir)/ideal/libcoot-ideal.la       \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la \
+-	$(top_builddir)/coords/libcoot-coords.la           \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la    \
+-	$(top_builddir)/db-main/libcoot-db-main.la         \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la        \
+-	$(top_builddir)/geometry/libcoot-geometry.la       \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la       \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la  \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la        \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la    \
+ 	$(top_builddir)/compat/libcoot-compat.la           \
+ 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+ test_helix_placement_LDADD = \
+ 	./libcoot-ligand.la \
+-	$(top_builddir)/ideal/libcoot-ideal.la       \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la \
+-	$(top_builddir)/coords/libcoot-coords.la           \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la    \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la        \
+-	$(top_builddir)/geometry/libcoot-geometry.la       \
+-	$(top_builddir)/db-main/libcoot-db-main.la         \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la       \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la  \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la        \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la    \
+ 	$(top_builddir)/compat/libcoot-compat.la           \
+ 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+@@ -95,19 +87,10 @@
+ 
+ test_fffear_in_coot_LDADD = \
+ 	./libcoot-ligand.la \
+-	$(top_builddir)/ideal/libcoot-ideal.la            \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coords/libcoot-coords.la          \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+-	$(top_builddir)/geometry/libcoot-geometry.la      \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coot-utils/libcoot-map-heavy.la   \
+-	$(top_builddir)/db-main/libcoot-db-main.la         \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+ 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+@@ -119,33 +102,15 @@
+ 
+ findligand_real_LDADD = \
+ 	./libcoot-ligand.la                          \
+-	$(top_builddir)/ideal/libcoot-ideal.la       \
+-	$(top_builddir)/geometry/libcoot-geometry.la \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la \
+-	$(top_builddir)/coords/libcoot-coords.la     \
+-	$(top_builddir)/db-main/libcoot-db-main.la         \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+ 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+ findwaters_real_LDADD = \
+ 	./libcoot-ligand.la                               \
+-	$(top_builddir)/ideal/libcoot-ideal.la            \
+-	$(top_builddir)/geometry/libcoot-geometry.la      \
+-	$(top_builddir)/coords/libcoot-coords.la          \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+-	$(top_builddir)/db-main/libcoot-db-main.la         \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+ 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+@@ -166,17 +131,8 @@
+ testdunbrack_SOURCES = testdunbrack.cc
+ 
+ testdunbrack_LDADD = ./libcoot-ligand.la \
+-	$(top_builddir)/ideal/libcoot-ideal.la       \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la \
+-	$(top_builddir)/geometry/libcoot-geometry.la \
+-	$(top_builddir)/coords/libcoot-coords.la           \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la    \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+-	$(top_builddir)/db-main/libcoot-db-main.la         \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la  \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la        \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+         $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+ # lib coot-coords depends on mmdb, even though Cartesian doesn't
+diff -urN coot-0.3.3.orig/Makefile.am coot-0.3.3/Makefile.am
+--- coot-0.3.3.orig/Makefile.am	2007-08-15 12:20:04.000000000 -0700
++++ coot-0.3.3/Makefile.am	2007-08-15 21:09:11.000000000 -0700
+@@ -25,10 +25,10 @@
+ 
+ # see configure.in for po intl 
+ SUBDIRS = auxil scheme python macros compat coot-utils surface coot-surface \
+-	skeleton ccp4mg-utils density-contour coords angles \
+-	mini-mol db-main  geometry  \
++	atom-utils skeleton ccp4mg-utils density-contour mini-mol coords angles \
++	db-main  geometry  \
+ 	ideal ligand high-res build \
+-	analysis sequence-view tw atom-utils src doc 
++	analysis sequence-view tw src doc 
+ 
+ # po, no po today.
+ 
+diff -urN coot-0.3.3.orig/mini-mol/Makefile.am coot-0.3.3/mini-mol/Makefile.am
+--- coot-0.3.3.orig/mini-mol/Makefile.am	2007-08-15 12:20:04.000000000 -0700
++++ coot-0.3.3/mini-mol/Makefile.am	2007-08-15 12:21:22.000000000 -0700
+@@ -32,8 +32,9 @@
+ testminimol_SOURCES = testminimol.cc
+ 
+ libcoot_mini_mol_la_SOURCES =  mini-mol.cc mini-mol-utils.cc
++libcoot_mini_mol_la_LIBADD = \
++	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
++	$(CLIPPER_LIBS)
+ 
+ testminimol_LDADD = libcoot-mini-mol.la \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+-	$(top_builddir)/coot-utils/libcoot-utils.la \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS)
++	$(MMDB_LIBS)
+diff -urN coot-0.3.3.orig/skeleton/Makefile.am coot-0.3.3/skeleton/Makefile.am
+--- coot-0.3.3.orig/skeleton/Makefile.am	2007-08-15 12:20:04.000000000 -0700
++++ coot-0.3.3/skeleton/Makefile.am	2007-08-15 17:20:44.000000000 -0700
+@@ -36,7 +36,7 @@
+ 
+ 
+ libcoot_skeleton_la_SOURCES = $(libskeleton_a_sources)
+-
++libcoot_skeleton_la_LIBADD = ../atom-utils/libcoot-atomutils.la
+ 
+ # bin_PROGRAMS = ncssearch test_various test_torsion test_theta_2
+ 
+diff -urN coot-0.3.3.orig/tw/Makefile.am coot-0.3.3/tw/Makefile.am
+--- coot-0.3.3.orig/tw/Makefile.am	2007-08-15 12:20:04.000000000 -0700
++++ coot-0.3.3/tw/Makefile.am	2007-08-15 12:21:22.000000000 -0700
+@@ -39,15 +39,15 @@
+ include_HEADERS = coot-tw.hh
+ 
+ libcoot_tw_la_SOURCES = tw.cc
++libcoot_tw_la_LIBADD = \
++	$(GTKCANVAS_LIBS) \
++	@GTK_LIBS@
+ 
+ noinst_PROGRAMS = coot-tiddly
+ 
+ coot_tiddly_SOURCES = tiddly.cc
+ 
+-coot_tiddly_LDADD = libcoot-tw.la \
+-	$(GTKCANVAS_LIBS) \
+-	@GTK_LIBS@
+-
++coot_tiddly_LDADD = libcoot-tw.la
+ 
+ # cootsound_LDADD = -L/sw/lib -lvorbisfile -logg -lao
+ 
diff --git a/sci-chemistry/coot/files/0.3.3-link-against-guile-gtk-properly.patch b/sci-chemistry/coot/files/0.3.3-link-against-guile-gtk-properly.patch
new file mode 100644
index 000000000000..d0f57b287426
--- /dev/null
+++ b/sci-chemistry/coot/files/0.3.3-link-against-guile-gtk-properly.patch
@@ -0,0 +1,15 @@
+diff -urN coot-0.3.3.orig/macros/guile-gtk.m4 coot-0.3.3/macros/guile-gtk.m4
+--- coot-0.3.3.orig/macros/guile-gtk.m4	2007-08-15 12:20:04.000000000 -0700
++++ coot-0.3.3/macros/guile-gtk.m4	2007-08-15 12:20:32.000000000 -0700
+@@ -66,9 +66,9 @@
+    # we have the variable coot_gtk2 in configure.in, which is either TRUE or FALSE
+    # Let's use that here.  Perhaps there is a better (set by gtk macro?) variable?
+    if test $coot_gtk2 = TRUE ; then
+-	GUILE_GTK_LIBS=$guile_gtk_prefix/lib/libguilegtk-2.0.la
++	GUILE_GTK_LIBS="-L$guile_gtk_prefix/lib -lguilegtk-2.0"
+    else 
+-	GUILE_GTK_LIBS=$guile_gtk_prefix/lib/libguilegtk-1.2.la
++	GUILE_GTK_LIBS="-L$guile_gtk_prefix/lib -lguilegtk-1.2"
+    fi
+    # do we need to set this in fact?
+    GUILE_GTK_CFLAGS="-I$guile_gtk_prefix/include"
diff --git a/sci-chemistry/coot/files/digest-coot-0.3.3 b/sci-chemistry/coot/files/digest-coot-0.3.3
new file mode 100644
index 000000000000..4646e842f696
--- /dev/null
+++ b/sci-chemistry/coot/files/digest-coot-0.3.3
@@ -0,0 +1,3 @@
+MD5 e4c5c250d7c14124bc6a835d4532df40 coot-0.3.3.tar.gz 3870046
+RMD160 b23ca227894a469456c5af0284d0bb8530c855b5 coot-0.3.3.tar.gz 3870046
+SHA256 f3a7d6f789846b1f7670d4dc3e61a430cbab811f2f22349b84f49e10aaa4a41c coot-0.3.3.tar.gz 3870046