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

(Portage version: 2.1.3.5)

5 files changed, 610 insertions, 1 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/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