coot fixes

as-needed patch not needed anymore
Same for reduce sed
rappermc patch added

4 files changed, 512 insertions, 21 deletions

diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index 1f9d06a8c..8ebcb8dbd 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -5,6 +5,7 @@ AUX 0.6_pre1-as-needed.patch 18539 RMD160 2596dac3eb33e1704f84a11613fdc52c42fe87
 AUX 0.6_pre1-gcc4.4.patch 299 RMD160 75374bd38981d4383d926a3b6529ef955a18e893 SHA1 e05d1caeb3dd13d101d417e7f2613402b6712005 SHA256 02c18e695086d70152b923af5d0aecd334bc18f1b6b955d3133c2ae7b6f218af
 AUX 0.6_pre1-test-rama.patch 497 RMD160 6db4732c088d6435dfa1eab0b036f5d37cf13df4 SHA1 dea0505ccdfae27c5632c1c57ce889024a8681bc SHA256 13eed941e596f5a8f1a7a266f8f7c44a359ab35d7df1dad6cae1d91461a7f3bf
 AUX 9999-as-needed.patch 18539 RMD160 2596dac3eb33e1704f84a11613fdc52c42fe8765 SHA1 b6d932312e38d7822866df6449226d90ea1c38c3 SHA256 1646003be0db635ff9b9ef7726adb06f4da8de8a4dbe77baa5074ec8a2faa68a
+AUX 9999-as-needed2.patch 18539 RMD160 2596dac3eb33e1704f84a11613fdc52c42fe8765 SHA1 b6d932312e38d7822866df6449226d90ea1c38c3 SHA256 1646003be0db635ff9b9ef7726adb06f4da8de8a4dbe77baa5074ec8a2faa68a
 AUX 9999-check-include.patch 833 RMD160 7b877f8973b06119779518b433b607665930a382 SHA1 c8a0c80d3a3f5e85592c9925b35c6d5462fc36ad SHA256 98a6c8ef47953501e360b1bdd568ac99d5a53749738d940939e9f6a47cf85cd1
 AUX 9999-gcc4.4.patch 299 RMD160 75374bd38981d4383d926a3b6529ef955a18e893 SHA1 e05d1caeb3dd13d101d417e7f2613402b6712005 SHA256 02c18e695086d70152b923af5d0aecd334bc18f1b6b955d3133c2ae7b6f218af
 AUX 9999-test-rama.patch 497 RMD160 6db4732c088d6435dfa1eab0b036f5d37cf13df4 SHA1 dea0505ccdfae27c5632c1c57ce889024a8681bc SHA256 13eed941e596f5a8f1a7a266f8f7c44a359ab35d7df1dad6cae1d91461a7f3bf
@@ -16,9 +17,9 @@ AUX imlib.m4 11371 RMD160 4470d0cf2d0f8298bea6565069acda8a44e1cd9d SHA1 c983c372
 AUX link-against-guile-gtk-properly.patch 800 RMD160 4215ea41c02e7db2c04dda191e0200cc1704d43c SHA1 5bd24ab8c651a147076289098956f545c6e431d6 SHA256 7805cdf4e34c532899a8c37eb19664fc95fc8bc440e770db7c87373a94e1fb2d
 DIST coot-0.5.2.tar.gz 10160364 RMD160 5cee5e8da6e4d2ce06016f6f8935b395e65ddbf9 SHA1 041cc947a68296701deb153c0932ee20a3437323 SHA256 6245f85dfb796ee7f3488c0790531f8d5e29a9f6ea18411ae539e3993e4ed2d6
 DIST coot-0.6-pre-1-revision-2312.tar.gz 11014498 RMD160 d509629d4a4aaa042699b255270d02f19af5c1e7 SHA1 4502d18aa14eb1f0f2725e877b7ddfab8a145efd SHA256 9ac5076502c1cb0a45e3dd6c59ef9f39e2732bdfca5441bf59f0af398ca1be85
-DIST greg-data.tar.gz 7853711 RMD160 3d736f3dfd0ad1a1fbe857ae3b6d412106375e6d SHA1 639db46bbd8ee5ff9764a011873ca635bc3c9351 SHA256 6ccdbec91c098b4e89666259cb93acec4dc0213e9762e5d3d3e9a8b96d9f0fcc
+DIST greg-data.tar.gz 7853712 RMD160 9dc7f9dc65786e3aa4ebdc58c280fffa32ed07d3 SHA1 eff196da7da65e4265cc289aba4c7717f5600916 SHA256 ce0c5ae438dcb14771f3339fe57d3b40bb8cd0a8cb37a237eeecc0bb69fb3e5d
 EBUILD coot-0.5.2.ebuild 3238 RMD160 80d71146f3b11a4283494bfb95e77667a5128c1f SHA1 72f982f9a9fa8bc22688f5a5bbae9488b3e5dafb SHA256 582a0d78796e8666825befbc2fe5a4256ea5a5512cded142480f70f14bca2e74
 EBUILD coot-0.6_pre1-r2312.ebuild 4318 RMD160 8164ef691b3ef718bdd0aad743789624d7021239 SHA1 e725804986286fb50de2def68b7218a2f5f8b4ee SHA256 81fef115c1b7972482bf6f578f0350abbbc68a685673bdbceb4fcde50d67a0ff
-EBUILD coot-9999.ebuild 4194 RMD160 025e880a348a1c856de8d1130cecb6179acffa51 SHA1 89413c8a0c9d2b516c6c0158beed5503e499f7fa SHA256 36de50557b876646276acbb7167b7ae4af291c4c662f189d7a5eef99d795e78f
+EBUILD coot-9999.ebuild 4176 RMD160 fd068d47dc3dce93a874be3f32829d5e439a8e2f SHA1 ef908eb88677069c451c199054cfd802312bbdb5 SHA256 70dff7bce3d644f83ea8f1950165222447c9a1135b35de0322ae110225683965
 MISC ChangeLog 6038 RMD160 44f05c3a14daf55c3b4f14f710790e7b83e4e83b SHA1 5c1d78bdb14cb3e748336c91d44bd746091b958f SHA256 58bb9a17e32402179e269cadb493468c519e96b5972f75a369db731ab89d9245
 MISC metadata.xml 316 RMD160 845cc100ac244efa5f02595717b5da635f87d2f1 SHA1 c870d2c52c44dee3bab8623e5b6095266f400813 SHA256 64f6dbcd3bb41b26fd7897089cd60ddb93f1ea7d75f9531bca94f28b07e21b2f
diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index 72ec9f637..8e7bb82d2 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -60,7 +60,7 @@ DEPEND="${RDEPEND}
 S="${WORKDIR}"
 
 PATCHES=(
-	"${FILESDIR}"/${PV}-as-needed.patch
+	"${FILESDIR}"/${PV}-rappermc.patch
 	"${FILESDIR}"/link-against-guile-gtk-properly.patch
 	"${FILESDIR}"/fix-namespace-error.patch
 	)
@@ -79,12 +79,6 @@ src_prepare() {
 		-e "s:lrfftw:lsrfftw: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" \
-		"${S}"/scheme/group-settings.scm
-
 	# So we don't need to depend on crazy old gtk and friends
 	cp "${FILESDIR}"/*.m4 "${S}"/macros/
 
@@ -119,20 +113,20 @@ src_configure() {
 }
 
 src_compile() {
-	# 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
-
+#	# 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
+#
 	emake || die "emake failed"
 
-	cp "${S}"/src/coot.py python/
+	cp "${S}"/src/coot.py python/ || die
 }
 
 src_test() {
diff --git a/sci-chemistry/coot/files/9999-as-needed2.patch b/sci-chemistry/coot/files/9999-as-needed2.patch
new file mode 100644
index 000000000..0cfce54dd
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-as-needed2.patch
@@ -0,0 +1,481 @@
+Index: mini-mol/Makefile.am
+===================================================================
+--- mini-mol/Makefile.am	(revision 2293)
++++ mini-mol/Makefile.am	(working copy)
+@@ -35,8 +35,9 @@
+ testminimol_SOURCES = testminimol.cc
+ 
+ libcoot_mini_mol_la_SOURCES =  mini-mol.cc mini-mol-utils.cc atom-quads.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)
+Index: coords/Makefile.am
+===================================================================
+--- coords/Makefile.am	(revision 2293)
++++ coords/Makefile.am	(working copy)
+@@ -40,3 +40,7 @@
+ 		 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
++
+Index: ligand/Makefile.am
+===================================================================
+--- ligand/Makefile.am	(revision 2293)
++++ ligand/Makefile.am	(working copy)
+@@ -49,6 +49,17 @@
+ 	torsion-general.cc rotamer-tables.cc primitive-chi-angles.cc dipole.cc\
+         base-pairing.cc backrub-rotamer.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)"' \
+ 	$(COOT_WINDOWS_CFLAGS)
+@@ -68,7 +79,6 @@
+ 
+ test_random_LDADD = \
+ 	./libcoot-ligand.la \
+-	$(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    \
+@@ -85,31 +95,14 @@
+ 
+ test_ligand_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)/coot-utils/libcoot-coord-utils.la  \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la        \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.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)/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)/coot-utils/libcoot-coord-utils.la  \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la        \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la       \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la    \
+@@ -120,18 +113,9 @@
+ 
+ test_fffear_in_coot_LDADD = \
+ 	./libcoot-ligand.la \
+-	$(top_builddir)/ideal/libcoot-ideal.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)/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)/mini-mol/libcoot-mini-mol.la      \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+ 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+@@ -143,23 +127,13 @@
+ 
+ findligand_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)/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)/mini-mol/libcoot-mini-mol.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)/ccp4mg-utils/libccp4mg-utils.la    \
+@@ -190,16 +164,7 @@
+ testdunbrack_SOURCES = testdunbrack.cc
+ 
+ testdunbrack_LDADD = ./libcoot-ligand.la \
+-	$(top_builddir)/ideal/libcoot-ideal.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       \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la \
+         $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+Index: analysis/Makefile.am
+===================================================================
+--- analysis/Makefile.am	(revision 2293)
++++ analysis/Makefile.am	(working copy)
+@@ -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) 	\
+Index: skeleton/Makefile.am
+===================================================================
+--- skeleton/Makefile.am	(revision 2293)
++++ skeleton/Makefile.am	(working copy)
+@@ -39,8 +39,8 @@
+ 
+ 
+ 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
+ 
+ # ncssearch_SOURCES = ncs-search.cc ncs-search.h
+Index: coot-surface/Makefile.am
+===================================================================
+--- coot-surface/Makefile.am	(revision 2293)
++++ coot-surface/Makefile.am	(working copy)
+@@ -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
+Index: high-res/Makefile.am
+===================================================================
+--- high-res/Makefile.am	(revision 2293)
++++ high-res/Makefile.am	(working copy)
+@@ -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)
+ 
+ check_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      \
+@@ -53,71 +56,60 @@
+ 	$(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
+Index: cootaneer/Makefile.am
+===================================================================
+--- cootaneer/Makefile.am	(revision 2293)
++++ cootaneer/Makefile.am	(working copy)
+@@ -34,6 +34,7 @@
+ 	buccaneer-sequence.cpp cootaneer-sequence.cpp \
+ 	buccaneer-lib.h buccaneer-prot.h \
+ 	buccaneer-sequence.h cootaneer-sequence.h
++libcootaneer_la_LIBADD = $(CLIPPER_LIBS)
+ 
+ subpkgdatadir = $(pkgdatadir)
+ subpkgdata_DATA = cootaneer-llk-2.40.dat 
+Index: geometry/Makefile.am
+===================================================================
+--- geometry/Makefile.am	(revision 2293)
++++ geometry/Makefile.am	(working copy)
+@@ -35,6 +35,9 @@
+ #	-DHAVE_SYS_STDTYPES_H
+ 
+ libcoot_geometry_la_SOURCES = protein-geometry.cc protein-geometry-mmdb.cc 
++libcoot_geometry_la_LIBADD = \
++	$(top_builddir)/coot-utils/libcoot-utils.la \
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+ # libcoot_geometry_la_CXXFLAGS = -g -O1
+ 
+@@ -44,12 +47,7 @@
+ 
+ test_read_components_SOURCES = test-read-components.cc test-read-components.hh
+ 
+-test_geometry_LDADD = ./libcoot-geometry.la         \
+-        $(top_builddir)/coot-utils/libcoot-utils.la \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS)
++test_geometry_LDADD = ./libcoot-geometry.la
++ 
++test_read_components_LDADD = ./libcoot-geometry.la
+ 
+-test_read_components_LDADD =  \
+-	./libcoot-geometry.la \
+-        $(top_builddir)/coot-utils/libcoot-utils.la   \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS)
+-
+Index: ideal/Makefile.am
+===================================================================
+--- ideal/Makefile.am	(revision 2293)
++++ ideal/Makefile.am	(working copy)
+@@ -54,6 +54,12 @@
+ 
+ 
+ libcoot_ideal_la_SOURCES = simple-restraint.cc  pepflip.cc regularize-minimol.cc lograma.cpp
++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 logramatest
+@@ -75,12 +81,8 @@
+         ./libcoot-ideal.la                                \
+ 	$(top_builddir)/geometry/libcoot-geometry.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       \
+-	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+ # add libcoot-map-utils for  the debugging density_around_point function
+ with_map_LDADD =  \
+@@ -88,22 +90,16 @@
+ 	$(top_builddir)/geometry/libcoot-geometry.la       \
+ 	$(top_builddir)/coords/libcoot-coords.la           \
+ 	$(top_builddir)/coot-utils/libcoot-map-utils.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        \
+-        $(top_builddir)/compat/libcoot-compat.la           \
+-	$(top_builddir)/mini-mol/libcoot-mini-mol.la       \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
++	$(top_builddir)/compat/libcoot-compat.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)
+ 
+ # Why do I need all these libraries to simply link a trivial test program?
+ # Badness....
+Index: tw/Makefile.am
+===================================================================
+--- tw/Makefile.am	(revision 2293)
++++ tw/Makefile.am	(working copy)
+@@ -39,14 +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
+Index: coot-utils/Makefile.am
+===================================================================
+--- coot-utils/Makefile.am	(revision 2293)
++++ coot-utils/Makefile.am	(working copy)
+@@ -49,6 +49,7 @@
+ # for simple things:
+ libcoot_utils_la_SOURCES = coot-utils.cc coot-fasta.cc atomic-numbers.cc \
+ 	gdk-keysyms.cc
++libcoot_coord_utils_la_LIBADD = $(CLIPPER_LIBS) libcoot-utils.la
+ 
+ # for pure coordinates (mmdb) things
+ libcoot_coord_utils_la_SOURCES = coot-coord-utils.cc \
+@@ -56,6 +57,7 @@
+ 
+ # 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 \
+@@ -63,24 +65,23 @@
+ 
+ # for (map) things that need to link mmdb and clipper:
+ libcoot_map_utils_la_SOURCES = coot-map-utils.cc peak-search.cc trim.cc xmap-stats.cc
++libcoot_map_utils_la_LIBADD = $(CLIPPER_LIBS)
+ 
+ # 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)
++	$(MMDB_LIBS)
+ 
+ testcootutils_SOURCES = test-utils.cc
+ testcootutils_LDADD = \
+ 	./libcoot-shelx.la \
+-	./libcoot-coord-utils.la \
+ 	./libcoot-utils.la \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS)
++  $(MMDB_LIBS)
+ 
+-
+Index: Makefile.am
+===================================================================
+--- Makefile.am	(revision 2293)
++++ Makefile.am	(working copy)
+@@ -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 greg-tests python-tests \
+-	analysis sequence-view tw atom-utils cootaneer src rama-data doc 
++	analysis sequence-view tw cootaneer src rama-data doc 
+ 
+ # po, no po today.
+ 
diff --git a/sci-chemistry/coot/files/9999-rappermc.patch b/sci-chemistry/coot/files/9999-rappermc.patch
new file mode 100644
index 000000000..1ecd9c529
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-rappermc.patch
@@ -0,0 +1,15 @@
+Index: /data/svn-src/coot/trunk/python/a_rapper_gui.py
+===================================================================
+--- /data/svn-src/coot/trunk/python/a_rapper_gui.py	(revision 2398)
++++ /data/svn-src/coot/trunk/python/a_rapper_gui.py	(working copy)
+@@ -20,8 +20,8 @@
+     home_dir = os.getenv('COOT_HOME')
+ else:
+     home_dir = os.getenv('HOME')
+-rapper_dir = os.path.join(os.path.normpath(home_dir), "rappermc")
+-rapper_command = "rapper"
++rapper_dir = "/usr/share/rapper"
++rapper_command = "rappermc"
+ 
+ def rapper_process():
+     #needed?