Merged sci-chemistry/coot from dberkholz-overlay to sci-overlay

version bump to 0.5.2
We now build against ccp4-libs

8 files changed, 1309 insertions, 0 deletions

diff --git a/sci-chemistry/coot/files/0.5.2-as-needed.patch b/sci-chemistry/coot/files/0.5.2-as-needed.patch
new file mode 100644
index 000000000..e66ec971d
--- /dev/null
+++ b/sci-chemistry/coot/files/0.5.2-as-needed.patch
@@ -0,0 +1,489 @@
+diff -ur coot-0.5-pre-1.orig/analysis/Makefile.am coot-0.5-pre-1/analysis/Makefile.am
+--- coot-0.5-pre-1.orig/analysis/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ coot-0.5-pre-1/analysis/Makefile.am	2008-07-13 16:40:40.000000000 -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 -ur coot-0.5-pre-1.orig/coords/Makefile.am coot-0.5-pre-1/coords/Makefile.am
+--- coot-0.5-pre-1.orig/coords/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ coot-0.5-pre-1/coords/Makefile.am	2008-07-13 16:40:40.000000000 -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 -ur coot-0.5-pre-1.orig/cootaneer/Makefile.am coot-0.5-pre-1/cootaneer/Makefile.am
+--- coot-0.5-pre-1.orig/cootaneer/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ coot-0.5-pre-1/cootaneer/Makefile.am	2008-07-13 16:40:40.000000000 -0700
+@@ -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 
+diff -ur coot-0.5-pre-1.orig/coot-surface/Makefile.am coot-0.5-pre-1/coot-surface/Makefile.am
+--- coot-0.5-pre-1.orig/coot-surface/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ coot-0.5-pre-1/coot-surface/Makefile.am	2008-07-13 16:40:40.000000000 -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 -ur coot-0.5-pre-1.orig/coot-utils/Makefile.am coot-0.5-pre-1/coot-utils/Makefile.am
+--- coot-0.5-pre-1.orig/coot-utils/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ coot-0.5-pre-1/coot-utils/Makefile.am	2008-07-13 16:40:40.000000000 -0700
+@@ -51,9 +51,11 @@
+ # for pure coordinates (mmdb) things
+ libcoot_coord_utils_la_SOURCES = coot-coord-utils.cc \
+ 	coot-coord-utils-nucleotides.cc coot-rama.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
+@@ -63,21 +65,20 @@
+ 
+ # 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)
+ 
+ 
+--- coot-0.5/geometry/Makefile.am	2008-09-08 15:22:01.000000000 +0200
++++ coot-0.5/geometry/Makefile.am.new	2008-11-20 12:01:08.000000000 +0100
+@@ -35,6 +35,10 @@
+ 
+ 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
+ 
+ noinst_PROGRAMS = test-geometry test-read-components
+@@ -43,12 +47,6 @@
+ 
+ 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_read_components_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
+
+diff -ur coot-0.5-pre-1.orig/high-res/Makefile.am coot-0.5-pre-1/high-res/Makefile.am
+--- coot-0.5-pre-1.orig/high-res/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ coot-0.5-pre-1/high-res/Makefile.am	2008-07-13 16:40:40.000000000 -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 -ur coot-0.5-pre-1.orig/ideal/Makefile.am coot-0.5-pre-1/ideal/Makefile.am
+--- coot-0.5-pre-1.orig/ideal/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ coot-0.5-pre-1/ideal/Makefile.am	2008-07-13 16:41:14.000000000 -0700
+@@ -44,6 +44,12 @@
+ AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS)
+ 
+ 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
+ # bin_PROGRAMS = 
+@@ -63,36 +69,25 @@
+ 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)
+ 
+ # add libcoot-map-utils for  the debugging density_around_point function
+ 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-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           \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
++	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
++	$(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....
+diff -ur coot-0.5-pre-1.orig/ligand/Makefile.am coot-0.5-pre-1/ligand/Makefile.am
+--- coot-0.5-pre-1.orig/ligand/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ coot-0.5-pre-1/ligand/Makefile.am	2008-07-13 16:40:40.000000000 -0700
+@@ -46,6 +46,16 @@
+ 	chi-angles.cc helix-placement.cc rigid-body.cc ideal-rna.cc           \
+ 	richardson-rotamers.cc richardson-rotamer.cc rotamer.cc               \
+ 	torsion-general.cc rotamer-tables.cc primitive-chi-angles.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)"' \
+@@ -83,35 +93,17 @@
+ 
+ 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)/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)
+ 
+@@ -119,19 +111,10 @@
+ 
+ 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)
+ 
+@@ -143,33 +126,15 @@
+ 
+ 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)
+ 
+@@ -190,17 +155,8 @@
+ 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 -ur coot-0.5-pre-1.orig/Makefile.am coot-0.5-pre-1/Makefile.am
+--- coot-0.5-pre-1.orig/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ coot-0.5-pre-1/Makefile.am	2008-07-13 16:40:40.000000000 -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 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 -ur coot-0.5-pre-1.orig/mini-mol/Makefile.am coot-0.5-pre-1/mini-mol/Makefile.am
+--- coot-0.5-pre-1.orig/mini-mol/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ coot-0.5-pre-1/mini-mol/Makefile.am	2008-07-13 16:40:40.000000000 -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 -ur coot-0.5-pre-1.orig/skeleton/Makefile.am coot-0.5-pre-1/skeleton/Makefile.am
+--- coot-0.5-pre-1.orig/skeleton/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ coot-0.5-pre-1/skeleton/Makefile.am	2008-07-13 16:40:40.000000000 -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 -ur coot-0.5-pre-1.orig/tw/Makefile.am coot-0.5-pre-1/tw/Makefile.am
+--- coot-0.5-pre-1.orig/tw/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ coot-0.5-pre-1/tw/Makefile.am	2008-07-13 16:40:40.000000000 -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/0.5.2-gcc-4.3.patch b/sci-chemistry/coot/files/0.5.2-gcc-4.3.patch
new file mode 100644
index 000000000..26377ed9d
--- /dev/null
+++ b/sci-chemistry/coot/files/0.5.2-gcc-4.3.patch
@@ -0,0 +1,10 @@
+--- coot-0.5-pre-1.orig/ligand/rotamer.cc	2008-07-01 18:14:54.000000000 -0700
++++ coot-0.5-pre-1/ligand/rotamer.cc	2008-07-01 18:15:10.000000000 -0700
+@@ -21,6 +21,7 @@
+  * 02110-1301, USA
+  */
+ 
++#include <cstring>
+ #include <fstream>
+ #include <stdexcept>
+ 
diff --git a/sci-chemistry/coot/files/fix-namespace-error.patch b/sci-chemistry/coot/files/fix-namespace-error.patch
new file mode 100644
index 000000000..5bf8a2d4b
--- /dev/null
+++ b/sci-chemistry/coot/files/fix-namespace-error.patch
@@ -0,0 +1,52 @@
+--- coot-utils/coot-coord-utils.cc.orig	2007-11-14 09:38:31.000000000 -0800
++++ coot-utils/coot-coord-utils.cc	2007-11-14 09:44:50.000000000 -0800
+@@ -395,28 +395,30 @@
+    return SelHnd;
+ }
+ 
+-std::ostream& coot::operator<< (std::ostream& s, const coot::atom_spec_t &spec) {
++namespace coot {
++   std::ostream& operator<< (std::ostream& s, const atom_spec_t &spec) {
+ 
+-   s << "[spec: ";
+-   s << "\"";
+-   s << spec.chain;
+-   s << "\" ";
+-   s << spec.resno;
+-   s << " ";
+-   s << "\"";
+-   s << spec.insertion_code;
+-   s << "\"";
+-   s << " ";
+-   s << "\"";
+-   s  << spec.atom_name;
+-   s << "\"";
+-   s << " ";
+-   s << "\"";
+-   s << spec.alt_conf;
+-   s << "\"]";
++      s << "[spec: ";
++      s << "\"";
++      s << spec.chain;
++      s << "\" ";
++      s << spec.resno;
++      s << " ";
++      s << "\"";
++      s << spec.insertion_code;
++      s << "\"";
++      s << " ";
++      s << "\"";
++      s  << spec.atom_name;
++      s << "\"";
++      s << " ";
++      s << "\"";
++      s << spec.alt_conf;
++      s << "\"]";
+ 
+-   return s;
++      return s;
+ 
++   }
+ }
+ 
+ 
diff --git a/sci-chemistry/coot/files/glib.m4 b/sci-chemistry/coot/files/glib.m4
new file mode 100644
index 000000000..b3c632b0e
--- /dev/null
+++ b/sci-chemistry/coot/files/glib.m4
@@ -0,0 +1,196 @@
+# Configure paths for GLIB
+# Owen Taylor     97-11-3
+
+dnl AM_PATH_GLIB([MINIMUM-VERSION, [ACTION-IF-FOUND [, ACTION-IF-NOT-FOUND [, MODULES]]]])
+dnl Test for GLIB, and define GLIB_CFLAGS and GLIB_LIBS, if "gmodule" or 
+dnl gthread is specified in MODULES, pass to glib-config
+dnl
+AC_DEFUN([AM_PATH_GLIB],
+[dnl 
+dnl Get the cflags and libraries from the glib-config script
+dnl
+AC_ARG_WITH(glib-prefix,[  --with-glib-prefix=PFX   Prefix where GLIB is installed (optional)],
+            glib_config_prefix="$withval", glib_config_prefix="")
+AC_ARG_WITH(glib-exec-prefix,[  --with-glib-exec-prefix=PFX Exec prefix where GLIB is installed (optional)],
+            glib_config_exec_prefix="$withval", glib_config_exec_prefix="")
+AC_ARG_ENABLE(glibtest, [  --disable-glibtest       Do not try to compile and run a test GLIB program],
+		    , enable_glibtest=yes)
+
+  if test x$glib_config_exec_prefix != x ; then
+     glib_config_args="$glib_config_args --exec-prefix=$glib_config_exec_prefix"
+     if test x${GLIB_CONFIG+set} != xset ; then
+        GLIB_CONFIG=$glib_config_exec_prefix/bin/glib-config
+     fi
+  fi
+  if test x$glib_config_prefix != x ; then
+     glib_config_args="$glib_config_args --prefix=$glib_config_prefix"
+     if test x${GLIB_CONFIG+set} != xset ; then
+        GLIB_CONFIG=$glib_config_prefix/bin/glib-config
+     fi
+  fi
+
+  for module in . $4
+  do
+      case "$module" in
+         gmodule) 
+             glib_config_args="$glib_config_args gmodule"
+         ;;
+         gthread) 
+             glib_config_args="$glib_config_args gthread"
+         ;;
+      esac
+  done
+
+  AC_PATH_PROG(GLIB_CONFIG, glib-config, no)
+  min_glib_version=ifelse([$1], ,0.99.7,$1)
+  AC_MSG_CHECKING(for GLIB - version >= $min_glib_version)
+  no_glib=""
+  if test "$GLIB_CONFIG" = "no" ; then
+    no_glib=yes
+  else
+    GLIB_CFLAGS=`$GLIB_CONFIG $glib_config_args --cflags`
+    GLIB_LIBS=`$GLIB_CONFIG $glib_config_args --libs`
+    glib_config_major_version=`$GLIB_CONFIG $glib_config_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\1/'`
+    glib_config_minor_version=`$GLIB_CONFIG $glib_config_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\2/'`
+    glib_config_micro_version=`$GLIB_CONFIG $glib_config_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\3/'`
+    if test "x$enable_glibtest" = "xyes" ; then
+      ac_save_CFLAGS="$CFLAGS"
+      ac_save_LIBS="$LIBS"
+      CFLAGS="$CFLAGS $GLIB_CFLAGS"
+      LIBS="$GLIB_LIBS $LIBS"
+dnl
+dnl Now check if the installed GLIB is sufficiently new. (Also sanity
+dnl checks the results of glib-config to some extent
+dnl
+      rm -f conf.glibtest
+      AC_TRY_RUN([
+#include <glib.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+int 
+main ()
+{
+  int major, minor, micro;
+  char *tmp_version;
+
+  system ("touch conf.glibtest");
+
+  /* HP/UX 9 (%@#!) writes to sscanf strings */
+  tmp_version = g_strdup("$min_glib_version");
+  if (sscanf(tmp_version, "%d.%d.%d", &major, &minor, &micro) != 3) {
+     printf("%s, bad version string\n", "$min_glib_version");
+     exit(1);
+   }
+
+  if ((glib_major_version != $glib_config_major_version) ||
+      (glib_minor_version != $glib_config_minor_version) ||
+      (glib_micro_version != $glib_config_micro_version))
+    {
+      printf("\n*** 'glib-config --version' returned %d.%d.%d, but GLIB (%d.%d.%d)\n", 
+             $glib_config_major_version, $glib_config_minor_version, $glib_config_micro_version,
+             glib_major_version, glib_minor_version, glib_micro_version);
+      printf ("*** was found! If glib-config was correct, then it is best\n");
+      printf ("*** to remove the old version of GLIB. You may also be able to fix the error\n");
+      printf("*** by modifying your LD_LIBRARY_PATH enviroment variable, or by editing\n");
+      printf("*** /etc/ld.so.conf. Make sure you have run ldconfig if that is\n");
+      printf("*** required on your system.\n");
+      printf("*** If glib-config was wrong, set the environment variable GLIB_CONFIG\n");
+      printf("*** to point to the correct copy of glib-config, and remove the file config.cache\n");
+      printf("*** before re-running configure\n");
+    } 
+  else if ((glib_major_version != GLIB_MAJOR_VERSION) ||
+	   (glib_minor_version != GLIB_MINOR_VERSION) ||
+           (glib_micro_version != GLIB_MICRO_VERSION))
+    {
+      printf("*** GLIB header files (version %d.%d.%d) do not match\n",
+	     GLIB_MAJOR_VERSION, GLIB_MINOR_VERSION, GLIB_MICRO_VERSION);
+      printf("*** library (version %d.%d.%d)\n",
+	     glib_major_version, glib_minor_version, glib_micro_version);
+    }
+  else
+    {
+      if ((glib_major_version > major) ||
+        ((glib_major_version == major) && (glib_minor_version > minor)) ||
+        ((glib_major_version == major) && (glib_minor_version == minor) && (glib_micro_version >= micro)))
+      {
+        return 0;
+       }
+     else
+      {
+        printf("\n*** An old version of GLIB (%d.%d.%d) was found.\n",
+               glib_major_version, glib_minor_version, glib_micro_version);
+        printf("*** You need a version of GLIB newer than %d.%d.%d. The latest version of\n",
+	       major, minor, micro);
+        printf("*** GLIB is always available from ftp://ftp.gtk.org.\n");
+        printf("***\n");
+        printf("*** If you have already installed a sufficiently new version, this error\n");
+        printf("*** probably means that the wrong copy of the glib-config shell script is\n");
+        printf("*** being found. The easiest way to fix this is to remove the old version\n");
+        printf("*** of GLIB, but you can also set the GLIB_CONFIG environment to point to the\n");
+        printf("*** correct copy of glib-config. (In this case, you will have to\n");
+        printf("*** modify your LD_LIBRARY_PATH enviroment variable, or edit /etc/ld.so.conf\n");
+        printf("*** so that the correct libraries are found at run-time))\n");
+      }
+    }
+  return 1;
+}
+],, no_glib=yes,[echo $ac_n "cross compiling; assumed OK... $ac_c"])
+       CFLAGS="$ac_save_CFLAGS"
+       LIBS="$ac_save_LIBS"
+     fi
+  fi
+  if test "x$no_glib" = x ; then
+     AC_MSG_RESULT(yes)
+     ifelse([$2], , :, [$2])     
+  else
+     AC_MSG_RESULT(no)
+     if test "$GLIB_CONFIG" = "no" ; then
+       echo "*** The glib-config script installed by GLIB could not be found"
+       echo "*** If GLIB was installed in PREFIX, make sure PREFIX/bin is in"
+       echo "*** your path, or set the GLIB_CONFIG environment variable to the"
+       echo "*** full path to glib-config."
+     else
+       if test -f conf.glibtest ; then
+        :
+       else
+          echo "*** Could not run GLIB test program, checking why..."
+          CFLAGS="$CFLAGS $GLIB_CFLAGS"
+          LIBS="$LIBS $GLIB_LIBS"
+          AC_TRY_LINK([
+#include <glib.h>
+#include <stdio.h>
+],      [ return ((glib_major_version) || (glib_minor_version) || (glib_micro_version)); ],
+        [ echo "*** The test program compiled, but did not run. This usually means"
+          echo "*** that the run-time linker is not finding GLIB or finding the wrong"
+          echo "*** version of GLIB. If it is not finding GLIB, you'll need to set your"
+          echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point"
+          echo "*** to the installed location  Also, make sure you have run ldconfig if that"
+          echo "*** is required on your system"
+	  echo "***"
+          echo "*** If you have an old version installed, it is best to remove it, although"
+          echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH"
+          echo "***"
+          echo "*** If you have a RedHat 5.0 system, you should remove the GTK package that"
+          echo "*** came with the system with the command"
+          echo "***"
+          echo "***    rpm --erase --nodeps gtk gtk-devel" ],
+        [ echo "*** The test program failed to compile or link. See the file config.log for the"
+          echo "*** exact error that occured. This usually means GLIB was incorrectly installed"
+          echo "*** or that you have moved GLIB since it was installed. In the latter case, you"
+          echo "*** may want to edit the glib-config script: $GLIB_CONFIG" ])
+          CFLAGS="$ac_save_CFLAGS"
+          LIBS="$ac_save_LIBS"
+       fi
+     fi
+     GLIB_CFLAGS=""
+     GLIB_LIBS=""
+     ifelse([$3], , :, [$3])
+  fi
+  AC_SUBST(GLIB_CFLAGS)
+  AC_SUBST(GLIB_LIBS)
+  rm -f conf.glibtest
+])
diff --git a/sci-chemistry/coot/files/gtk.m4 b/sci-chemistry/coot/files/gtk.m4
new file mode 100644
index 000000000..beb1859e3
--- /dev/null
+++ b/sci-chemistry/coot/files/gtk.m4
@@ -0,0 +1,199 @@
+# Configure paths for GTK+
+# Owen Taylor     97-11-3
+AC_DEFUN([GTK_AC_DIVERT_BEFORE_HELP],
+[ifdef([m4_divert_text], [m4_divert_text([NOTICE],[$1])],
+       [ifdef([AC_DIVERT], [AC_DIVERT([NOTICE],[$1])],
+              [AC_DIVERT_PUSH(AC_DIVERSION_NOTICE)dnl
+$1
+AC_DIVERT_POP()])])])
+dnl AM_PATH_GTK([MINIMUM-VERSION, [ACTION-IF-FOUND [, ACTION-IF-NOT-FOUND [, MODULES]]]])
+dnl Test for GTK, and define GTK_CFLAGS and GTK_LIBS
+dnl
+AC_DEFUN([AM_PATH_GTK],
+[dnl 
+dnl Get the cflags and libraries from the gtk-config script
+dnl
+AC_ARG_WITH(gtk-prefix,[  --with-gtk-prefix=PFX   Prefix where GTK is installed (optional)],
+            gtk_config_prefix="$withval", gtk_config_prefix="")
+AC_ARG_WITH(gtk-exec-prefix,[  --with-gtk-exec-prefix=PFX Exec prefix where GTK is installed (optional)],
+            gtk_config_exec_prefix="$withval", gtk_config_exec_prefix="")
+AC_ARG_ENABLE(gtktest, [  --disable-gtktest       Do not try to compile and run a test GTK program],
+		    , enable_gtktest=yes)
+
+  for module in . $4
+  do
+      case "$module" in
+         gthread) 
+             gtk_config_args="$gtk_config_args gthread"
+         ;;
+      esac
+  done
+
+  if test x$gtk_config_exec_prefix != x ; then
+     gtk_config_args="$gtk_config_args --exec-prefix=$gtk_config_exec_prefix"
+     if test x${GTK_CONFIG+set} != xset ; then
+        GTK_CONFIG=$gtk_config_exec_prefix/bin/gtk-config
+     fi
+  fi
+  if test x$gtk_config_prefix != x ; then
+     gtk_config_args="$gtk_config_args --prefix=$gtk_config_prefix"
+     if test x${GTK_CONFIG+set} != xset ; then
+        GTK_CONFIG=$gtk_config_prefix/bin/gtk-config
+     fi
+  fi
+
+  AC_PATH_PROG(GTK_CONFIG, gtk-config, no)
+  min_gtk_version=ifelse([$1], ,0.99.7,$1)
+  AC_MSG_CHECKING(for GTK - version >= $min_gtk_version)
+  no_gtk=""
+  if test "$GTK_CONFIG" = "no" ; then
+    no_gtk=yes
+  else
+    GTK_CFLAGS=`$GTK_CONFIG $gtk_config_args --cflags`
+    GTK_LIBS=`$GTK_CONFIG $gtk_config_args --libs`
+    gtk_config_major_version=`$GTK_CONFIG $gtk_config_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\1/'`
+    gtk_config_minor_version=`$GTK_CONFIG $gtk_config_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\2/'`
+    gtk_config_micro_version=`$GTK_CONFIG $gtk_config_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\3/'`
+    if test "x$enable_gtktest" = "xyes" ; then
+      ac_save_CFLAGS="$CFLAGS"
+      ac_save_LIBS="$LIBS"
+      CFLAGS="$CFLAGS $GTK_CFLAGS"
+      LIBS="$GTK_LIBS $LIBS"
+dnl
+dnl Now check if the installed GTK is sufficiently new. (Also sanity
+dnl checks the results of gtk-config to some extent
+dnl
+      rm -f conf.gtktest
+      AC_TRY_RUN([
+#include <gtk/gtk.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+int 
+main ()
+{
+  int major, minor, micro;
+  char *tmp_version;
+
+  system ("touch conf.gtktest");
+
+  /* HP/UX 9 (%@#!) writes to sscanf strings */
+  tmp_version = g_strdup("$min_gtk_version");
+  if (sscanf(tmp_version, "%d.%d.%d", &major, &minor, &micro) != 3) {
+     printf("%s, bad version string\n", "$min_gtk_version");
+     exit(1);
+   }
+
+  if ((gtk_major_version != $gtk_config_major_version) ||
+      (gtk_minor_version != $gtk_config_minor_version) ||
+      (gtk_micro_version != $gtk_config_micro_version))
+    {
+      printf("\n*** 'gtk-config --version' returned %d.%d.%d, but GTK+ (%d.%d.%d)\n", 
+             $gtk_config_major_version, $gtk_config_minor_version, $gtk_config_micro_version,
+             gtk_major_version, gtk_minor_version, gtk_micro_version);
+      printf ("*** was found! If gtk-config was correct, then it is best\n");
+      printf ("*** to remove the old version of GTK+. You may also be able to fix the error\n");
+      printf("*** by modifying your LD_LIBRARY_PATH enviroment variable, or by editing\n");
+      printf("*** /etc/ld.so.conf. Make sure you have run ldconfig if that is\n");
+      printf("*** required on your system.\n");
+      printf("*** If gtk-config was wrong, set the environment variable GTK_CONFIG\n");
+      printf("*** to point to the correct copy of gtk-config, and remove the file config.cache\n");
+      printf("*** before re-running configure\n");
+    } 
+#if defined (GTK_MAJOR_VERSION) && defined (GTK_MINOR_VERSION) && defined (GTK_MICRO_VERSION)
+  else if ((gtk_major_version != GTK_MAJOR_VERSION) ||
+	   (gtk_minor_version != GTK_MINOR_VERSION) ||
+           (gtk_micro_version != GTK_MICRO_VERSION))
+    {
+      printf("*** GTK+ header files (version %d.%d.%d) do not match\n",
+	     GTK_MAJOR_VERSION, GTK_MINOR_VERSION, GTK_MICRO_VERSION);
+      printf("*** library (version %d.%d.%d)\n",
+	     gtk_major_version, gtk_minor_version, gtk_micro_version);
+    }
+#endif /* defined (GTK_MAJOR_VERSION) ... */
+  else
+    {
+      if ((gtk_major_version > major) ||
+        ((gtk_major_version == major) && (gtk_minor_version > minor)) ||
+        ((gtk_major_version == major) && (gtk_minor_version == minor) && (gtk_micro_version >= micro)))
+      {
+        return 0;
+       }
+     else
+      {
+        printf("\n*** An old version of GTK+ (%d.%d.%d) was found.\n",
+               gtk_major_version, gtk_minor_version, gtk_micro_version);
+        printf("*** You need a version of GTK+ newer than %d.%d.%d. The latest version of\n",
+	       major, minor, micro);
+        printf("*** GTK+ is always available from ftp://ftp.gtk.org.\n");
+        printf("***\n");
+        printf("*** If you have already installed a sufficiently new version, this error\n");
+        printf("*** probably means that the wrong copy of the gtk-config shell script is\n");
+        printf("*** being found. The easiest way to fix this is to remove the old version\n");
+        printf("*** of GTK+, but you can also set the GTK_CONFIG environment to point to the\n");
+        printf("*** correct copy of gtk-config. (In this case, you will have to\n");
+        printf("*** modify your LD_LIBRARY_PATH enviroment variable, or edit /etc/ld.so.conf\n");
+        printf("*** so that the correct libraries are found at run-time))\n");
+      }
+    }
+  return 1;
+}
+],, no_gtk=yes,[echo $ac_n "cross compiling; assumed OK... $ac_c"])
+       CFLAGS="$ac_save_CFLAGS"
+       LIBS="$ac_save_LIBS"
+     fi
+  fi
+  if test "x$no_gtk" = x ; then
+     AC_MSG_RESULT(yes)
+     ifelse([$2], , :, [$2])     
+  else
+     AC_MSG_RESULT(no)
+     if test "$GTK_CONFIG" = "no" ; then
+       echo "*** The gtk-config script installed by GTK could not be found"
+       echo "*** If GTK was installed in PREFIX, make sure PREFIX/bin is in"
+       echo "*** your path, or set the GTK_CONFIG environment variable to the"
+       echo "*** full path to gtk-config."
+     else
+       if test -f conf.gtktest ; then
+        :
+       else
+          echo "*** Could not run GTK test program, checking why..."
+          CFLAGS="$CFLAGS $GTK_CFLAGS"
+          LIBS="$LIBS $GTK_LIBS"
+          AC_TRY_LINK([
+#include <gtk/gtk.h>
+#include <stdio.h>
+],      [ return ((gtk_major_version) || (gtk_minor_version) || (gtk_micro_version)); ],
+        [ echo "*** The test program compiled, but did not run. This usually means"
+          echo "*** that the run-time linker is not finding GTK or finding the wrong"
+          echo "*** version of GTK. If it is not finding GTK, you'll need to set your"
+          echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point"
+          echo "*** to the installed location  Also, make sure you have run ldconfig if that"
+          echo "*** is required on your system"
+	  echo "***"
+          echo "*** If you have an old version installed, it is best to remove it, although"
+          echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH"
+          echo "***"
+          echo "*** If you have a RedHat 5.0 system, you should remove the GTK package that"
+          echo "*** came with the system with the command"
+          echo "***"
+          echo "***    rpm --erase --nodeps gtk gtk-devel" ],
+        [ echo "*** The test program failed to compile or link. See the file config.log for the"
+          echo "*** exact error that occured. This usually means GTK was incorrectly installed"
+          echo "*** or that you have moved GTK since it was installed. In the latter case, you"
+          echo "*** may want to edit the gtk-config script: $GTK_CONFIG" ])
+          CFLAGS="$ac_save_CFLAGS"
+          LIBS="$ac_save_LIBS"
+       fi
+     fi
+     GTK_CFLAGS=""
+     GTK_LIBS=""
+     ifelse([$3], , :, [$3])
+  fi
+  AC_SUBST(GTK_CFLAGS)
+  AC_SUBST(GTK_LIBS)
+  rm -f conf.gtktest
+])
diff --git a/sci-chemistry/coot/files/gtkgl.m4 b/sci-chemistry/coot/files/gtkgl.m4
new file mode 100644
index 000000000..5de62525e
--- /dev/null
+++ b/sci-chemistry/coot/files/gtkgl.m4
@@ -0,0 +1,47 @@
+dnl
+dnl AM_PATH_GTKGL([ACTION-IF-FOUND [, ACTION-IF-NOT-FOUND]])
+dnl
+AC_DEFUN([AM_PATH_GTKGL],
+  [
+    AC_REQUIRE([AM_PATH_GTK])
+    
+    AC_ARG_WITH(gtkgl-prefix, [  --with-gtkgl-prefix=DIR prefix where GtkGLArea is installed ])
+    if test -n "${with_gtkgl_pefix}"; then
+      gtkgl__Idir="-I${with_gtkgl_prefix}/include"
+      gtkgl__Ldir="-L${with_gtkgl_prefix}/lib"
+    fi
+    
+    GTKGL_CFLAGS=""
+    GTKGL_LIBS=""
+    
+    AC_LANG_SAVE
+    AC_LANG_C
+    AC_CHECK_LIB(gtkgl, gdk_gl_query,
+      [
+        ac_save_CPPFLAGS="${CPPFLAGS}"
+        CPPFLAGS="${CPPFLAGS} ${GTK_CFLAGS} ${gtkgl__Idir}"
+        AC_CHECK_HEADER(gtkgl/gtkglarea.h,
+          [
+            have_gtkgl=yes
+            GTKGL_CFLAGS="${GTK_CFLAGS} ${gtkgl__Idir}"
+            GTKGL_LIBS="${gtkgl__Ldir} -lgtkgl"
+          ],
+          have_gtkgl=no
+        )
+        CPPGLAGS="${ac_save_CPPFLAGS}"
+      ],
+      have_gtkgl=no,
+      ${gtkgl__Ldir}
+    )
+    AC_LANG_RESTORE
+    
+    if test "X${have_gtkgl}" = Xyes; then
+      ifelse([$1], , :, [$1])
+    else
+      ifelse([$2], , :, [$2])
+    fi
+    
+    AC_SUBST(GTKGL_CFLAGS)
+    AC_SUBST(GTKGL_LIBS)
+  ]
+)
diff --git a/sci-chemistry/coot/files/imlib.m4 b/sci-chemistry/coot/files/imlib.m4
new file mode 100644
index 000000000..cbff0c932
--- /dev/null
+++ b/sci-chemistry/coot/files/imlib.m4
@@ -0,0 +1,301 @@
+# Configure paths for IMLIB
+# Frank Belew     98-8-31
+# stolen from Manish Singh
+# Shamelessly stolen from Owen Taylor
+
+dnl AM_PATH_IMLIB([MINIMUM-VERSION, [ACTION-IF-FOUND [, ACTION-IF-NOT-FOUND]]])
+dnl Test for IMLIB, and define IMLIB_CFLAGS and IMLIB_LIBS
+dnl
+AC_DEFUN(AM_PATH_IMLIB,
+[dnl 
+dnl Get the cflags and libraries from the imlib-config script
+dnl
+AC_ARG_WITH(imlib-prefix,[  --with-imlib-prefix=PFX   Prefix where IMLIB is installed (optional)],
+            imlib_prefix="$withval", imlib_prefix="")
+AC_ARG_WITH(imlib-exec-prefix,[  --with-imlib-exec-prefix=PFX Exec prefix where IMLIB is installed (optional)],
+            imlib_exec_prefix="$withval", imlib_exec_prefix="")
+AC_ARG_ENABLE(imlibtest, [  --disable-imlibtest       Do not try to compile and run a test IMLIB program],
+		    , enable_imlibtest=yes)
+
+  if test x$imlib_exec_prefix != x ; then
+     imlib_args="$imlib_args --exec-prefix=$imlib_exec_prefix"
+     if test x${IMLIB_CONFIG+set} != xset ; then
+        IMLIB_CONFIG=$imlib_exec_prefix/bin/imlib-config
+     fi
+  fi
+  if test x$imlib_prefix != x ; then
+     imlib_args="$imlib_args --prefix=$imlib_prefix"
+     if test x${IMLIB_CONFIG+set} != xset ; then
+        IMLIB_CONFIG=$imlib_prefix/bin/imlib-config
+     fi
+  fi
+
+  AC_PATH_PROG(IMLIB_CONFIG, imlib-config, no)
+  min_imlib_version=ifelse([$1], ,1.8.2,$1)
+  AC_MSG_CHECKING(for IMLIB - version >= $min_imlib_version)
+  no_imlib=""
+  if test "$IMLIB_CONFIG" = "no" ; then
+    no_imlib=yes
+  else
+    IMLIB_CFLAGS=`$IMLIB_CONFIG $imlibconf_args --cflags`
+    IMLIB_LIBS=`$IMLIB_CONFIG $imlibconf_args --libs`
+
+    imlib_major_version=`$IMLIB_CONFIG $imlib_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\1/'`
+    imlib_minor_version=`$IMLIB_CONFIG $imlib_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\2/'`
+    imlib_micro_version=`$IMLIB_CONFIG $imlib_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\3/'`
+    if test "x$enable_imlibtest" = "xyes" ; then
+      ac_save_CFLAGS="$CFLAGS"
+      ac_save_LIBS="$LIBS"
+      CFLAGS="$CFLAGS $IMLIB_CFLAGS"
+      LIBS="$LIBS $IMLIB_LIBS"
+dnl
+dnl Now check if the installed IMLIB is sufficiently new. (Also sanity
+dnl checks the results of imlib-config to some extent
+dnl
+      rm -f conf.imlibtest
+      AC_TRY_RUN([
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <Imlib.h>
+
+char*
+my_strdup (char *str)
+{
+  char *new_str;
+  
+  if (str)
+    {
+      new_str = malloc ((strlen (str) + 1) * sizeof(char));
+      strcpy (new_str, str);
+    }
+  else
+    new_str = NULL;
+  
+  return new_str;
+}
+
+int main ()
+{
+  int major, minor, micro;
+  char *tmp_version;
+
+  system ("touch conf.imlibtest");
+
+  /* HP/UX 9 (%@#!) writes to sscanf strings */
+  tmp_version = my_strdup("$min_imlib_version");
+  if (sscanf(tmp_version, "%d.%d.%d", &major, &minor, &micro) != 3) {
+     printf("%s, bad version string\n", "$min_imlib_version");
+     exit(1);
+   }
+
+    if (($imlib_major_version > major) ||
+        (($imlib_major_version == major) && ($imlib_minor_version > minor)) ||
+	(($imlib_major_version == major) && ($imlib_minor_version == minor) &&
+	($imlib_micro_version >= micro)))
+    {
+      return 0;
+    }
+  else
+    {
+      printf("\n*** 'imlib-config --version' returned %d.%d, but the minimum version\n", $imlib_major_version, $imlib_minor_version);
+      printf("*** of IMLIB required is %d.%d. If imlib-config is correct, then it is\n", major, minor);
+      printf("*** best to upgrade to the required version.\n");
+      printf("*** If imlib-config was wrong, set the environment variable IMLIB_CONFIG\n");
+      printf("*** to point to the correct copy of imlib-config, and remove the file\n");
+      printf("*** config.cache before re-running configure\n");
+      return 1;
+    }
+}
+
+],, no_imlib=yes,[echo $ac_n "cross compiling; assumed OK... $ac_c"])
+       CFLAGS="$ac_save_CFLAGS"
+       LIBS="$ac_save_LIBS"
+     fi
+  fi
+  if test "x$no_imlib" = x ; then
+     AC_MSG_RESULT(yes)
+     ifelse([$2], , :, [$2])     
+  else
+     AC_MSG_RESULT(no)
+     if test "$IMLIB_CONFIG" = "no" ; then
+       echo "*** The imlib-config script installed by IMLIB could not be found"
+       echo "*** If IMLIB was installed in PREFIX, make sure PREFIX/bin is in"
+       echo "*** your path, or set the IMLIB_CONFIG environment variable to the"
+       echo "*** full path to imlib-config."
+     else
+       if test -f conf.imlibtest ; then
+        :
+       else
+          echo "*** Could not run IMLIB test program, checking why..."
+          CFLAGS="$CFLAGS $IMLIB_CFLAGS"
+          LIBS="$LIBS $IMLIB_LIBS"
+          AC_TRY_LINK([
+#include <stdio.h>
+#include <Imlib.h>
+],      [ return 0; ],
+        [ echo "*** The test program compiled, but did not run. This usually means"
+          echo "*** that the run-time linker is not finding IMLIB or finding the wrong"
+          echo "*** version of IMLIB. If it is not finding IMLIB, you'll need to set your"
+          echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point"
+          echo "*** to the installed location  Also, make sure you have run ldconfig if that"
+          echo "*** is required on your system"
+	  echo "***"
+          echo "*** If you have an old version installed, it is best to remove it, although"
+          echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH"],
+        [ echo "*** The test program failed to compile or link. See the file config.log for the"
+          echo "*** exact error that occured. This usually means IMLIB was incorrectly installed"
+          echo "*** or that you have moved IMLIB since it was installed. In the latter case, you"
+          echo "*** may want to edit the imlib-config script: $IMLIB_CONFIG" ])
+          CFLAGS="$ac_save_CFLAGS"
+          LIBS="$ac_save_LIBS"
+       fi
+     fi
+     IMLIB_CFLAGS=""
+     IMLIB_LIBS=""
+     ifelse([$3], , :, [$3])
+  fi
+  AC_SUBST(IMLIB_CFLAGS)
+  AC_SUBST(IMLIB_LIBS)
+  rm -f conf.imlibtest
+])
+
+# Check for gdk-imlib
+AC_DEFUN(AM_PATH_GDK_IMLIB,
+[dnl 
+dnl Get the cflags and libraries from the imlib-config script
+dnl
+AC_ARG_WITH(imlib-prefix,[  --with-imlib-prefix=PFX   Prefix where IMLIB is installed (optional)],
+            imlib_prefix="$withval", imlib_prefix="")
+AC_ARG_WITH(imlib-exec-prefix,[  --with-imlib-exec-prefix=PFX Exec prefix where IMLIB is installed (optional)],
+            imlib_exec_prefix="$withval", imlib_exec_prefix="")
+AC_ARG_ENABLE(imlibtest, [  --disable-imlibtest       Do not try to compile and run a test IMLIB program],
+		    , enable_imlibtest=yes)
+
+  if test x$imlib_exec_prefix != x ; then
+     imlib_args="$imlib_args --exec-prefix=$imlib_exec_prefix"
+     if test x${IMLIB_CONFIG+set} != xset ; then
+        IMLIB_CONFIG=$imlib_exec_prefix/bin/imlib-config
+     fi
+  fi
+  if test x$imlib_prefix != x ; then
+     imlib_args="$imlib_args --prefix=$imlib_prefix"
+     if test x${IMLIB_CONFIG+set} != xset ; then
+        IMLIB_CONFIG=$imlib_prefix/bin/imlib-config
+     fi
+  fi
+
+  AC_PATH_PROG(IMLIB_CONFIG, imlib-config, no)
+  min_imlib_version=ifelse([$1], ,1.8.2,$1)
+  AC_MSG_CHECKING(for IMLIB - version >= $min_imlib_version)
+  no_imlib=""
+  if test "$IMLIB_CONFIG" = "no" ; then
+    no_imlib=yes
+  else
+    GDK_IMLIB_CFLAGS=`$IMLIB_CONFIG $imlibconf_args --cflags-gdk`
+    GDK_IMLIB_LIBS=`$IMLIB_CONFIG $imlibconf_args --libs-gdk`
+
+    imlib_major_version=`$IMLIB_CONFIG $imlib_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\1/'`
+    imlib_minor_version=`$IMLIB_CONFIG $imlib_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\2/'`
+    if test "x$enable_imlibtest" = "xyes" ; then
+      ac_save_CFLAGS="$CFLAGS"
+      ac_save_LIBS="$LIBS"
+      CFLAGS="$CFLAGS $GDK_IMLIB_CFLAGS"
+      LIBS="$LIBS $GDK_IMLIB_LIBS"
+dnl
+dnl Now check if the installed IMLIB is sufficiently new. (Also sanity
+dnl checks the results of imlib-config to some extent
+dnl
+      rm -f conf.imlibtest
+      AC_TRY_RUN([
+#include <stdio.h>
+#include <stdlib.h>
+#include <gdk_imlib.h>
+
+int main ()
+{
+  int major, minor;
+  char *tmp_version;
+
+  system ("touch conf.gdkimlibtest");
+
+  /* HP/UX 9 (%@#!) writes to sscanf strings */
+  tmp_version = g_strdup("$min_imlib_version");
+  if (sscanf(tmp_version, "%d.%d", &major, &minor) != 2) {
+     printf("%s, bad version string\n", "$min_imlib_version");
+     exit(1);
+   }
+
+    if (($imlib_major_version > major) ||
+        (($imlib_major_version == major) && ($imlib_minor_version >= minor)))
+    {
+      return 0;
+    }
+  else
+    {
+      printf("\n*** 'imlib-config --version' returned %d.%d, but the minimum version\n", $imlib_major_version, $imlib_minor_version);
+      printf("*** of IMLIB required is %d.%d. If imlib-config is correct, then it is\n", major, minor);
+      printf("*** best to upgrade to the required version.\n");
+      printf("*** If imlib-config was wrong, set the environment variable IMLIB_CONFIG\n");
+      printf("*** to point to the correct copy of imlib-config, and remove the file\n");
+      printf("*** config.cache before re-running configure\n");
+      return 1;
+    }
+}
+
+],, no_imlib=yes,[echo $ac_n "cross compiling; assumed OK... $ac_c"])
+       CFLAGS="$ac_save_CFLAGS"
+       LIBS="$ac_save_LIBS"
+     fi
+  fi
+  if test "x$no_imlib" = x ; then
+     AC_MSG_RESULT(yes)
+     ifelse([$2], , :, [$2])     
+  else
+     AC_MSG_RESULT(no)
+     if test "$IMLIB_CONFIG" = "no" ; then
+       echo "*** The imlib-config script installed by IMLIB could not be found"
+       echo "*** If IMLIB was installed in PREFIX, make sure PREFIX/bin is in"
+       echo "*** your path, or set the IMLIB_CONFIG environment variable to the"
+       echo "*** full path to imlib-config."
+     else
+       if test -f conf.gdkimlibtest ; then
+        :
+       else
+          echo "*** Could not run IMLIB test program, checking why..."
+          CFLAGS="$CFLAGS $GDK_IMLIB_CFLAGS"
+          LIBS="$LIBS $GDK_IMLIB_LIBS"
+          AC_TRY_LINK([
+#include <stdio.h>
+#include <gdk_imlib.h>
+],      [ return 0; ],
+        [ echo "*** The test program compiled, but did not run. This usually means"
+          echo "*** that the run-time linker is not finding IMLIB or finding the wrong"
+          echo "*** version of IMLIB. If it is not finding IMLIB, you'll need to set your"
+          echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point"
+          echo "*** to the installed location  Also, make sure you have run ldconfig if that"
+          echo "*** is required on your system"
+	  echo "***"
+          echo "*** If you have an old version installed, it is best to remove it, although"
+          echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH"],
+        [ echo "*** The test program failed to compile or link. See the file config.log for the"
+          echo "*** exact error that occured. This usually means IMLIB was incorrectly installed"
+          echo "*** or that you have moved IMLIB since it was installed. In the latter case, you"
+          echo "*** may want to edit the imlib-config script: $IMLIB_CONFIG" ])
+          CFLAGS="$ac_save_CFLAGS"
+          LIBS="$ac_save_LIBS"
+       fi
+     fi
+     IMLIB_CFLAGS=""
+     IMLIB_LIBS=""
+     ifelse([$3], , :, [$3])
+  fi
+  AC_SUBST(GDK_IMLIB_CFLAGS)
+  AC_SUBST(GDK_IMLIB_LIBS)
+  rm -f conf.gdkimlibtest
+])
diff --git a/sci-chemistry/coot/files/link-against-guile-gtk-properly.patch b/sci-chemistry/coot/files/link-against-guile-gtk-properly.patch
new file mode 100644
index 000000000..e30a0d4c9
--- /dev/null
+++ b/sci-chemistry/coot/files/link-against-guile-gtk-properly.patch
@@ -0,0 +1,15 @@
+diff -ur coot-0.4-pre-1.orig/macros/guile-gtk.m4 coot-0.4-pre-1/macros/guile-gtk.m4
+--- coot-0.4-pre-1.orig/macros/guile-gtk.m4	2007-11-07 18:25:15.000000000 -0800
++++ coot-0.4-pre-1/macros/guile-gtk.m4	2007-11-07 18:25:20.000000000 -0800
+@@ -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$guile_gtk_prefix/lib -lguilegtk-2.1"
+    else 
+-	GUILE_GTK_LIBS=$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"