coot prereleases added

4 files changed, 514 insertions, 12 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
index e66ec971d..2db2ecf84 100644
--- a/sci-chemistry/coot/files/0.5.2-as-needed.patch
+++ b/sci-chemistry/coot/files/0.5.2-as-needed.patch
@@ -1,4 +1,3 @@
-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 @@
@@ -17,7 +16,6 @@ diff -ur coot-0.5-pre-1.orig/analysis/Makefile.am coot-0.5-pre-1/analysis/Makefi
  	$(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 @@
@@ -28,7 +26,6 @@ diff -ur coot-0.5-pre-1.orig/coords/Makefile.am coot-0.5-pre-1/coords/Makefile.a
 +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 @@
@@ -39,7 +36,6 @@ diff -ur coot-0.5-pre-1.orig/cootaneer/Makefile.am coot-0.5-pre-1/cootaneer/Make
  
  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 @@
@@ -47,7 +43,6 @@ diff -ur coot-0.5-pre-1.orig/coot-surface/Makefile.am coot-0.5-pre-1/coot-surfac
  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 @@
@@ -116,7 +111,6 @@ diff -ur coot-0.5-pre-1.orig/coot-utils/Makefile.am coot-0.5-pre-1/coot-utils/Ma
  
 +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 @@
@@ -233,7 +227,6 @@ diff -ur coot-0.5-pre-1.orig/high-res/Makefile.am coot-0.5-pre-1/high-res/Makefi
 -
 +	$(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 @@
@@ -291,7 +284,6 @@ diff -ur coot-0.5-pre-1.orig/ideal/Makefile.am coot-0.5-pre-1/ideal/Makefile.am
  
  # 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 @@
@@ -419,7 +411,6 @@ diff -ur coot-0.5-pre-1.orig/ligand/Makefile.am coot-0.5-pre-1/ligand/Makefile.a
          $(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 @@
@@ -436,7 +427,6 @@ diff -ur coot-0.5-pre-1.orig/Makefile.am coot-0.5-pre-1/Makefile.am
  
  # 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 @@
@@ -452,7 +442,6 @@ diff -ur coot-0.5-pre-1.orig/mini-mol/Makefile.am coot-0.5-pre-1/mini-mol/Makefi
 -	$(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 @@
@@ -464,7 +453,6 @@ diff -ur coot-0.5-pre-1.orig/skeleton/Makefile.am coot-0.5-pre-1/skeleton/Makefi
  
  # 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 @@
diff --git a/sci-chemistry/coot/files/0.6_pre1-as-needed.patch b/sci-chemistry/coot/files/0.6_pre1-as-needed.patch
new file mode 100644
index 000000000..0e12d61b5
--- /dev/null
+++ b/sci-chemistry/coot/files/0.6_pre1-as-needed.patch
@@ -0,0 +1,475 @@
+diff -ur analysis/Makefile.am analysis/Makefile.am
+--- analysis/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ 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 coords/Makefile.am coords/Makefile.am
+--- coords/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ 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 cootaneer/Makefile.am cootaneer/Makefile.am
+--- cootaneer/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ 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-surface/Makefile.am coot-surface/Makefile.am
+--- coot-surface/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ 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-utils/Makefile.am coot-utils/Makefile.am
+--- coot-utils/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ 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)
+ 
+ 
+--- geometry/Makefile.am	2008-09-08 15:22:01.000000000 +0200
++++ 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 ideal/Makefile.am ideal/Makefile.am
+--- ideal/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ 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 mini-mol/Makefile.am mini-mol/Makefile.am
+--- mini-mol/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ 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 skeleton/Makefile.am skeleton/Makefile.am
+--- skeleton/Makefile.am	2008-07-13 16:40:27.000000000 -0700
++++ 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
+ 
+--- high-res/Makefile.am	2009-01-06 20:19:20.000000000 +0100
++++ high-res/Makefile.am.new	2009-06-03 10:13:35.000000000 +0200
+@@ -39,13 +39,17 @@
+ 
+ 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 +57,60 @@
+ 	$(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
+--- ligand/Makefile.am	2009-02-06 00:50:01.000000000 +0100
++++ ligand/Makefile.am.new	2009-06-03 10:29:30.000000000 +0200
+@@ -50,6 +50,18 @@
+ 	torsion-general.cc rotamer-tables.cc primitive-chi-angles.cc dipole.cc\
+         base-pairing.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)
+@@ -69,52 +81,25 @@
+ 
+ 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_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)
+ 
+@@ -122,19 +107,10 @@
+ 
+ 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)
+ 
+@@ -146,23 +122,13 @@
+ 
+ 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       \
+@@ -193,17 +159,8 @@
+ 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
+--- tw/Makefile.am	2007-04-20 16:12:16.000000000 +0200
++++ tw/Makefile.am.new	2009-06-03 10:31:17.000000000 +0200
+@@ -39,14 +39,16 @@
+ 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
+--- Makefile.am	2009-01-06 15:50:23.000000000 +0100
++++ Makefile.am.new	2009-06-03 10:35:59.000000000 +0200
+@@ -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/0.6_pre1-gcc-4.3.patch b/sci-chemistry/coot/files/0.6_pre1-gcc-4.3.patch
new file mode 100644
index 000000000..26377ed9d
--- /dev/null
+++ b/sci-chemistry/coot/files/0.6_pre1-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/0.6_pre1-gtk.patch b/sci-chemistry/coot/files/0.6_pre1-gtk.patch
new file mode 100644
index 000000000..57a5eb346
--- /dev/null
+++ b/sci-chemistry/coot/files/0.6_pre1-gtk.patch
@@ -0,0 +1,29 @@
+#--- src/c-interface-gui.cc	2009-05-26 01:30:03.000000000 +0200
+#+++ src/c-interface-gui.cc.new	2009-06-03 11:14:25.000000000 +0200
+#@@ -74,6 +74,7 @@
+# #include "cmtz-interface.hh"
+# #include "mmdb.h"  // for centre of molecule
+# #include "clipper/core/clipper_instance.h"
+#+#include <gtk/gtk.h>
+# 
+# #if (GTK_MAJOR_VERSION > 2 || (GTK_MAJOR_VERSION == 2 && GTK_MINOR_VERSION > 5))
+# #define HAVE_GTK_COMBO_BOX_GET_ACTIVE_TEXT
+--- src/c-interface-gui.cc	2009-06-03 11:55:35.000000000 +0200
++++ src/c-interface-gui.cc.new	2009-06-03 13:12:19.000000000 +0200
+@@ -5355,11 +5355,12 @@
+ #if (GTK_MAJOR_VERSION > 1)
+ #if (GTK_MAJOR_VERSION > 2) || (GTK_MINOR_VERSION > 14) 
+    for (int i=0; i<5; i++)
+-      gtk_scale_add_mark(GTK_RANGE(h_scale),
++      gtk_scale_add_mark(GTK_SCALE(h_scale),
+ 			 float (i-2) * 0.5 * sharpening_limit,
+-			 GTK_POS_BOTTOM);
+-   gtk_scale_add_mark(GTK_RANGE(h_scale), -sharpening_limit, GTK_POS_BOTTOM, "Blur");
+-   gtk_scale_add_mark(GTK_RANGE(h_scale),  sharpening_limit, GTK_POS_BOTTOM, "Sharp");
++			 GTK_POS_BOTTOM,
++			 "");
++   gtk_scale_add_mark(GTK_SCALE(h_scale), -sharpening_limit, GTK_POS_BOTTOM, "Blur");
++   gtk_scale_add_mark(GTK_SCALE(h_scale),  sharpening_limit, GTK_POS_BOTTOM, "Sharp");
+ #endif   
+ #endif
+