HOMEPAGE corrected bug 285068

bumped prerelease to r2312 which will be the version of the second
prerelease
Included src_test in prerelease

8 files changed, 440 insertions, 366 deletions

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 58741a151..302d21af8 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,17 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*coot-0.6_pre1-r2312 (16 Sep 2009)
+
+  16 Sep 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  files/0.6_pre1-as-needed.patch, -coot-0.6_pre1-r2042.ebuild,
+  files/0.6_pre1-gcc4.4.patch, +coot-0.6_pre1-r2312.ebuild,
+  +files/0.6_pre1-test-rama.patch, coot-0.5.2.ebuild, coot-9999.ebuild:
+  HOMEPAGE corrected bug 285068
+  bumped prerelease to r2312 which will be the version of the second
+  prerelease
+  Included src_test in prerelease
+
   13 Sep 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
   files/9999-test-rama.patch, coot-9999.ebuild:
   src_test is working now (rev. 2296)
diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index 7524d3252..9b139a86c 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -1,8 +1,9 @@
 AUX 0.5.2-as-needed.patch 19562 RMD160 7c242801251cbd11a8143df793a832a860c5aacb SHA1 a7d6552e5a3bbdf4e28ac995a31b3c3059241dab SHA256 9f5be12beb7691eb1e187923b95edc5890e385fecb2ef2ecb5eb9991858bebc1
 AUX 0.5.2-gcc-4.3.patch 260 RMD160 e6d72c24d7dc02e84c67198f3e82aa4215df9b77 SHA1 1dd99a49d35181808a9e30a1f41ab63b6077dda0 SHA256 2d215b8009449e2f234eeb6c1e08da1f2e7804fedcf5e1d69997a6d8355d37da
 AUX 0.5.2-gcc-4.4.patch 257 RMD160 d1ec251cda36ac201a8baa84d7dad542e72e0c7b SHA1 069af29c1de34e6af94ff463ca04e3fb3c19c209 SHA256 761db5b8cb4cc11050b833df1f87b9ea5d9ca8b3637d7e7b1f5b4f6b7d795177
-AUX 0.6_pre1-as-needed.patch 19465 RMD160 7bb47b98e929f7219cbe82d415dd94d27369ecdb SHA1 76aec121e7f3454cd38d5e3a1fb87126e15537f6 SHA256 d374ae451805701c08c9872e7a73f51062e75ae61cbf5cee6af2d9a6f64232d0
-AUX 0.6_pre1-gcc4.4.patch 257 RMD160 d1ec251cda36ac201a8baa84d7dad542e72e0c7b SHA1 069af29c1de34e6af94ff463ca04e3fb3c19c209 SHA256 761db5b8cb4cc11050b833df1f87b9ea5d9ca8b3637d7e7b1f5b4f6b7d795177
+AUX 0.6_pre1-as-needed.patch 18539 RMD160 2596dac3eb33e1704f84a11613fdc52c42fe8765 SHA1 b6d932312e38d7822866df6449226d90ea1c38c3 SHA256 1646003be0db635ff9b9ef7726adb06f4da8de8a4dbe77baa5074ec8a2faa68a
+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-check-include.patch 833 RMD160 7b877f8973b06119779518b433b607665930a382 SHA1 c8a0c80d3a3f5e85592c9925b35c6d5462fc36ad SHA256 98a6c8ef47953501e360b1bdd568ac99d5a53749738d940939e9f6a47cf85cd1
 AUX 9999-gcc4.4.patch 299 RMD160 75374bd38981d4383d926a3b6529ef955a18e893 SHA1 e05d1caeb3dd13d101d417e7f2613402b6712005 SHA256 02c18e695086d70152b923af5d0aecd334bc18f1b6b955d3133c2ae7b6f218af
@@ -14,10 +15,10 @@ AUX gtkgl.m4 1137 RMD160 9f9712aeaa4efaf07a8c1c483abd4098ac823ef7 SHA1 f7bb50edc
 AUX imlib.m4 11371 RMD160 4470d0cf2d0f8298bea6565069acda8a44e1cd9d SHA1 c983c372cb6cca546bb3fd739f68199a94a741c8 SHA256 04fcea84564608fff1b8049170f4dd571e9b30723c29c46e31855fab26b84a91
 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-2042.tar.gz 10888679 RMD160 25fa2990351b13fb94d1a070d6310c1e0191ce2f SHA1 f21a24f55c0e99ba12b9cacf7e7e1908a9f3a7ab SHA256 bef648ac407b900af3383f63a138ddbdff96695542633b1ed88b5947e38a03e5
-DIST greg-data.tar.gz 7853712 RMD160 2e2ffbe882411345187115111c31fa55d75b7082 SHA1 29a6b99c44eaf32a05f0a7c79599a95116472035 SHA256 733ddb40a1083792b60bf916524dcea0dc315cb7cb4864720564c51afb24c171
-EBUILD coot-0.5.2.ebuild 3234 RMD160 61dd2c58155350889e8120b0f7fe9361daf3aa7b SHA1 0ee99faaafc1c349569fb71342c8269732430c30 SHA256 b6a5ff0fdee3afa51befde1849cbb55bc9212067e43b88a37b3b82f9cbb10edf
-EBUILD coot-0.6_pre1-r2042.ebuild 2901 RMD160 f822c42328b42dcf6a07f5ee08809d9f6e237853 SHA1 76779628a94b71d90c824ace661c22715b15075b SHA256 5ca5ea32aca7f754fa8ef8aacf3fb80eaed06545036a64f67ac4f60e0987b1da
-EBUILD coot-9999.ebuild 4511 RMD160 8d672d885a26998e0e8be74acad99e2da945e280 SHA1 d6f0263105e9b82d68b16e918f635f86b6e4d4ce SHA256 992e8efaa0e4989beb875fa6da39a7e0dc106efebf39f5ccb4e544f83eb0dffa
-MISC ChangeLog 5456 RMD160 39121e6e8ab037f473ad41025a66202b03f2b647 SHA1 c6a7025b903806f3befbaa67b27d72e6feecc45d SHA256 615727258ba1ea95e83a895bc4dc15b0c1eca3ecef5dfb763dae164e3c6ba1ac
+DIST coot-0.6-pre-1-revision-2312.tar.gz 11014498 RMD160 d509629d4a4aaa042699b255270d02f19af5c1e7 SHA1 4502d18aa14eb1f0f2725e877b7ddfab8a145efd SHA256 9ac5076502c1cb0a45e3dd6c59ef9f39e2732bdfca5441bf59f0af398ca1be85
+DIST greg-data.tar.gz 7853709 RMD160 a2a78ab380eec094eec3e9132466033942b92463 SHA1 3af3eebc3d08b20ff71235c9fe6b0d5fabc04984 SHA256 335eeac63489f51c4939feed14545e0246ccee0df8a7ea153bd65a7bd26889ba
+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 4302 RMD160 750af92cdc476479443b4fef4c3b3ee1b99b450f SHA1 ddef0fab3025b39cd706ffb6249b39dd83c10349 SHA256 b373954286b3804acdb97b3f09a6c1f43210b8da4cba674dba6fad4106af7211
+MISC ChangeLog 5893 RMD160 31b798f5a2f269a81f4f7c3ea623ff6a2b35d79e SHA1 fe0fa8952d84a428445c805854b314c0f1c9a9f7 SHA256 30d6ff5bc1c407f78231e792f2abd581d093bbd448878dfd2a9c6aaff13e17ca
 MISC metadata.xml 316 RMD160 845cc100ac244efa5f02595717b5da635f87d2f1 SHA1 c870d2c52c44dee3bab8623e5b6095266f400813 SHA256 64f6dbcd3bb41b26fd7897089cd60ddb93f1ea7d75f9531bca94f28b07e21b2f
diff --git a/sci-chemistry/coot/coot-0.5.2.ebuild b/sci-chemistry/coot/coot-0.5.2.ebuild
index 5878affef..3761537bc 100644
--- a/sci-chemistry/coot/coot-0.5.2.ebuild
+++ b/sci-chemistry/coot/coot-0.5.2.ebuild
@@ -10,11 +10,11 @@ MY_PV=${PV}
 MY_P=${PN}-${MY_PV}
 
 DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~emsley/coot/"
+HOMEPAGE="http://www.biop.ox.ac.uk/coot/"
 if [[ ${MY_PV} = *pre* ]]; then
-	SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/pre-release/${MY_S_P}.tar.gz"
+	SRC_URI="http://www.biop.ox.ac.uk/coot/software/source/pre-releases/${MY_S_P}.tar.gz"
 else
-	SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/${MY_P}.tar.gz"
+	SRC_URI="http://www.biop.ox.ac.uk/coot/software/source/releases/${MY_P}.tar.gz"
 fi
 LICENSE="GPL-3"
 SLOT="0"
diff --git a/sci-chemistry/coot/coot-0.6_pre1-r2042.ebuild b/sci-chemistry/coot/coot-0.6_pre1-r2312.ebuild
index cd9d4026f..74c9e9792 100644
--- a/sci-chemistry/coot/coot-0.6_pre1-r2042.ebuild
+++ b/sci-chemistry/coot/coot-0.6_pre1-r2312.ebuild
@@ -13,48 +13,61 @@ MY_PV=${PV}
 MY_P=${PN}-${MY_PV}
 
 DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~emsley/coot/"
+HOMEPAGE="http://www.biop.ox.ac.uk/coot/"
 if [[ ${MY_PV} = *pre* ]]; then
-	SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/pre-release/${MY_S_P}.tar.gz"
+	SRC_URI="http://www.biop.ox.ac.uk/coot/software/source/pre-releases/${MY_S_P}.tar.gz"
 else
-	SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/${MY_P}.tar.gz"
+	SRC_URI="http://www.biop.ox.ac.uk/coot/software/source/releases/${MY_P}.tar.gz"
 fi
+SRC_URI="
+	${SRC_URI}
+	test? ( http://www.biop.ox.ac.uk/coot/devel/greg-data.tar.gz  )"
 
 SLOT="0"
 LICENSE="GPL-3"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
+IUSE="test"
 
-RDEPEND="x11-libs/gtkglext
-	virtual/glut
-	dev-lang/python
-	>=x11-libs/gtk+-2.2
+SCIDEPS="
+	>=sci-libs/ccp4-libs-6.1
+	>=sci-libs/clipper-20090520
+	>=sci-libs/coot-data-2
+	>=sci-libs/gsl-1.3
+	sci-chemistry/reduce
+	sci-chemistry/refmac
+	sci-chemistry/probe"
+
+XDEPS="
 	gnome-base/libgnomecanvas
-	dev-python/pygtk
 	gnome-base/librsvg
-	=x11-libs/guile-gtk-2.1
-	dev-scheme/guile-gui
+	virtual/glut
+	>=x11-libs/gtk+-2.2
+	x11-libs/gtkglext"
+
+SCHEMEDEPS="
 	dev-scheme/net-http
 	dev-scheme/goosh
-	dev-scheme/guile-www
+	dev-scheme/guile-gui
 	>=dev-scheme/guile-lib-0.1.6
-	>=sci-libs/gsl-1.3
-	sci-libs/coot-data
-	sci-chemistry/reduce
-	sci-chemistry/refmac
-	sci-chemistry/probe
-	>=sci-libs/ccp4-libs-6.1
-	>=sci-libs/clipper-20090210
+	dev-scheme/guile-www
+	=x11-libs/guile-gtk-2.1"
+
+RDEPEND="
+	${SCIDEPS}
+	${XDEPS}
+	${SCHEMEDEPS}
+	dev-python/pygtk
 	>=dev-libs/gmp-4.2.2-r2"
 DEPEND="${RDEPEND}
-	dev-lang/swig"
+	dev-lang/swig
+	test? ( dev-scheme/greg )"
 
 #S="${WORKDIR}/${MY_P}"
 S="${WORKDIR}/${MY_S2_P}"
 
 PATCHES=(
 	"${FILESDIR}"/${PV}-as-needed.patch
-	"${FILESDIR}"/${PV}-gcc4.4.patch
+	"${FILESDIR}"/${PV}-test-rama.patch
 	"${FILESDIR}"/link-against-guile-gtk-properly.patch
 	"${FILESDIR}"/fix-namespace-error.patch
 	)
@@ -89,6 +102,7 @@ src_configure() {
 		--with-clipper-prefix=/usr \
 		--with-mmdb-prefix=/usr \
 		--with-ssmlib-prefix=/usr \
+		--with-gtkgl-prefix=/usr \
 		--with-guile \
 		--with-python=/usr \
 		--with-guile-gtk \
@@ -110,12 +124,55 @@ src_compile() {
 	popd
 
 	emake || die "emake failed"
-}
 
-src_install() {
-	base_src_install
+	cp "${S}"/src/coot.py python/
+}
 
-	# Install misses this
-	insinto /usr/share/coot/python
-	doins "${S}"/src/coot.py
+src_test() {
+#	emake check || die
+
+	ln -sf ../data "${S}"/data
+
+	mkdir "${T}"/coot_test
+
+	export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
+	export COOT_SCHEME_DIR="${S}/scheme/"
+	export COOT_RESOURCES_FILE="${S}/cootrc"
+	export COOT_PIXMAPS_DIR="${S}/pixmaps"
+	export COOT_DATA_DIR="${S}"
+	export COOT_PYTHON_DIR="${S}/python"
+	export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
+	export PYTHONHOME=/usr
+	export CCP4_SCR="${T}"/coot_test
+
+	export TESTROOT="${S}"
+
+	cat > command-line-greg.scm <<- EOF
+	(use-modules (ice-9 greg))
+		(set! greg-tools (list "greg-tests"))
+			(set! greg-debug #t)
+			(set! greg-verbose 5)
+			(let ((r (greg-test-run)))
+				(if r
+				(coot-real-exit 0)
+				(coot-real-exit 1)))
+	EOF
+
+	sed \
+		-e "s:HOME:TESTROOT:g" \
+		-i greg-tests/begin.grg \
+		|| die
+
+	einfo "Running test with following paths ..."
+	einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES"
+	einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR"
+	einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE"
+	einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR"
+	einfo "COOT_DATA_DIR $COOT_DATA_DIR"
+	einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR"
+	einfo "PYTHONPATH $PYTHONPATH"
+	einfo "PYTHONHOME $PYTHONHOME"
+	einfo "CCP4_SCR ${CCP4_SCR}"
+
+	"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
 }
diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index ce9c2f002..3e70a7e7a 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -15,12 +15,7 @@ MY_P=${PN}-${MY_PV}
 ESVN_REPO_URI="http://coot.googlecode.com/svn/trunk"
 
 DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~emsley/coot/"
-#if [[ ${MY_PV} = *pre* ]]; then
-#	SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/pre-release/${MY_S_P}.tar.gz"
-#else
-#	SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/${MY_P}.tar.gz"
-#fi
+HOMEPAGE="http://www.biop.ox.ac.uk/coot/"
 SRC_URI="test? ( http://www.biop.ox.ac.uk/coot/devel/greg-data.tar.gz )"
 
 SLOT="0"
diff --git a/sci-chemistry/coot/files/0.6_pre1-as-needed.patch b/sci-chemistry/coot/files/0.6_pre1-as-needed.patch
index 6d45efac3..0cfce54dd 100644
--- a/sci-chemistry/coot/files/0.6_pre1-as-needed.patch
+++ b/sci-chemistry/coot/files/0.6_pre1-as-needed.patch
@@ -1,210 +1,202 @@
-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
+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
  
-@@ -16,7 +17,6 @@
+ 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)
  
- 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 \
+ 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
-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 
++
+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_geometry_la_LIBADD = \
-+      $(top_builddir)/coot-utils/libcoot-utils.la \
-+      $(CLIPPER_LIBS) $(MMDB_LIBS)
++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  \
++	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la
 +
- # libcoot_geometry_la_CXXFLAGS = -g -O1
+ AM_CXXFLAGS = \
+ 	-DPKGDATADIR='"$(pkgdatadir)"' \
+ 	$(COOT_WINDOWS_CFLAGS)
+@@ -68,7 +79,6 @@
  
- noinst_PROGRAMS = test-geometry test-read-components
-@@ -43,12 +47,6 @@
+ 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_read_components_SOURCES = test-read-components.cc test-read-components.hh
+ 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_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_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_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)
+ 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)
  
- 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)
+@@ -143,23 +127,13 @@
  
- 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       \
+ 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       \
--	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-+	$(CLIPPER_LIBS) $(MMDB_LIBS)
+-	$(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)
  
- # add libcoot-map-utils for  the debugging density_around_point function
- with_map_LDADD =  \
-         ./libcoot-ideal.la                                 \
+ findwaters_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)/coot-utils/libcoot-map-utils.la   \
--	$(top_builddir)/coot-utils/libcoot-shelx.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)/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)
+ 	$(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)
  
- 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)
+Index: analysis/Makefile.am
+===================================================================
+--- analysis/Makefile.am	(revision 2293)
++++ analysis/Makefile.am	(working copy)
+@@ -9,6 +9,7 @@
+ 	$(MMDB_CXXFLAGS)
  
- # 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_analysis_la_SOURCES = bfkurt.cc
++libcoot_analysis_la_LIBADD = $(top_builddir)/coot-utils/libcoot-coord-utils.la
  
- 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)
+ bin_PROGRAMS = bfactan
  
- 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 @@
+@@ -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
  
---- 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 @@
+ # 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
@@ -212,7 +204,6 @@ diff -ur skeleton/Makefile.am skeleton/Makefile.am
 +	$(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
  
@@ -223,7 +214,7 @@ diff -ur skeleton/Makefile.am skeleton/Makefile.am
  	$(top_builddir)/db-main/libcoot-db-main.la        \
  	$(top_builddir)/ideal/libcoot-ideal.la            \
  	$(top_builddir)/geometry/libcoot-geometry.la      \
-@@ -53,71 +57,60 @@
+@@ -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 \
@@ -299,152 +290,116 @@ diff -ur skeleton/Makefile.am skeleton/Makefile.am
  
  
  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
+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)
  
-+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 @@
+ 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
  
- 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)
+ 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)
  
- 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)
+ # libcoot_geometry_la_CXXFLAGS = -g -O1
  
- 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)
+@@ -44,12 +47,7 @@
  
-@@ -122,19 +107,10 @@
+ test_read_components_SOURCES = test-read-components.cc test-read-components.hh
  
- 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)
+-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
  
-@@ -146,23 +122,13 @@
+-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 @@
  
- 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    \
+ 
+ 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)/coot-utils/libcoot-shelx.la        \
- 	$(top_builddir)/compat/libcoot-compat.la           \
- 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 	$(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)
  
- findwaters_real_LDADD = \
- 	./libcoot-ligand.la                                \
--	$(top_builddir)/ideal/libcoot-ideal.la             \
+ # 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)/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-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-coord-utils.la  \
  	$(top_builddir)/coot-utils/libcoot-utils.la        \
--	$(top_builddir)/coot-utils/libcoot-shelx.la       \
-         $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+-        $(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)
  
- # 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 @@
+ 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
  
@@ -457,8 +412,59 @@ diff -ur skeleton/Makefile.am skeleton/Makefile.am
  
  
  # 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
+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 
@@ -473,13 +479,3 @@ diff -ur skeleton/Makefile.am skeleton/Makefile.am
  
  # po, no po today.
  
---- coot-utils/Makefile.am.orig	2009-06-07 17:40:00.000000000 -0700
-+++ coot-utils/Makefile.am	2009-06-07 17:39:07.000000000 -0700
-@@ -63,6 +63,7 @@
- 
- # 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
diff --git a/sci-chemistry/coot/files/0.6_pre1-gcc4.4.patch b/sci-chemistry/coot/files/0.6_pre1-gcc4.4.patch
index d754a519c..b7cd75662 100644
--- a/sci-chemistry/coot/files/0.6_pre1-gcc4.4.patch
+++ b/sci-chemistry/coot/files/0.6_pre1-gcc4.4.patch
@@ -1,11 +1,10 @@
---- coot-utils/coot-utils.cc	2008-12-10 01:22:01.000000000 +0100
-+++ coot-utils/coot-utils.cc.new	2009-08-06 00:31:18.000000000 +0200
-@@ -47,7 +47,7 @@
+--- coot-utils/coot-utils.cc	2009-08-06 00:02:51.000000000 +0200
++++ coot-utils/coot-utils.cc.new	2009-08-06 00:06:13.000000000 +0200
+@@ -25,6 +25,7 @@
  
- #include "clipper/core/hkl_compute.h"
- #include "coot-utils.hh"
--
+ #include <stdexcept> // for string_to_int.
+ #include <sstream>   // ditto.
 +#include <cstdio>
  
- 
- std::string
+ #include "coot-sysdep.h"
+ #if defined _MSC_VER
diff --git a/sci-chemistry/coot/files/0.6_pre1-test-rama.patch b/sci-chemistry/coot/files/0.6_pre1-test-rama.patch
new file mode 100644
index 000000000..96bfbf60c
--- /dev/null
+++ b/sci-chemistry/coot/files/0.6_pre1-test-rama.patch
@@ -0,0 +1,15 @@
+--- src/graphics-info.h	(revision 2296)
++++ src/graphics-info.h	(working copy)
+@@ -798,12 +798,10 @@
+       // guess we shall rather use COOT_DATA_DIR and only as fallback PKGDATADIR?!
+       // maybe only for windows!?
+       std::string tables_dir = PKGDATADIR;
+-#ifdef WINDOWS_MINGW
+       char *data_dir = getenv("COOT_DATA_DIR");
+       if (data_dir) {
+ 	tables_dir = data_dir;
+       }
+-#endif // MINGW
+       tables_dir += "/rama-data";
+       rot_prob_tables.set_tables_dir(tables_dir);
+