sci-chemistry/coot: Fix for latest HEAD

Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher <jlec@gentoo.org>

6 files changed, 127 insertions, 1087 deletions

diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index 662c585ec..2dca079db 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -1 +1 @@
-DIST greg-data.tar.gz 8142259 SHA256 6f3e1c1bc540c8355583ce2e1807cc9f6a2f7b466384382a843942f96b1d31a1 SHA512 6ce97b72f3f984c0d2dc1eb4a259412761736bfaec23867eba46919b6c6444698dc0b0e717c1a095aa713b2a4726d4229aed5964d89a74f7c1f2aa058f4891bf WHIRLPOOL 65db8c976f481a765e1301526cc7af6939ceb4c1cc26f3c1d5e628512a9c34bc4a10e8380d10ab4773976def9b3e07cf84b2cdc1da821750118c405b2f8b34d4
+DIST greg-data.tar.gz 8677037 SHA256 d936795853406f3c2a3dfd6f37a07a7df677e96b2d023d9302668aa49b7f06cb SHA512 28396a5fa64af61e8932b565c6593ed27c4708e6a59158d62c94005bea9fa8c46562b6caba97011209a40705e5ec6711b949138dd8a23bb954df2ab4dfa9bb33 WHIRLPOOL cb85234ece76314661bcfa424904224ac554c41fc63655857f3ba1bd2f0bf8e457c55dd1f42ffecffb9a8582ff759277b0fb9a40ca2393bf47b6a09fdd04ce1e
diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index 1ea16a346..d6b0be981 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
 
 AUTOTOOLS_AUTORECONF="true"
 
-inherit autotools-utils python-single-r1 subversion toolchain-funcs versionator
+inherit autotools-utils git-r3 python-single-r1 toolchain-funcs versionator
 
 MY_S2_PV=$(replace_version_separator 2 - ${PV})
 MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
@@ -17,9 +17,9 @@ MY_PV=${PV}
 MY_P=${PN}-${MY_PV}
 
 DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
-HOMEPAGE="http://www.biop.ox.ac.uk/coot/"
-SRC_URI="test? ( http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/data/greg-data.tar.gz )"
-ESVN_REPO_URI="http://coot.googlecode.com/svn/trunk"
+HOMEPAGE="https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/"
+SRC_URI="test? ( https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/data/greg-data.tar.gz )"
+EGIT_REPO_URI="https://github.com/pemsley/coot.git"
 
 SLOT="0"
 LICENSE="GPL-3"
@@ -31,25 +31,26 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 AUTOTOOLS_IN_SOURCE_BUILD=1
 
 SCIDEPS="
-	>=sci-libs/ccp4-libs-6.1
+	sci-libs/libccp4
 	sci-libs/clipper
 	>=sci-libs/coot-data-2
 	>=sci-libs/gsl-1.3
-	>=sci-libs/mmdb-1.23
-	sci-libs/ssm
+	sci-libs/fftw:2.1=
+	sci-libs/mmdb:2
 	sci-libs/monomer-db
+	sci-libs/ssm
 	sci-chemistry/reduce
-	sci-chemistry/refmac
 	sci-chemistry/probe"
 
 XDEPS="
 	gnome-base/libgnomecanvas
 	gnome-base/librsvg:2
-	media-libs/libpng
+	media-libs/libpng:0=
 	media-libs/freeglut
 	x11-libs/gtk+:2
 	x11-libs/goocanvas:0
-	x11-libs/gtkglext"
+	x11-libs/gtkglext
+	virtual/opengl"
 
 SCHEMEDEPS="
 	dev-scheme/net-http
@@ -63,18 +64,23 @@ RDEPEND="
 	${XDEPS}
 	${SCHEMEDEPS}
 	${PYTHON_DEPS}
+	dev-db/sqlite:3
+	dev-libs/boost:0=[python,${PYTHON_USEDEP}]
+	dev-libs/glib:2
+	>=dev-libs/gmp-4.2.2-r2:0=
+	dev-python/pygobject:2[${PYTHON_USEDEP}]
 	dev-python/pygtk:2[${PYTHON_USEDEP}]
-	>=dev-libs/gmp-4.2.2-r2
 	>=net-misc/curl-7.19.6
-	net-dns/libidn"
+	net-dns/libidn
+	sys-libs/readline:0=
+	"
 DEPEND="${RDEPEND}
+	virtual/pkgconfig
 	>=sys-devel/libtool-2.4-r2
 	dev-lang/swig
 	sys-devel/bc
 	test? ( dev-scheme/greg )"
 
-S="${WORKDIR}"
-
 pkg_setup() {
 	if use openmp; then
 		tc-has-openmp || die "Please use an OPENMP capable compiler"
@@ -83,53 +89,44 @@ pkg_setup() {
 }
 
 PATCHES=(
-	"${FILESDIR}"/${PV}-pc.patch
+	"${FILESDIR}"/${P}-desktop.patch
 	"${FILESDIR}"/${P}-sandbox-icons.patch
+	"${FILESDIR}"/${P}-libtool.patch
+	"${FILESDIR}"/${P}-libguile.patch
 )
 
 src_unpack() {
-	subversion_src_unpack
+	git-r3_src_unpack
 	if use test; then
+		cd "${S}" || die
 		unpack ${A}
-		ln -sf . "${S}"/coot-ccp4
+		ln -sf . "${S}"/coot-ccp4 || die
 	fi
 }
 
 src_prepare() {
 	sed \
 		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
-		-i configure.in || die
+		-i configure.ac || die
 
 	autotools-utils_src_prepare
-
-	cat >> src/svn-revision.cc <<- EOF
-	extern "C" {
-	int svn_revision() {
-		return  ${ESVN_WC_REVISION:-0};
-	}
-	}
-	EOF
 }
 
 src_configure() {
 	# All the --with's are used to activate various parts.
 	# Yes, this is broken behavior.
 	local myeconfargs=(
-		--includedir='${prefix}/include/coot'
 		--with-goocanvas-prefix="${EPREFIX}/usr"
-		--with-guile
+		--with-guile="${EPREFIX}/usr"
 		--with-python="${EPREFIX}/usr"
 		--with-guile-gtk
-		--with-pygtk
-		$(use_enable openmp)
+		--with-pygtk="${EPREFIX}/usr"
+		--with-sqlite3
+		--with-boost="${EPREFIX}/usr"
 		)
 	autotools-utils_src_configure
 }
 
-src_compile() {
-	autotools-utils_src_compile
-	cp "${S}"/src/coot_gtk2.py python/coot.py || die
-}
 src_test() {
 	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
 	mkdir "${T}"/coot_test || die
@@ -143,10 +140,11 @@ src_test() {
 	export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
 	export PYTHONHOME="${EPREFIX}"/usr/
 	export CCP4_SCR="${T}"/coot_test/
-	export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/"
+	export CLIBD_MON="${EPREFIX}/usr/share/data/monomers/"
+	export COOT_REF_STRUCTS="${EPREFIX}/usr/share/data/monomers/"
 	export SYMINFO="${S}/syminfo.lib"
 
-	export COOT_TEST_DATA_DIR="${S}"/data/greg-data/
+	export COOT_TEST_DATA_DIR="${S}"/greg-data/
 
 	cat > command-line-greg.scm <<- EOF
 	(use-modules (ice-9 greg))
@@ -172,6 +170,6 @@ src_test() {
 	einfo "CLIBD_MON ${CLIBD_MON}"
 	einfo "SYMINFO ${SYMINFO}"
 
-	"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
-	"${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die
+	"${S}"/src/coot-bin --no-graphics --script command-line-greg.scm || die
+	"${S}"/src/coot-bin --no-graphics --script python-tests/coot_unittest.py || die
 }
diff --git a/sci-chemistry/coot/files/9999-pc.patch b/sci-chemistry/coot/files/9999-pc.patch
deleted file mode 100644
index 32d08e119..000000000
--- a/sci-chemistry/coot/files/9999-pc.patch
+++ /dev/null
@@ -1,1047 +0,0 @@
-diff --git a/ChangeLog b/ChangeLog
-index 46f6362..fd3fd9a 100644
---- a/ChangeLog
-+++ b/ChangeLog
-@@ -1963,7 +1963,7 @@
- 2005-01-29  Paul Emsley  <paulemsley@ysbl.york.ac.uk>
- 
- 	* macros/mmdb-ssm.m4 (AM_WITH_MMDBSSM): use $with_ssmlib_prefix in
--	MMDBSSM_CXXFLAGS [Oops].  Hopefully fixes problems spotted by Joel
-+	MMDBSSM_CFLAGS [Oops].  Hopefully fixes problems spotted by Joel
- 	Bard and Joseph Toth.
- 
- 	* src/graphics-info-pick.cc: (symmetry_atom_pick): tried to add
-@@ -2256,14 +2256,14 @@
- 
- 2004-11-20  Paul Emsley  <paulemsley@ysbl.york.ac.uk>
- 
--	* coords/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS [for
-+	* coords/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS [for
- 	coot-close.cc usage].
- 
- 2004-11-19  Paul Emsley  <paulemsley@ysbl.york.ac.uk>
- 
--	* sequence-view/Makefile.am (INCLUDES): added CLIPPER_CXXFLAGS
-+	* sequence-view/Makefile.am (INCLUDES): added CLIPPER_CFLAGS
- 
--	* analysis/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS
-+	* analysis/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS
- 
- 2004-11-16  Paul Emsley  <emsley@localhost>
- 
-@@ -2273,7 +2273,7 @@
-  
- 2004-11-15  Paul Emsley  <emsley@localhost>
- 
--	* coot-utils/Makefile.am: add MMDB_CXXFLAGS to INCLUDE [thanks 
-+	* coot-utils/Makefile.am: add MMDB_CFLAGS to INCLUDE [thanks 
-           Joseph Toth].
- 
- 	* surface/CXXSphereNode.h: removed the ; again!
-diff --git a/analysis/Makefile.am b/analysis/Makefile.am
-index 8a873dc..ef4a9cf 100644
---- a/analysis/Makefile.am
-+++ b/analysis/Makefile.am
-@@ -8,8 +8,8 @@ pkgincludedir = $(includedir)/coot/analysis
- 
- INCLUDES = \
- 	-I$(top_srcdir) \
--	$(CLIPPER_CXXFLAGS)		\
--	$(MMDB_CXXFLAGS)
-+	$(CLIPPER_CFLAGS)		\
-+	$(MMDB_CFLAGS)
- 
- libcoot_analysis_la_SOURCES = bfkurt.cc mogul.cc kolmogorov.hh kolmogorov.cc cablam.hh cablam.cc
- 
-diff --git a/angles/Makefile.am b/angles/Makefile.am
-index b89276d..935ce06 100644
---- a/angles/Makefile.am
-+++ b/angles/Makefile.am
-@@ -7,7 +7,7 @@ EXTRA_DIST = \
- pkginclude_HEADERS = AngleInfo.h ncube.h wrapped-ncube.h
- pkgincludedir = $(includedir)/coot/angles
- 
--INCLUDES = $(CLIPPER_CXXFLAGS)
-+INCLUDES = $(CLIPPER_CFLAGS)
- 
- libcoot_AngleInfo_a_sources = AngleInfo.cc AngleInfo.h  \
- 	AngleInfo-angle-torsions-autogen.cc AngleInfo-theta_2-autogen.cc
-diff --git a/auxil/catcheck/Makefile.am b/auxil/catcheck/Makefile.am
-index 41e1766..69e6091 100644
---- a/auxil/catcheck/Makefile.am
-+++ b/auxil/catcheck/Makefile.am
-@@ -1,7 +1,7 @@
- 
- EXTRA_DIST = Makefile.simple
- 
--INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) 
-+INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) 
- 
- check_PROGRAMS = catcheck
- 
-diff --git a/auxil/catcheck/Makefile.simple b/auxil/catcheck/Makefile.simple
-index 5157398..0e25fb2 100644
---- a/auxil/catcheck/Makefile.simple
-+++ b/auxil/catcheck/Makefile.simple
-@@ -1,17 +1,17 @@
- 
--# CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
-+# CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
- 
- 
- BASE = /home/paule/autobuild/Linux-kalypso-pre-release
--CLIPPER_CXXFLAGS = -I$(BASE)/include
--MMDB_CXXFLAGS = -I$(BASE)/include/mmdb
-+CLIPPER_CFLAGS = -I$(BASE)/include
-+MMDB_CFLAGS = -I$(BASE)/include/mmdb
- 
- CLIPPER_LIBS = -L$(BASE)/lib -lclipper-ccp4 \
- 	-lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
- 	-lclipper-core -lccp4c -L$(BASE)/lib \
- 	-L$(BASE) -lmmdb -lm -lrfftw -lfftw -lz -lm
- 
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
- LDLIBS = $(CLIPPER_LIBS)
- 
- catcheck: catcheck.cc catcheck.hh
-diff --git a/auxil/rama/Makefile.am b/auxil/rama/Makefile.am
-index cdbb54e..12c6731 100644
---- a/auxil/rama/Makefile.am
-+++ b/auxil/rama/Makefile.am
-@@ -1,7 +1,7 @@
- 
- EXTRA_DIST = Makefile.simple fit-rama.scm run.scm test-arr.scm
- 
--INCLUDES =  $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+INCLUDES =  $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
- 
- 
- check_PROGRAMS = rama-data rama-doughnut 
-diff --git a/auxil/rama/Makefile.simple b/auxil/rama/Makefile.simple
-index 10fe22e..715a270 100644
---- a/auxil/rama/Makefile.simple
-+++ b/auxil/rama/Makefile.simple
-@@ -1,12 +1,12 @@
- 
--CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
-+CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
- 
- CLIPPER_LIBS = -L/Users/paulemsley/ccp4/ysbl-distro-based/lib -lclipper-ccp4 \
- 	-lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
- 	-lclipper-core -lccp4c -L/Users/paulemsley/ccp4/ysbl-distro-based/lib \
- 	-L/Users/paulemsley/ccp4/ysbl-distro-based -lmmdb -lm -lrfftw -lfftw -lz -lm
- 
--INCLUDES = $(CLIPPER_CXXFLAGS)
-+INCLUDES = $(CLIPPER_CFLAGS)
- LDLIBS = $(CLIPPER_LIBS)
- 
- rama-data: rama-data.cc
-diff --git a/auxil/sec-str/Makefile.am b/auxil/sec-str/Makefile.am
-index 81f79e8..bfef73a 100644
---- a/auxil/sec-str/Makefile.am
-+++ b/auxil/sec-str/Makefile.am
-@@ -1,6 +1,6 @@
- 
- EXTRA_DIST = Makefile.simple sec-str-dist-check.cc sec-str-dist-check.hh
--INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) 
-+INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) 
- 
- #check_PROGRAMS = sec-str-dist-check
- 
-diff --git a/auxil/sec-str/Makefile.simple b/auxil/sec-str/Makefile.simple
-index eb6db20..8b22930 100644
---- a/auxil/sec-str/Makefile.simple
-+++ b/auxil/sec-str/Makefile.simple
-@@ -1,27 +1,27 @@
- 
--#CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
-+#CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
- 
- #CLIPPER_LIBS = -L/Users/paulemsley/ccp4/ysbl-distro-based/lib -lclipper-ccp4 \
- #	-lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
- #	-lclipper-core -lccp4c -L/Users/paulemsley/ccp4/ysbl-distro-based/lib \
- #	-L/Users/paulemsley/ccp4/ysbl-distro-based -lmmdb -lm -lrfftw -lfftw -lz -lm
- 
--#INCLUDES = $(CLIPPER_CXXFLAGS)
-+#INCLUDES = $(CLIPPER_CFLAGS)
- #LDLIBS = $(CLIPPER_LIBS)
- 
- 
- # 
- 
- BASE = /home/paule/autobuild/Linux-kalypso-pre-release
--CLIPPER_CXXFLAGS = -I$(BASE)/include
--MMDB_CXXFLAGS = -I$(BASE)/include/mmdb
-+CLIPPER_CFLAGS = -I$(BASE)/include
-+MMDB_CFLAGS = -I$(BASE)/include/mmdb
- 
- CLIPPER_LIBS = -L$(BASE)/lib -lclipper-ccp4 \
- 	-lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
- 	-lclipper-core -lccp4c -L$(BASE)/lib \
- 	-L$(BASE) -lmmdb -lm -lrfftw -lfftw -lz -lm
- 
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
- LDLIBS = $(CLIPPER_LIBS)
- 
- sec-str-dist-check: sec-str-dist-check.cc sec-str-dist-check.hh
-diff --git a/auxil/strand-analysis/Makefile.am b/auxil/strand-analysis/Makefile.am
-index 11686ba..9c24b3b 100644
---- a/auxil/strand-analysis/Makefile.am
-+++ b/auxil/strand-analysis/Makefile.am
-@@ -3,8 +3,8 @@ EXTRA_DIST = Makefile.simple strand-analysis.cc
- 
- 
- INCLUDES = -I$(top_srcdir)/auxil/sec-str \
--	$(MMDB_CXXFLAGS) 	         \
--	$(CLIPPER_CXXFLAGS) 		
-+	$(MMDB_CFLAGS) 	         \
-+	$(CLIPPER_CFLAGS) 		
- 
- 
- check_PROGRAMS = 
-diff --git a/auxil/strand-analysis/Makefile.simple b/auxil/strand-analysis/Makefile.simple
-index d5c21a4..2f58b8d 100644
---- a/auxil/strand-analysis/Makefile.simple
-+++ b/auxil/strand-analysis/Makefile.simple
-@@ -2,13 +2,13 @@
- 
- CLIPPER = /Users/paulemsley/ccp4/ysbl-distro-based
- 
--CLIPPER_CXXFLAGS = -I$(CLIPPER)/include
-+CLIPPER_CFLAGS = -I$(CLIPPER)/include
- 
- CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-ccp4 \
- 	-lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
- 	-lclipper-core -lccp4c -lmmdb -lm -lrfftw -lfftw -lz -lm
- 
--INCLUDES = -I../sec-str $(CLIPPER_CXXFLAGS)
-+INCLUDES = -I../sec-str $(CLIPPER_CFLAGS)
- LDLIBS = $(CLIPPER_LIBS)
- 
- .cc:
-diff --git a/auxil/vectors/Makefile.am b/auxil/vectors/Makefile.am
-index 8826587..4a8d72e 100644
---- a/auxil/vectors/Makefile.am
-+++ b/auxil/vectors/Makefile.am
-@@ -1,6 +1,6 @@
- 
- EXTRA_DIST = Makefile.simple diff-vec.cc
--INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
-+INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
- check_PROGRAMS = 
- 
- #diff_vec_SOURCES = diff-vec.cc
-diff --git a/build/Makefile.am b/build/Makefile.am
-index 6afe5a3..748341b 100644
---- a/build/Makefile.am
-+++ b/build/Makefile.am
-@@ -25,8 +25,8 @@ pkgincludedir = $(includedir)/coot/build
- 
- INCLUDES =  \
- 	-I$(top_srcdir) \
--	$(CLIPPER_CXXFLAGS) \
--	$(MMDB_CXXFLAGS)
-+	$(CLIPPER_CFLAGS) \
-+	$(MMDB_CFLAGS)
- 
- noinst_PROGRAMS = testcabuild
- 
-diff --git a/ccp4mg-utils/Makefile.am b/ccp4mg-utils/Makefile.am
-index 7734f09..c58fe1d 100644
---- a/ccp4mg-utils/Makefile.am
-+++ b/ccp4mg-utils/Makefile.am
-@@ -26,7 +26,7 @@ pkgincludedir = $(includedir)/coot/ccp4mg-utils
- EXTRA_DIST = convert.sh get-new-utils.sh
- 
- INCLUDES =  \
--	$(MMDB_CXXFLAGS) \
-+	$(MMDB_CFLAGS) \
- 	$(LIBPNG_CFLAGS)
- 
- libccp4mg_utils_la_SOURCES = geomutil.cc mgtree.cc cartesian.cc \
-diff --git a/ccp4mg-utils/mmut/Makefile.am b/ccp4mg-utils/mmut/Makefile.am
-index d0651db..d4e0bf8 100755
---- a/ccp4mg-utils/mmut/Makefile.am
-+++ b/ccp4mg-utils/mmut/Makefile.am
-@@ -70,9 +70,9 @@ INCLUDES = \
- 	$(LIBGLADE_CFLAGS)		\
- 	@GTK_CFLAGS@ 			\
- 	$(GLUT_CFLAGS)			\
--	$(MMDBSSM_CXXFLAGS) 		\
--	$(MMDB_CXXFLAGS) 		\
--	$(CLIPPER_CXXFLAGS) 		
-+	$(MMDBSSM_CFLAGS) 		\
-+	$(MMDB_CFLAGS) 		\
-+	$(CLIPPER_CFLAGS) 		
- 
- #	$(WITH_SCRIPT_CFLAGS) 
- 
-diff --git a/ccp4mg-utils/pygl/Makefile.am b/ccp4mg-utils/pygl/Makefile.am
-index a7e68b5..e26a6c8 100755
---- a/ccp4mg-utils/pygl/Makefile.am
-+++ b/ccp4mg-utils/pygl/Makefile.am
-@@ -108,9 +108,9 @@ INCLUDES = \
- 	$(LIBGLADE_CFLAGS)		\
- 	@GTK_CFLAGS@ 			\
- 	$(GLUT_CFLAGS)			\
--	$(MMDBSSM_CXXFLAGS) 		\
--	$(MMDB_CXXFLAGS) 		\
--	$(CLIPPER_CXXFLAGS) 		
-+	$(MMDBSSM_CFLAGS) 		\
-+	$(MMDB_CFLAGS) 		\
-+	$(CLIPPER_CFLAGS) 		
- 
- #	$(WITH_SCRIPT_CFLAGS) 
- 
-diff --git a/ccp4mg-utils/util/Makefile.am b/ccp4mg-utils/util/Makefile.am
-index 399f453..3d2ff55 100755
---- a/ccp4mg-utils/util/Makefile.am
-+++ b/ccp4mg-utils/util/Makefile.am
-@@ -73,9 +73,9 @@ INCLUDES = \
- 	$(LIBGLADE_CFLAGS)		\
- 	@GTK_CFLAGS@ 			\
- 	$(GLUT_CFLAGS)			\
--	$(MMDBSSM_CXXFLAGS) 		\
--	$(MMDB_CXXFLAGS) 		\
--	$(CLIPPER_CXXFLAGS) 		
-+	$(MMDBSSM_CFLAGS) 		\
-+	$(MMDB_CFLAGS) 		\
-+	$(CLIPPER_CFLAGS) 		
- 
- #	$(WITH_SCRIPT_CFLAGS) 
- 
-diff --git a/configure.in b/configure.in
-index cc549a5..d56f856 100644
---- a/configure.in
-+++ b/configure.in
-@@ -108,14 +108,18 @@ esac
- 
- 
- dnl Check for MMDB.
--AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)
-+PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2],,[AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)])
- 
--AM_WITH_MMDBSSM
-+PKG_CHECK_MODULES([MMDBSSM],[ssm],,[AM_WITH_MMDBSSM])
- AM_WITH_CCP4SRS
- 
- dnl Check for Clipper.  we exit if clipper is not found.
- #
--AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper]))
-+PKG_CHECK_MODULES([CLIPPER], [clipper libccp4c], [
-+  CLIPPER_LIBS="${CLIPPER_LIBS} -lrfftw -lfftw"; AC_SUBST([CLIPPER_LIBS])
-+  ], [
-+  AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper]))
-+  ])
- 
- # we set default coot_guile to true
- coot_guile=true
-@@ -186,11 +190,15 @@ AM_PATH_LIBGLADE
- 
- dnl =========================== GooCanvas ================================
- 
--AM_PATH_GOOCANVAS
--# give something for the preprocessor to chew on...
--if test "$GOOCANVAS_CFLAGS" != "" ; then
--   GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"
--fi
-+PKG_CHECK_MODULES([GOOCANVAS], [goocanvas],
-+	[GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"; AC_SUBST(GOOCANVAS_CFLAGS)],
-+	[
-+		AM_PATH_GOOCANVAS
-+		# give something for the preprocessor to chew on...
-+		if test "$GOOCANVAS_CFLAGS" != "" ; then
-+   		GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"
-+		fi
-+	])
- 
- AC_ARG_WITH(enhanced-ligand-tools, [ --with-enhanced-ligand-tools with optional complicated/experimental ligand-related dependencies ],
-  coot_enhanced_ligand_additions="true",
-diff --git a/coords/Makefile.am b/coords/Makefile.am
-index 05fdf70..1e1c5d2 100644
---- a/coords/Makefile.am
-+++ b/coords/Makefile.am
-@@ -29,7 +29,7 @@ INCLUDES = \
- 	-I$(top_srcdir) \
- 	$(ENHANCED_LIGAND_TOOLS_CFLAGS)      \
- 	$(RDKIT_CXXFLAGS) 		\
--	$(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+	$(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
- 
- AM_CXXFLAGS = \
- 	-DPKGDATADIR='"$(pkgdatadir)"' \
-diff --git a/coot-surface/Makefile.am b/coot-surface/Makefile.am
-index d2243d6..2434219 100644
---- a/coot-surface/Makefile.am
-+++ b/coot-surface/Makefile.am
-@@ -19,7 +19,7 @@
- # 02110-1301, USA
- 
- INCLUDES = -I$(top_srcdir) \
--	$(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(GTKGL_CFLAGS) $(GLUT_CFLAGS)
-+	$(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(GTKGL_CFLAGS) $(GLUT_CFLAGS)
- 
- lib_LTLIBRARIES = libcoot-surface.la
- 
-diff --git a/coot-utils/Makefile.am b/coot-utils/Makefile.am
-index 87810dc..c5b05b4 100644
---- a/coot-utils/Makefile.am
-+++ b/coot-utils/Makefile.am
-@@ -34,11 +34,10 @@ pkginclude_HEADERS = peak-search.hh coot-trim.hh \
- 	read-sm-cif.hh bonded-pairs.hh tree.hh helix-analysis.hh elastic.hh 
- pkgincludedir = $(includedir)/coot/coot-utils
- 
--
- INCLUDES = \
- 	-I$(top_srcdir)	\
--	$(CLIPPER_CXXFLAGS) 		\
--	$(MMDB_CXXFLAGS) 		\
-+	$(CLIPPER_CFLAGS) 		\
-+	$(MMDB_CFLAGS) 		\
- 	$(GSL_CFLAGS)			\
- 	$(WITH_GUILE_CFLAGS)		\
- 	$(WITH_PYTHON_CFLAGS)
-diff --git a/cootaneer/Makefile.am b/cootaneer/Makefile.am
-index 3a1d720..cfca0fd 100644
---- a/cootaneer/Makefile.am
-+++ b/cootaneer/Makefile.am
-@@ -20,7 +20,7 @@
- EXTRA_DIST = 		\
- 	cootaneer-llk-2.40.dat
- 
--INCLUDES = 	$(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) 
-+INCLUDES = 	$(CLIPPER_CFLAGS) $(MMDB_CFLAGS) 
- 
- cootaneer_demo_SOURCES = cootaneer-demo.cpp
- 
-diff --git a/cootilus/Makefile.am b/cootilus/Makefile.am
-index 7e4169d..4492014 100644
---- a/cootilus/Makefile.am
-+++ b/cootilus/Makefile.am
-@@ -20,7 +20,7 @@
- EXTRA_DIST = 		\
- 	nautilus_lib.pdb
- 
--INCLUDES = 	$(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) 
-+INCLUDES = 	$(CLIPPER_CFLAGS) $(MMDB_CFLAGS) 
- 
- cootilus_demo_SOURCES = cootilus-demo.cpp
- 
-diff --git a/db-main/Makefile.am b/db-main/Makefile.am
-index 3a85b9e..1a11cdf 100644
---- a/db-main/Makefile.am
-+++ b/db-main/Makefile.am
-@@ -6,7 +6,7 @@ AM_CXXFLAGS = \
- 	-DDATADIR='"$(datadir)"'
- 
- INCLUDES = -I$(top_srcdir) \
--   $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
-+   $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
- 
- pkginclude_HEADERS = db-main.hh db-strands.hh
- pkgincludedir = $(includedir)/coot/db-main
-diff --git a/db-main/Makefile.simple b/db-main/Makefile.simple
-index cec561d..c207a43 100644
---- a/db-main/Makefile.simple
-+++ b/db-main/Makefile.simple
-@@ -19,7 +19,7 @@ CLIPPER = $(HOME)/crystal
- MCCP4   = $(HOME)/crystal
- 
- CXX = g++
--MMDB_CXXFLAGS = -I$(MMDB)/include 
-+MMDB_CFLAGS = -I$(MMDB)/include 
- FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
- 
- MMDB_LIBS = -L$(MMDB)/lib -lmmdb 
-@@ -28,9 +28,9 @@ CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-contrib \
- 	-L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
- 
- MCCP4_CFLAGS = -I$(MCCP4)/include
--CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
-+CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
- 
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MCCP4_CFLAGS) $(MMDB_CXXFLAGS) -I../mini-mol
-+INCLUDES = $(CLIPPER_CFLAGS) $(MCCP4_CFLAGS) $(MMDB_CFLAGS) -I../mini-mol
- 
- CXXFLAGS = -g $(INCLUDES)
- LDFLAGS = -static -L../mini-mol -lcoot-mini-mol $(CLIPPER_LIBS) $(MMDB_LIBS) 
-@@ -44,4 +44,4 @@ libcoot-db-main.a: db-main.o
- db-main.o: db-main.cc db-main.hh
- 
- testmmdbbits: testmmdbbits.cc
--	$(CXX) $(MMDB_CXXFLAGS) $(MMDB_LIBS) $? -o $@
-+	$(CXX) $(MMDB_CFLAGS) $(MMDB_LIBS) $? -o $@
-diff --git a/density-contour/Makefile.am b/density-contour/Makefile.am
-index 7f705e8..f5dcc00 100644
---- a/density-contour/Makefile.am
-+++ b/density-contour/Makefile.am
-@@ -20,7 +20,7 @@
- 
- COORD_INCLUDES = -I$(top_srcdir)
- 
--INCLUDES = $(COORD_INCLUDES) $(CLIPPER_CXXFLAGS) 
-+INCLUDES = $(COORD_INCLUDES) $(CLIPPER_CFLAGS) 
- 
- lib_LTLIBRARIES = libcoot-isosurface.la
- 
-diff --git a/geometry/Makefile.am b/geometry/Makefile.am
-index 6dd665f..57aaa04 100644
---- a/geometry/Makefile.am
-+++ b/geometry/Makefile.am
-@@ -26,7 +26,7 @@ pkginclude_HEADERS =  protein-geometry.hh read-sbase.hh lbg-graph.hh srs-interfa
- pkgincludedir = $(includedir)/coot/geometry
- 
- INCLUDES = -I$(top_srcdir) \
--	 $(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS)
-+	 $(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS)
- 
- AM_CXXFLAGS = \
- 	-DDATADIR='"$(datadir)"'       \
-diff --git a/geometry/Makefile.simple b/geometry/Makefile.simple
-index 370b2fa..c3b0106 100644
---- a/geometry/Makefile.simple
-+++ b/geometry/Makefile.simple
-@@ -46,7 +46,7 @@ MCCP4   = $(HOME)/mapview
- 
- 
- CXX = g++
--MMDB_CXXFLAGS = -I$(MMDB)/include 
-+MMDB_CFLAGS = -I$(MMDB)/include 
- FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
- 
- MMDB_LIBS = -L$(MMDB)/lib -lmmdb 
-@@ -55,9 +55,9 @@ CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-contrib \
- 	-L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
- 
- MCCP4_CFLAGS = -I$(MCCP4)/include
--CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
-+CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
- 
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -I$(top_srcdir)/coords 
-+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) -I$(top_srcdir)/coords 
- 
- top_srcdir = ..
- 
-diff --git a/high-res/Makefile.am b/high-res/Makefile.am
-index cf81182..3a2af5c 100644
---- a/high-res/Makefile.am
-+++ b/high-res/Makefile.am
-@@ -29,8 +29,8 @@ AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS)
- 
- INCLUDES = \
- 	-I$(top_srcdir)   \
--	$(MMDB_CXXFLAGS)  \
--	$(CLIPPER_CXXFLAGS)
-+	$(MMDB_CFLAGS)  \
-+	$(CLIPPER_CFLAGS)
- 
- libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \
- 	sequence-assignment.cc
-diff --git a/ideal/Makefile.am b/ideal/Makefile.am
-index e52c271..c5c8e6a 100644
---- a/ideal/Makefile.am
-+++ b/ideal/Makefile.am
-@@ -33,11 +33,11 @@ pkgincludedir = $(includedir)/coot/ideal
- 
- INCLUDES = \
- 	-I$(top_srcdir) \
--	$(CLIPPER_CXXFLAGS)        \
--	$(MMDB_CXXFLAGS)
-+	$(CLIPPER_CFLAGS)        \
-+	$(MMDB_CFLAGS)
- 
- AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS) $(COOT_WINDOWS_CFLAGS) \
--     $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) $(COOT_GSL_FLAGS) 
-+     $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) $(COOT_GSL_FLAGS) 
- AM_LDFLAGS = $(GSL_LIBS) $(MMDB_LIBS) $(CLIPPER_LIBS)
- 
- 
-diff --git a/ideal/Makefile.simple b/ideal/Makefile.simple
-index 3c32c3c..0abd514 100644
---- a/ideal/Makefile.simple
-+++ b/ideal/Makefile.simple
-@@ -44,7 +44,7 @@ MMDB    = $(HOME)/mapview
- 
- 
- CXX = g++
--MMDB_CXXFLAGS = -I$(MMDB)/include 
-+MMDB_CFLAGS = -I$(MMDB)/include 
- FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
- 
- MMDB_LIBS = -L$(MMDB)/lib -lmmdb 
-@@ -53,9 +53,9 @@ CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-contrib \
- 	-L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
- 
- MCCP4_CFLAGS = -I$(MCCP4)/include
--CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
-+CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
- 
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) \
-+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) \
- 	-I$(top_srcdir)/coords  \
- 	-I$(top_srcdir)/geometry
- 
-diff --git a/lbg/Makefile.am b/lbg/Makefile.am
-index df74b90..7f54567 100644
---- a/lbg/Makefile.am
-+++ b/lbg/Makefile.am
-@@ -6,7 +6,7 @@ INCLUDES = \
-         $(GSL_CFLAGS) \
-         $(GOOCANVAS_CFLAGS) \
-         $(GTK_CFLAGS) \
--	$(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS) \
-+	$(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS) \
- 	$(COOT_WINDOWS_CFLAGS) \
- 	$(ENHANCED_LIGAND_TOOLS_CFLAGS)      \
- 	$(RDKIT_CXXFLAGS) \
-diff --git a/lbg/Makefile.simple b/lbg/Makefile.simple
-index 48d091b..5b148b4 100644
---- a/lbg/Makefile.simple
-+++ b/lbg/Makefile.simple
-@@ -24,11 +24,11 @@ GSL_LDFLAGS=$(CRYST)/lib/libgsl.la  $(CRYST)/lib/libgslcblas.la -lm
- MMDB=$(CRYST)
- # MMDB=$(HOME)/test/mmdb
- 
--MMDB_CXXFLAGS=-I$(MMDB)/include/mmdb
-+MMDB_CFLAGS=-I$(MMDB)/include/mmdb
- MMDB_LDFLAGS=$(MMDB)/lib/libmmdb.la
- 
- CLIPPER=$(CRYST)
--CLIPPER_CXXFLAGS=-I$(CLIPPER)/include
-+CLIPPER_CFLAGS=-I$(CLIPPER)/include
- CLIPPER_LDFLAGS=$(CLIPPER)/lib/libclipper-core.la \
-         $(CLIPPER)/lib/librfftw.la \
-         $(CLIPPER)/lib/libfftw.la
-@@ -40,7 +40,7 @@ LIDIA_CORE_CXXFLAGS = -I ../lidia-core
- LIDIA_CORE_LDFLAGS = $(COOT_INSTALLED)/lib/libcoot-lidia-core.la
- 
- 
--CXXFLAGS=-g -O2 $(EXTRA_FLAGS) $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(LIDIA_CORE_CXXFLAGS) \
-+CXXFLAGS=-g -O2 $(EXTRA_FLAGS) $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(LIDIA_CORE_CXXFLAGS) \
-     -I$(top_srcdir)/compat
- 
- lbg:  lbg.o wmolecule.o lbg-callbacks.o lbg-search.o some-coot-utils.o residue-circles.o
-diff --git a/lidia-core/Makefile.am b/lidia-core/Makefile.am
-index 72b28ca..2a184b4 100644
---- a/lidia-core/Makefile.am
-+++ b/lidia-core/Makefile.am
-@@ -24,13 +24,13 @@ pkgincludedir = $(includedir)/coot/lidia-core
- 
- #  20110408 I add a CResidue,dictionary_residue_restraints_t constructor to molfile_molecule_t
- # simple
--#INCLUDES = $(CLIPPER_CXXFLAGS)
-+#INCLUDES = $(CLIPPER_CFLAGS)
- #
- INCLUDES = \
- 	 -I$(top_srcdir) \
- 	$(ENHANCED_LIGAND_TOOLS_CFLAGS)      \
- 	$(RDKIT_CXXFLAGS) 		\
--        $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+        $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
- 
- libcoot_lidia_core_la_SOURCES = lbg-shared.cc lbg-molfile.cc lig-build.cc rdkit-interface.cc \
- 	cod-types.cc
-diff --git a/ligand/Makefile.am b/ligand/Makefile.am
-index 202979e..5173204 100644
---- a/ligand/Makefile.am
-+++ b/ligand/Makefile.am
-@@ -27,7 +27,7 @@ INCLUDES = \
- 	-I$(top_srcdir) \
- 	$(COOT_GSL_FLAGS)		\
- 	$(GSL_CFLAGS)			\
--	$(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) 
-+	$(CLIPPER_CFLAGS) $(MMDB_CFLAGS) 
- 
- pkginclude_HEADERS = ligand.hh residue_by_phi_psi.hh wligand.hh monomer-utils.hh \
- 	chi-angles.hh dunbrack.hh helix-placement.hh fast-ss-search.hh        \
-diff --git a/macros/clipper.m4 b/macros/clipper.m4
-index da11e74..ad2af81 100644
---- a/macros/clipper.m4
-+++ b/macros/clipper.m4
-@@ -56,7 +56,7 @@ if test x$clipper_prefix != x; then
-  #
-  # should use clipper-config --cflags
-  #
-- CLIPPER_CXXFLAGS="-I$clipper_prefix/include"
-+ CLIPPER_CFLAGS="-I$clipper_prefix/include"
-  # -I$clipper_prefix/cctbx
-  
-  # yes, libmmtz.a is in -L$clipper_prefix/umtz!
-@@ -75,7 +75,7 @@ if test x$clipper_prefix != x; then
-  #
-  ccp4c=ccp4c
- 
-- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -l$ccp4c $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
-+ CLIPPER_LIBS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -l$ccp4c $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
-  # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx 
- 
- 
-@@ -102,8 +102,8 @@ else
-  # this needs to be 'configured' - typically either s or blank.
-  fftw_pre=
- 
-- CLIPPER_CXXFLAGS="$CCP4_CFLAGS"
-- CLIPPER_LDOPTS="-lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-minimol -lclipper-cns -lclipper-core $CCP4_LIBS $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
-+ CLIPPER_CFLAGS="$CCP4_CFLAGS"
-+ CLIPPER_LIBS="-lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-minimol -lclipper-cns -lclipper-core $CCP4_LIBS $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
- fi
- 
- # BL: workaround needed for new MinGW
-@@ -113,17 +113,17 @@ ac_cv_build_alias=${ac_cv_build_alias:=$build_alias}
- case $ac_cv_build_alias in
-         # BL says:: same as for cygwin in mingw
-         MINGW*|Mingw*|*mingw*|Cygwin*|CYGWIN*|*cygwin*)
--                CLIPPER_LDOPTS=$CLIPPER_LDOPTS
-+                CLIPPER_LIBS=$CLIPPER_LIBS
- 	;; 
- 	*)
--		CLIPPER_LDOPTS=$CLIPPER_LDOPTS" -lpthread"
-+		CLIPPER_LIBS=$CLIPPER_LIBS" -lpthread"
-         ;;
- esac
- 
- AC_MSG_CHECKING([for Clipper])
- 
--	LIBS="$save_LIBS $CLIPPER_LDOPTS"
--	CFLAGS="$save_CFLAGS $CLIPPER_CXXFLAGS"
-+	LIBS="$save_LIBS $CLIPPER_LIBS"
-+	CFLAGS="$save_CFLAGS $CLIPPER_CFLAGS"
- 	# AC_TRY_LINK uses the c compiler, so we will temporarily 
- 	# reassign $CC to the c++ compiler.
-  	#
-@@ -140,7 +140,7 @@ if test x$have_clipper = xyes; then
- 
-  LIBS="$saved_LIBS"
-  CFLAGS="$saved_CFLAGS"
-- CLIPPER_LIBS="$CLIPPER_LDOPTS"
-+ CLIPPER_LIBS="$CLIPPER_LIBS"
-  ifelse([$1], , :, [$1])
- 
- else
-@@ -148,12 +148,12 @@ else
-  LIBS="$saved_LIBS"
-  CFLAGS="$saved_CFLAGS"
-  CLIPPER_LIBS=""
-- CLIPPER_CXXFLAGS=""
-+ CLIPPER_CFLAGS=""
-  ifelse([$2], , :, [$2])
- 
- fi
- 
--AC_SUBST(CLIPPER_CXXFLAGS)
-+AC_SUBST(CLIPPER_CFLAGS)
- AC_SUBST(CLIPPER_LIBS)
- 
- ])
-diff --git a/macros/clipper.m4.old b/macros/clipper.m4.old
-index de8ab65..4c1b418 100644
---- a/macros/clipper.m4.old
-+++ b/macros/clipper.m4.old
-@@ -34,7 +34,7 @@ if test x$clipper_prefix != x; then
-  # should ideally be CLIPPER_CFLAGS="-I$clipper_prefix/include", and the like
-  # when clipper and dependencies get installed.
-  #  
-- CLIPPER_CXXFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include"
-+ CLIPPER_CFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include"
- # -I$clipper_prefix/cctbx
-  
-  # yes, libmmtz.a is in -L$clipper_prefix/umtz!
-@@ -45,20 +45,20 @@ if test x$clipper_prefix != x; then
-  # HACK! FIXME
-  # added lz, we should have proper autoconf check for this.
-  #
-- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper -L$clipper_prefix/mccp4 -lmccp4 $MMDB_LIBS -L$clipper_prefix/fftw/lib -lrfftw -lfftw -lz -lm"
-+ CLIPPER_LIBS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper -L$clipper_prefix/mccp4 -lmccp4 $MMDB_LIBS -L$clipper_prefix/fftw/lib -lrfftw -lfftw -lz -lm"
- # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx 
- else
-  # the compiler looks in the "standard" places for clipper.  In real life,
-  # it would be quite unlikely that clipper would be installed in /usr/include, 
-  # /usr/lib etc. so this code will not usually find the right dependencies.
-- CLIPPER_CXXFLAGS=""
-- CLIPPER_LDOPTS=""
-+ CLIPPER_CFLAGS=""
-+ CLIPPER_LIBS=""
- fi
- 
- AC_MSG_CHECKING([for Clipper])
- 
--	LIBS="$save_LIBS $CLIPPER_LDOPTS"
--	CFLAGS="$save_CFLAGS $CLIPPER_CXXFLAGS"
-+	LIBS="$save_LIBS $CLIPPER_LIBS"
-+	CFLAGS="$save_CFLAGS $CLIPPER_CFLAGS"
- 	# AC_TRY_LINK uses the c compiler, so we will temporarily 
- 	# reassign $CC to the c++ compiler.
-  	#
-@@ -72,7 +72,7 @@ if test x$have_clipper = xyes; then
- 
-  LIBS="$saved_LIBS"
-  CFLAGS="$saved_CFLAGS"
-- CLIPPER_LIBS="$CLIPPER_LDOPTS"
-+ CLIPPER_LIBS="$CLIPPER_LIBS"
-  ifelse([$1], , :, [$1])
- 
- else
-@@ -80,12 +80,12 @@ else
-  LIBS="$saved_LIBS"
-  CFLAGS="$saved_CFLAGS"
-  CLIPPER_LIBS=""
-- CLIPPER_CXXFLAGS=""
-+ CLIPPER_CFLAGS=""
-  ifelse([$2], , :, [$2])
- 
- fi
- 
--AC_SUBST(CLIPPER_CXXFLAGS)
-+AC_SUBST(CLIPPER_CFLAGS)
- AC_SUBST(CLIPPER_LIBS)
- 
- ])
-diff --git a/macros/goo-canvas.m4 b/macros/goo-canvas.m4
-index e2494a5..89c908e 100644
---- a/macros/goo-canvas.m4
-+++ b/macros/goo-canvas.m4
-@@ -35,8 +35,7 @@ if test x$goocanvas_prefix != x; then
-   # SGI compiler CC (CXX=CC) needs -lm to link maths library, but 
-   # GCC c++ does not.
-   #
--  GOOCANVAS_LDOPTS="-L$goocanvas_prefix/lib -lgoocanvas"
--
-+  GOOCANVAS_LIBS="-L$goocanvas_prefix/lib -lgoocanvas"
- else
-   # the compiler looks in the "standard" places for GOOCANVAS. (or uses pkgconfig)
- 
-@@ -54,18 +53,16 @@ else
-     break;;
-   esac
-   if test -z "${PKG_CONFIG}"; then
--     GOOCANVAS_LDOPTS="-lgoocanvas"
-+     GOOCANVAS_LIBS="-lgoocanvas"
-   else
--     GOOCANVAS_LDOPTS=`$PKG_CONFIG goocanvas --libs`
-+     GOOCANVAS_LIBS=`$PKG_CONFIG goocanvas --libs`
-   fi
- fi
- 
- AC_MSG_CHECKING([for Goocanvas])
- 
--LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS"
-+LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS"
- CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS"
--
--
- dnl # 20130929: why do I do this?  I don't remember.  Using libtool 
- dnl # in this way is not a good idea (configure makes libtool).
- dnl #
-@@ -85,18 +82,15 @@ dnl     # note that we use ./libtool (running in the build dir) because $LIBTOOL
- dnl     CXX="libtool --mode=link $CXX"
- dnl     break;;
- dnl esac
--
--
- AC_LANG_PUSH(C++)
- AC_TRY_LINK([#include "goocanvas.h"] ,[ GooCanvas *a;  ], have_goocanvas=yes, have_goocanvas=no)
- AC_LANG_POP
--
- AC_MSG_RESULT($have_goocanvas)
- 
- if test x$have_goocanvas = xyes; then
- 
-  GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS"
-- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS"
-+ GOOCANVAS_LIBS="$GOOCANVAS_LIBS"
- 
- ifelse([$1], , :, [$1])
- 
-diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
-index 25dc502..21646a5 100644
---- a/macros/mmdb-ssm.m4
-+++ b/macros/mmdb-ssm.m4
-@@ -34,11 +34,11 @@ if test x$with_ssmlib_prefix != x; then
- 
-    if test -r "$with_ssmlib_prefix/include/ssm/ssm_superpose.h"; then
- 
--      MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
-+      MMDBSSM_CFLAGS="-DHAVE_SSMLIB"
-       # AFAICS, ssm does not put its libs in $acl_libdirstem
-       # MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
-       MMDBSSM_LIBS="-L$with_ssmlib_prefix/lib -lssm"
--      ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/include"
-+      ac_MMDBSSM_CFLAGS="-I$with_ssmlib_prefix/include"
- 
-       # saved_LIBS="$LIBS"
-       # saved_CPPFLAGS="$CPPFLAGS"
-@@ -50,11 +50,11 @@ if test x$with_ssmlib_prefix != x; then
-    else 
-       AC_MSG_FAILURE([ --with-ssmlib-prefix specified but include files not found])
-    fi
--   MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
-+   MMDBSSM_CFLAGS="$MMDBSSM_CFLAGS $ac_MMDBSSM_CFLAGS"
-   
- else 
- 
--   MMDBSSM_CXXFLAGS=""
-+   MMDBSSM_CFLAGS=""
-    MMDBSSM_LIBS=""
-    with_ssmlib_prefix=no 
- 
-@@ -62,6 +62,6 @@ fi
- 
- AC_MSG_RESULT([$with_ssmlib_prefix])
- 
--AC_SUBST(MMDBSSM_CXXFLAGS)
-+AC_SUBST(MMDBSSM_CFLAGS)
- AC_SUBST(MMDBSSM_LIBS)
- ])
-diff --git a/macros/mmdb.m4 b/macros/mmdb.m4
-index 7c1cbcf..72613f3 100644
---- a/macros/mmdb.m4
-+++ b/macros/mmdb.m4
-@@ -55,7 +55,7 @@ if test x$mmdb_prefix != x; then
- 	# --with-mmdb=/some/thing
- 	#
- 
-- # should ideally be MMDB_CXXFLAGS="-I$MMDB_prefix/include", and the like
-+ # should ideally be MMDB_CFLAGS="-I$MMDB_prefix/include", and the like
-  # when MMDB and dependencies get installed - we infact, include both
-  # directories.
-  #  
-@@ -69,7 +69,7 @@ lib/src
- lib/src/mmdb'
- for ac_dir in $ac_mmdb_dirs; do
-    if test -r "$mmdb_prefix/$ac_dir/mmdb/mmdb_manager.h"; then
--      ac_MMDB_CXXFLAGS="-I$mmdb_prefix/$ac_dir"
-+      ac_MMDB_CFLAGS="-I$mmdb_prefix/$ac_dir"
-       break
-    fi
- done
-@@ -82,14 +82,14 @@ else
-  # the compiler looks in the "standard" places for MMDB.  In real life,
-  # it would be quite unlikely that MMDB would be installed in /usr/include, 
-  # /usr/lib etc. so this code will not usually find the right dependencies.
-- ac_MMDB_CXXFLAGS=""
-+ ac_MMDB_CFLAGS=""
-  ac_MMDB_LDOPTS="-lmmdb -lm"
- fi
- 
- AC_MSG_CHECKING([for MMDB])
- 
- 	LIBS="$save_LIBS $ac_MMDB_LDOPTS"
--	CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS"
-+	CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CFLAGS"
- 	#
- 	# AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
- 	# temporarily reassign $CC to the c++ compiler.
-@@ -118,7 +118,7 @@ if test x$have_mmdb = xyes; then
-     CLINKR_FLAG=-DMMDB_WITHOUT_LINKR
-  fi
-  CXXFLAGS="$saved_CXXFLAGS"
-- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS $HASH_FLAG $CISPEP_FLAG $CLINKR_FLAG"
-+ MMDB_CFLAGS="$ac_MMDB_CFLAGS $HASH_FLAG $CISPEP_FLAG $CLINKR_FLAG"
-  MMDB_LIBS="$ac_MMDB_LDOPTS"
- ifelse([$1], , :, [$1])
- 
-@@ -134,12 +134,12 @@ else
-  LIBS="$saved_LIBS"
-  CXXFLAGS="$saved_CXXFLAGS"
-  MMDB_LIBS=""
-- MMDB_CXXFLAGS=""
-+ MMDB_CFLAGS=""
-  ifelse([$2], , :, [$2])
- 
- fi
- 
--AC_SUBST(MMDB_CXXFLAGS)
-+AC_SUBST(MMDB_CFLAGS)
- AC_SUBST(MMDB_LIBS)
- 
- ])
-diff --git a/mini-mol/Makefile.am b/mini-mol/Makefile.am
-index 2f6e3a3..4865b0b 100644
---- a/mini-mol/Makefile.am
-+++ b/mini-mol/Makefile.am
-@@ -25,8 +25,8 @@ pkgincludedir = $(includedir)/coot/mini-mol
- 
- INCLUDES =  \
- 	-I$(top_srcdir) \
--	$(CLIPPER_CXXFLAGS)    \
--	$(MMDB_CXXFLAGS)
-+	$(CLIPPER_CFLAGS)    \
-+	$(MMDB_CFLAGS)
- 
- AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS)
- 
-diff --git a/protein_db/Makefile.am b/protein_db/Makefile.am
-index 268fcf6..cdd5c9e 100644
---- a/protein_db/Makefile.am
-+++ b/protein_db/Makefile.am
-@@ -19,7 +19,7 @@
- 
- lib_LTLIBRARIES=libcoot-protein-db.la
- 
--INCLUDES= $(CLIPPER_CXXFLAGS)  $(MMDB_CXXFLAGS)
-+INCLUDES= $(CLIPPER_CFLAGS)  $(MMDB_CFLAGS)
- 
- pkginclude_HEADERS=protein_db.h  protein_db_utils.h rna_db.h
- pkgincludedir = $(includedir)/coot/protein_db
-diff --git a/sequence-view/Makefile.am b/sequence-view/Makefile.am
-index 7af6384..742e6d7 100644
---- a/sequence-view/Makefile.am
-+++ b/sequence-view/Makefile.am
-@@ -55,9 +55,9 @@ INCLUDES = \
- 	-I$(top_srcdir)/analysis	\
- 	-I$(top_srcdir)/cootaneer	\
- 	-I$(top_srcdir)/src     	\
--	$(CLIPPER_CXXFLAGS) 		\
--	$(MMDB_CXXFLAGS) 		\
--	$(MMDBSSM_CXXFLAGS) 		\
-+	$(CLIPPER_CFLAGS) 		\
-+	$(MMDB_CFLAGS) 		\
-+	$(MMDBSSM_CFLAGS) 		\
- 	$(GLUT_CFLAGS)			\
- 	$(CANVAS_CFLAGS) 		\
- 	$(GTKGL_CONTEXT_CFLAGS)		\
-diff --git a/skeleton/Makefile.am b/skeleton/Makefile.am
-index 54872fe..bef7d0e 100644
---- a/skeleton/Makefile.am
-+++ b/skeleton/Makefile.am
-@@ -23,7 +23,7 @@ lib_LTLIBRARIES=libcoot-skeleton.la
- 
- INCLUDES = \
- 	  -I$(top_srcdir) \
--	 $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) 
-+	 $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) 
- 
- AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS)
- 
-diff --git a/src/Makefile.am b/src/Makefile.am
-index af5276b..d0ab482 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -195,11 +195,11 @@ INCLUDES = \
-         $(GOOCANVAS_CFLAGS)             \
- 	@GTK_CFLAGS@ 			\
- 	$(GLUT_CFLAGS)			\
--	$(MMDBSSM_CXXFLAGS) 		\
--	$(MMDB_CXXFLAGS) 		\
-+	$(MMDBSSM_CFLAGS) 		\
-+	$(MMDB_CFLAGS) 		\
- 	$(CCP4SRS_CXXFLAGS) 		\
- 	$(GSL_CFLAGS)			\
--	$(CLIPPER_CXXFLAGS) 		\
-+	$(CLIPPER_CFLAGS) 		\
- 	$(PYGTK_CFLAGS)                 \
- 	$(GLOB_CFLAGS)                 \
- 	$(CURL_CFLAGS)                 
-diff --git a/surface/Makefile.am b/surface/Makefile.am
-index 3de5953..2461f58 100644
---- a/surface/Makefile.am
-+++ b/surface/Makefile.am
-@@ -1,5 +1,5 @@
- 
--INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(FFTW_CXXFLAGS)
-+INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(FFTW_CXXFLAGS)
- 
- AM_CXXFLAGS = $(OPENMP_CFLAGS)
- 
diff --git a/sci-chemistry/coot/files/coot-9999-desktop.patch b/sci-chemistry/coot/files/coot-9999-desktop.patch
new file mode 100644
index 000000000..c264dd5a7
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-9999-desktop.patch
@@ -0,0 +1,21 @@
+ coot.desktop | 7 +++----
+ 1 file changed, 3 insertions(+), 4 deletions(-)
+
+diff --git a/coot.desktop b/coot.desktop
+index 74aecf3..8668018 100644
+--- a/coot.desktop
++++ b/coot.desktop
+@@ -1,10 +1,9 @@
+ [Desktop Entry]
+ Type=Application
+-Encoding=UTF-8
+ Name=Coot
+ Comment=Macromolecular model builder
+ Exec=coot
+-Icon=coot.png
++Icon=coot
+ Terminal=true
+-Categories=Science;Graphics
+-MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile
++Categories=Science;Graphics;
++MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile;
diff --git a/sci-chemistry/coot/files/coot-9999-libguile.patch b/sci-chemistry/coot/files/coot-9999-libguile.patch
new file mode 100644
index 000000000..cbaccefb2
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-9999-libguile.patch
@@ -0,0 +1,29 @@
+ src/graphics-info-modelling.cc | 1 +
+ src/graphics-info.cc           | 2 ++
+ 2 files changed, 3 insertions(+)
+
+diff --git a/src/graphics-info-modelling.cc b/src/graphics-info-modelling.cc
+index 05a63ad..4b7d129 100644
+--- a/src/graphics-info-modelling.cc
++++ b/src/graphics-info-modelling.cc
+@@ -102,6 +102,7 @@
+ 
+ #include "utils/coot-utils.hh"
+ 
++#include <libguile.h>
+ 
+ // Idealize the geometry without considering the map.
+ //
+diff --git a/src/graphics-info.cc b/src/graphics-info.cc
+index e2f9d52..76b6769 100644
+--- a/src/graphics-info.cc
++++ b/src/graphics-info.cc
+@@ -92,6 +92,8 @@
+ #include "cc-interface-scripting.hh"
+ #endif
+ 
++#include <libguile.h>
++
+ // A few non-class members - should be somewhere else, I guess.
+ // 
+ void initialize_graphics_molecules() { 
diff --git a/sci-chemistry/coot/files/coot-9999-libtool.patch b/sci-chemistry/coot/files/coot-9999-libtool.patch
new file mode 100644
index 000000000..10c43ad55
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-9999-libtool.patch
@@ -0,0 +1,39 @@
+ configure.ac    |  2 +-
+ lbg/Makefile.am | 11 -----------
+ 2 files changed, 1 insertion(+), 12 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 73d6ed7..b04dcd6 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -69,7 +69,7 @@ AC_LIB_PREPARE_MULTILIB
+ 
+ AC_SUBST(COOT_STDTYPES)
+ 
+-EXPORT_DYNAMIC_FLAG_SPEC=$export_dynamic_flag_spec
++eval EXPORT_DYNAMIC_FLAG_SPEC=\"$export_dynamic_flag_spec\"
+ AC_SUBST(EXPORT_DYNAMIC_FLAG_SPEC)
+ 
+ 
+diff --git a/lbg/Makefile.am b/lbg/Makefile.am
+index 1277afe..a79ebe0 100644
+--- a/lbg/Makefile.am
++++ b/lbg/Makefile.am
+@@ -43,17 +43,6 @@ pkginclude_HEADERS = lbg.hh wmolecule.hh  flev-annotations.hh graphics-c-interfa
+ 	lbg-drag-and-drop.hh qed-interface.hh alerts.hh pi-stacking.hh
+ pkgincludedir = $(includedir)/coot/lbg
+ 
+-# 20140521
+-# lidia_LDFLAGS = -Wl,--export-dynamic
+-# 
+-# Now we use EXPORT_DYNAMIC_FLAG_SPEC which usually evaluates to ${wl}--export-dynamic
+-# (but not for MacOSX, where it Does The Right Thing (hopefully)).
+-# We manually set the value of wl here, but maybe the Right Thing To Do for that is 
+-# run (eval) $($LIBTOOL --config | grep ^wl).  How do I do that here though?  
+-# I don't understand.  Maybe the setting of wl should be done in configure?  But then
+-# I have to force the output of libtool.  Bleugh.  Hmm...
+-# Anyway, thankyou Gary Vaughan.
+-wl=-Wl,
+ lidia_LDFLAGS = $(EXPORT_DYNAMIC_FLAG_SPEC)
+ 
+ # res spec output operator means we include libcoot-coord-utils