initial commit

13 files changed, 468 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..78c42f9ac0d0
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,69 @@
+# Generated by mksrcinfo v8
+# Tue Jan 22 10:03:04 UTC 2019
+pkgbase = coot-git
+	pkgdesc = Crystallographic Object-Oriented Toolkit for model building, completion and validation
+	pkgver = r7765.900be3e39
+	pkgrel = 1
+	url = http://lmb.bioch.ox.ac.uk/coot/
+	arch = i686
+	arch = x86_64
+	license = GPL
+	depends = guile1.8
+	depends = guile1.8-lib
+	depends = guile1.8-gtk
+	depends = guile1.8-gui
+	depends = gtkglext
+	depends = libccp4>=6.5.1-2
+	depends = clipper>=2.1.20170202-3
+	depends = goocanvas1
+	depends = gsl
+	depends = libgnomecanvas
+	depends = imlib
+	depends = swig
+	depends = freeglut
+	depends = libgl
+	depends = gtk2
+	depends = cairo
+	depends = libssm>=1.4.0-2
+	depends = zlib
+	depends = curl
+	depends = python2
+	depends = pygtk
+	depends = gtkglarea
+	depends = which
+	depends = bc
+	depends = sqlite
+	depends = rdkit-python2<=2017_09_3-1
+	depends = mmdb2>=2.0.12-4
+	conflicts = coot
+	source = coot::git+https://github.com/pemsley/coot.git
+	source = https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/refmac-monomer-library.tar.gz
+	source = https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/reference-structures.tar.gz
+	source = coot-configure.ac.patch
+	source = coot-makefile.patch
+	source = coot-guile.patch
+	source = coot-libguile.patch
+	source = coot-utils.patch
+	source = coot-lbg.patch
+	source = coot-python.patch
+	source = coot-lidia.patch
+	source = coot-pyrogen.patch
+	source = coot-dynarama.patch
+	source = coot.in
+	sha256sums = SKIP
+	sha256sums = 03562eec612103a48bd114cfe0d171943e88f94b84610d16d542cda138e5f36b
+	sha256sums = 44db38506f0f90c097d4855ad81a82a36b49cd1e3ffe7d6ee4728b15109e281a
+	sha256sums = 2babfbc3cb798868d9e22f19ee49d12981fac35e3dfba2d8f7318716f59f673c
+	sha256sums = 9ad5a56116748ab5b1f77b2a4b2e3df47847ff881579105dff6589ed60ac8eb4
+	sha256sums = c15e844536f512c2d5524391dbc046a889a0d5f8c23336b854508e453e226911
+	sha256sums = aa1e18d4ef43fb61e85aba05d13797f9aa2beb1da220405f1eb6058ac36eb60b
+	sha256sums = 059d57dc092feb8134a95e6fa452a2d807ccb3666da374f4a023e5684e3a0dfa
+	sha256sums = 423a50d27639376c52e6987877acea908d854decb48c7c2452f7f5ecb92b60e9
+	sha256sums = f4747e1fc7a3387f42b6c40358f999404761a0282ee6be3c621091d9d5d88099
+	sha256sums = dd2eb7c66ff2fa6f68a9d1e834e1911d2a1669a76ed29b5dbd6863619edcba18
+	sha256sums = b07517bdf9fcee43cf13533902ef333adcdaa45e60905628dfefc98ff55e95b5
+	sha256sums = 485f305444fbe8ec3df3add5df68c5f2f7524507211f94bdecf2fa110c28c014
+	sha256sums = 5ba4e0d9bdc4db0bab403b8f9aadb1320af60e91f9ed87e81dc680425375590b
+
+pkgname = coot-git
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..b64bfb1c8027
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,116 @@
+# Maintainer: Alexander Minges <alexander.minges@gmail.com>
+pkgname=coot-git
+pkgver=r7765.900be3e39
+pkgrel=1
+pkgdesc="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
+arch=('i686' 'x86_64')
+url="http://lmb.bioch.ox.ac.uk/coot/"
+license=('GPL')
+conflicts=('coot')
+depends=('guile1.8' 'guile1.8-lib' 'guile1.8-gtk' 'guile1.8-gui' 'gtkglext' 'libccp4>=6.5.1-2' 'clipper>=2.1.20170202-3' 'goocanvas1' 'gsl' 'libgnomecanvas' 'imlib' 'swig'
+         'freeglut' 'libgl' 'gtk2' 'cairo' 'libssm>=1.4.0-2' 'zlib' 'curl' 'python2' 'pygtk' 'gtkglarea' 'which' 'bc' 'sqlite' 'rdkit-python2<=2017_09_3-1' 'mmdb2>=2.0.12-4')
+_pkgname=coot
+source=(coot::git+https://github.com/pemsley/coot.git
+        https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/$_pkgname/dependencies/refmac-monomer-library.tar.gz
+        https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/$_pkgname/dependencies/reference-structures.tar.gz
+        coot-configure.ac.patch
+        coot-makefile.patch
+        coot-guile.patch
+        coot-libguile.patch
+        coot-utils.patch
+        coot-lbg.patch
+        coot-python.patch
+        coot-lidia.patch
+        coot-pyrogen.patch
+        coot-dynarama.patch
+        coot.in
+        )
+
+sha256sums=('SKIP'
+            '03562eec612103a48bd114cfe0d171943e88f94b84610d16d542cda138e5f36b'
+            '44db38506f0f90c097d4855ad81a82a36b49cd1e3ffe7d6ee4728b15109e281a'
+            '2babfbc3cb798868d9e22f19ee49d12981fac35e3dfba2d8f7318716f59f673c'
+            '9ad5a56116748ab5b1f77b2a4b2e3df47847ff881579105dff6589ed60ac8eb4'
+            'c15e844536f512c2d5524391dbc046a889a0d5f8c23336b854508e453e226911'
+            'aa1e18d4ef43fb61e85aba05d13797f9aa2beb1da220405f1eb6058ac36eb60b'
+            '059d57dc092feb8134a95e6fa452a2d807ccb3666da374f4a023e5684e3a0dfa'
+            '423a50d27639376c52e6987877acea908d854decb48c7c2452f7f5ecb92b60e9'
+            'f4747e1fc7a3387f42b6c40358f999404761a0282ee6be3c621091d9d5d88099'
+            'dd2eb7c66ff2fa6f68a9d1e834e1911d2a1669a76ed29b5dbd6863619edcba18'
+            'b07517bdf9fcee43cf13533902ef333adcdaa45e60905628dfefc98ff55e95b5'
+            '485f305444fbe8ec3df3add5df68c5f2f7524507211f94bdecf2fa110c28c014'
+            '5ba4e0d9bdc4db0bab403b8f9aadb1320af60e91f9ed87e81dc680425375590b')
+
+pkgver() {
+  cd "$_pkgname"
+  printf "r%s.%s" "$(git rev-list --count HEAD)" "$(git rev-parse --short HEAD)"
+}
+
+prepare() {
+
+  cd "$srcdir/$_pkgname"
+
+  patch -Np0 -i "$srcdir/coot-configure.ac.patch"
+  patch -Np0 -i "$srcdir/coot-makefile.patch"
+  patch -Np0 -i "$srcdir/coot-guile.patch"
+  patch -Np1 -i "$srcdir/coot-libguile.patch"
+  patch -Np0 -i "$srcdir/coot-utils.patch"
+  patch -Np0 -i "$srcdir/coot-lbg.patch"
+  patch -Np0 -i "$srcdir/coot-python.patch"
+  patch -Np0 -i "$srcdir/coot-lidia.patch"
+  patch -Np0 -i "$srcdir/coot-pyrogen.patch"
+  patch -NRtp0 -i "$srcdir/coot-dynarama.patch"
+
+  iconv -f iso8859-1 -t utf-8 README > README.conv && mv -f README.conv README
+
+  cp $srcdir/coot.in src/
+
+}
+
+build() {
+  cd "$srcdir/$_pkgname"
+
+  aclocal -I macros
+  libtoolize --automake --copy
+  autoconf
+  automake --copy --add-missing --gnu
+
+  # Work around coot's code not beeing completely standard compliant
+  CXXFLAGS="${CXXFLAGS} -fpermissive"
+
+  ./configure --prefix=/usr \
+              --with-python \
+              --with-guile \
+              --with-guile-gtk \
+              --with-pygtk \
+              --with-sqlite3 \
+              --with-boost \
+              --with-boost-python \
+              --disable-static \
+              --with-enhanced-ligand-tools RDKIT_LIBS="-lRDKitMolDraw2D -lRDKitForceFieldHelpers -lRDKitDescriptors -lRDKitForceField -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDistGeomHelpers -lRDKitDistGeometry -lRDKitAlignment -lRDKitEigenSolvers -lRDKitDepictor -lRDKitMolChemicalFeatures -lRDKitFileParsers  -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7" RDKIT_CXXFLAGS="-I/usr/include/rdkit"
+
+  make
+}
+
+package() {
+  cd "$srcdir/$_pkgname"
+  make DESTDIR="$pkgdir/" install
+  sed -i 's|COOT_PYTHON_DIR=|COOT_PYTHON_DIR=/usr/lib/python2.7/site-packages/coot|' src/$_pkgname
+  sed -i 's|COOT_REFMAC_LIB_DIR=|COOT_REFMAC_LIB_DIR=/usr/share/coot/lib/|' src/$_pkgname
+  install -p -m 755 src/$_pkgname $pkgdir/usr/bin
+
+  # remove shebang from python scripts
+  for lib in $(find $pkgdir/usr/lib/python2.7/site-packages/$_pkgname/ -name "*.py"); do
+    sed '/\/usr\/bin\/env/d' $lib > $lib.new &&
+    touch -r $lib $lib.new &&
+    mv $lib.new $lib
+  done
+
+  chmod 644 $pkgdir/usr/lib/python2.7/site-packages/$_pkgname/$_pkgname.py
+
+  install -d $pkgdir/usr/share/$_pkgname/reference-structures
+  install -Dm644 $srcdir/reference-structures/*.pdb $pkgdir/usr/share/$_pkgname/reference-structures/
+
+  install -d $pkgdir/usr/share/$_pkgname/lib/data/monomers
+  cp -r $srcdir/monomers/* $pkgdir/usr/share/$_pkgname/lib/data/monomers/
+}
diff --git a/coot-configure.ac.patch b/coot-configure.ac.patch
new file mode 100644
index 000000000000..54ea352f0536
--- /dev/null
+++ b/coot-configure.ac.patch
@@ -0,0 +1,28 @@
+--- configure.ac.orig	2016-12-30 12:57:26.843081999 -0500
++++ configure.ac	2016-12-30 12:58:11.963460565 -0500
+@@ -45,11 +45,11 @@
+ 
+ # AC_PROG_INTLTOOL, no, not today.  Mac compilation problems, no perl/ XML or something.
+ # BL says Lets do some testing and use old style if needed
+-AC_MSG_CHECKING([which libtool initialization strategy to adopt])
+-AC_MSG_RESULT([m4_ifset([LT_INIT],[LT-INIT],[AC-PROG-LIBTOOL])])
+-m4_ifset([LT_INIT],
+-[LT_INIT],
+-[AC_PROG_LIBTOOL])
++# AC_MSG_CHECKING([which libtool initialization strategy to adopt])
++# AC_MSG_RESULT([m4_ifset([LT_INIT],[LT-INIT],[AC-PROG-LIBTOOL])])
++# m4_ifset([LT_INIT],
++# [LT_INIT],
++# [AC_PROG_LIBTOOL])
+ 
+ GNOME_COMPILE_WARNINGS
+ GNOME_CXX_WARNINGS
+@@ -148,7 +148,7 @@
+ AM_WITH_GUILE(, [echo optional guile\?],,)
+ if test x$coot_guile = xtrue ; then
+    GUILE_FLAGS
+-   AM_GUILE_LIB
++   # AM_GUILE_LIB
+    # guile-gui depends on a gui interface being present.  If it is, force check for guile-gui
+    if test x$with_guile_gtk != x ; then
+       AM_GUILE_GUI
diff --git a/coot-dynarama.patch b/coot-dynarama.patch
new file mode 100644
index 000000000000..7af8d00acb3c
--- /dev/null
+++ b/coot-dynarama.patch
@@ -0,0 +1,20 @@
+--- src/dynarama-main.cc.orig	2018-07-10 13:29:01.850708482 +0200
++++ src/dynarama-main.cc	2018-04-01 02:17:29.000000000 +0200
+@@ -23,8 +23,6 @@
+ 
+ #ifdef HAVE_GOOCANVAS
+ 
+-#include <gtk/gtk.h>
+-
+ #ifdef __GNU_LIBRARY__
+ #include "compat/coot-getopt.h"
+ #else
+@@ -35,6 +33,8 @@
+ 
+ #include <sys/stat.h>
+ 
++#include <gtk/gtk.h>
++
+ #ifdef HAVE_GOOCANVAS
+ #include <goocanvas.h>
+ #endif
diff --git a/coot-guile.patch b/coot-guile.patch
new file mode 100644
index 000000000000..44dd1462a020
--- /dev/null
+++ b/coot-guile.patch
@@ -0,0 +1,27 @@
+--- macros/guile_orig.m4	2013-07-31 00:25:19.715073145 -0700
++++ macros/guile.m4	2013-07-31 00:27:01.763927099 -0700
+@@ -72,21 +72,21 @@
+ # The variables are marked for substitution, as by @code{AC_SUBST}.
+ #
+ AC_DEFUN([GUILE_PROGS],
+- [AC_PATH_PROG(GUILE,guile)
++ [AC_PATH_PROG(GUILE,guile1.8)
+   if test x$with_guile = xyes ; then 
+      if test "$GUILE" = "" ; then
+ 	AC_MSG_ERROR([guile required but not found])
+      fi
+   fi
+   AC_SUBST(GUILE)
+-  AC_PATH_PROG(GUILE_CONFIG,guile-config)
++  AC_PATH_PROG(GUILE_CONFIG,guile-config1.8)
+   if test x$with_guile = xyes ; then 
+      if test "$GUILE_CONFIG" = "" ; then
+         AC_MSG_ERROR([guile-config required but not found])
+      fi
+   fi
+   AC_SUBST(GUILE_CONFIG)
+-  AC_PATH_PROG(GUILE_TOOLS,guile-tools)
++  AC_PATH_PROG(GUILE_TOOLS,guile-tools1.8)
+   AC_SUBST(GUILE_TOOLS)
+  ])
+ 
diff --git a/coot-lbg.patch b/coot-lbg.patch
new file mode 100644
index 000000000000..312737bc5c63
--- /dev/null
+++ b/coot-lbg.patch
@@ -0,0 +1,11 @@
+--- lbg/lbg.cc_orig	2016-11-09 21:27:32.074363190 -0500
++++ lbg/lbg.cc	2016-11-09 21:27:47.836327788 -0500
+@@ -4873,7 +4873,7 @@
+       } 
+    } else {
+ 
+-      PyObject *pName = PyString_FromString("lidia.fetch");
++      PyObject *pName = PyString_FromString("coot.lidia.fetch");
+       PyObject *pModule = PyImport_Import(pName);
+       if (pModule == NULL) {
+ 	 std::cout << "NULL pModule" << std::endl;
diff --git a/coot-libguile.patch b/coot-libguile.patch
new file mode 100644
index 000000000000..cbaccefb2947
--- /dev/null
+++ b/coot-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/coot-lidia.patch b/coot-lidia.patch
new file mode 100644
index 000000000000..aeb0c933ef71
--- /dev/null
+++ b/coot-lidia.patch
@@ -0,0 +1,10 @@
+--- lidia-core/use-rdkit.hh.old	2017-06-15 20:46:21.245950862 +0200
++++ lidia-core/use-rdkit.hh	2017-06-15 20:46:28.492679795 +0200
+@@ -5,6 +5,7 @@
+ #include <vector>
+ #include <algorithm>
+ #include <string>
++#include <queue>
+
+ #ifndef WINDOWS_MINGW
+ #define ENABLE_NLS // fixes dcgettext() header problems on including
diff --git a/coot-makefile.patch b/coot-makefile.patch
new file mode 100644
index 000000000000..316e0446e83b
--- /dev/null
+++ b/coot-makefile.patch
@@ -0,0 +1,35 @@
+--- src/Makefile.am_orig	2016-11-09 16:13:53.942706012 -0500
++++ src/Makefile.am	2016-11-09 16:15:08.263956290 -0500
+@@ -457,7 +457,9 @@
+    EXTRA_DIST += coot_wrap_python_pre.cc 
+ endif
+ if COOT_USE_PYTHON
+-   dist_python_PYTHON = coot.py coot.pth
++   # dist_python_PYTHON = coot.py coot.pth
++   pythondir = $(pkgdatadir)/python
++   dist_pkgpython_SCRIPTS = coot.py
+ endif
+ 
+ 
+--- lbg/Makefile.am_orig	2016-11-09 16:46:09.161705178 -0500
++++ lbg/Makefile.am	2016-11-09 21:51:45.630944576 -0500
+@@ -73,8 +73,8 @@
+ # 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)
++# wl=-Wl,
++# lidia_LDFLAGS = $(EXPORT_DYNAMIC_FLAG_SPEC)
+ 
+ # res spec output operator means we include libcoot-coord-utils
+ # (if that is annoying, then remove it and expand it by hand)
+@@ -106,7 +106,7 @@
+ test_srs_standalone_SOURCES = test-srs-standalone.cc
+ test_srs_standalone_LDADD = $(CCP4SRS_LIBS) $(MMDB_LIBS)
+ 
+-pkgpythondir=$(pythondir)/lidia
++pkgpythondir=$(pythondir)/coot/lidia
+ 
+ dist_pkgpython_PYTHON = \
+     __init__.py fetch.py
diff --git a/coot-pyrogen.patch b/coot-pyrogen.patch
new file mode 100644
index 000000000000..655abac7172b
--- /dev/null
+++ b/coot-pyrogen.patch
@@ -0,0 +1,22 @@
+--- pyrogen/pyrogen.in.old	2016-06-29 05:00:18.000000000 +0200
++++ pyrogen/pyrogen.in	2017-06-15 22:11:34.872817885 +0200
+@@ -7,11 +7,11 @@
+ 
+ systype=$(uname)
+ 
+-if [ $systype = Darwin ] ; then 
++if [ $systype = Darwin ] ; then
+    prfx=$(dirname "$current_exe_dir")
+    if [ -z "$DYLD_FALLBACK_LIBRARY_PATH" ] ;  then
+ 	DYLD_FALLBACK_LIBRARY_PATH=$prfx/lib
+-   else 
++   else
+ 	DYLD_FALLBACK_LIBRARY_PATH=$prfx/lib:${DYLD_FALLBACK_LIBRARY_PATH}
+    fi
+    export DYLD_FALLBACK_LIBRARY_PATH
+@@ -22,4 +22,4 @@
+ 
+ export PATH=$prfx/bin:$PATH
+
+-python -m pyrogen "${@}"
++python2 -m pyrogen "${@}"
diff --git a/coot-python.patch b/coot-python.patch
new file mode 100644
index 000000000000..f163ed7b794b
--- /dev/null
+++ b/coot-python.patch
@@ -0,0 +1,17 @@
+--- macros/with-python.m4.orig	2013-08-17 11:46:15.000000000 +0200
++++ macros/with-python.m4	2013-09-10 11:45:57.205754025 +0200
+@@ -41,12 +41,12 @@
+    # be $PYTHON:
+    #
+    if test x$PYTHON = x ; then
+-      PYTHON=python
++      PYTHON=python2
+    fi
+    # Similar for python-config
+    #
+    if test x$PYTHON_CONFIG = x ; then
+-      PYTHON_CONFIG=python-config
++      PYTHON_CONFIG=python2-config
+    fi
+ 
+    # Check to see if python exists:
diff --git a/coot-utils.patch b/coot-utils.patch
new file mode 100644
index 000000000000..6342f93a7952
--- /dev/null
+++ b/coot-utils.patch
@@ -0,0 +1,20 @@
+--- coot-utils/coot-shelx.hh_orig	2016-04-07 22:05:10.753625059 -0400
++++ coot-utils/coot-shelx.hh	2016-04-07 22:05:43.366973568 -0400
+@@ -33,6 +33,7 @@
+ 
+ #include <mmdb2/mmdb_manager.h>
+ #include "clipper/core/cell.h"
++#include "coot-coord-utils.hh"
+ 
+ namespace coot {
+ 
+--- coot-utils/coot-hole.hh_orig	2016-04-07 22:05:55.561054355 -0400
++++ coot-utils/coot-hole.hh	2016-04-07 22:06:16.954432665 -0400
+@@ -4,6 +4,7 @@
+ #include "clipper/core/xmap.h"
+ #include "clipper/core/nxmap.h"
+ 
++#include "coot-map-utils.hh"
+ #include "utils/coot-utils.hh"
+ #include "geometry/protein-geometry.hh"
+ 
diff --git a/coot.in b/coot.in
new file mode 100644
index 000000000000..1be2adf79aaf
--- /dev/null
+++ b/coot.in
@@ -0,0 +1,64 @@
+#!/bin/sh
+# -*-shell-script-*-
+# coot wrapper script
+# Copyright 2004, 2005, 2006, 2007 University of York
+# written by Paul Emsley
+
+COOT_PREFIX="/usr"
+current_exe_dir="/usr/libexec"
+
+coot_real=$current_exe_dir/coot-bin
+# echo coot-real is at $coot_real
+
+# ----------------------------------------------------------------------------
+# ----------------------------------------------------------------------------
+# If the COOT_PREFIX is correct, then these should not need modification
+# i.e.  nothing below here need be changed.
+# ----------------------------------------------------------------------------
+# ----------------------------------------------------------------------------
+#
+prefix=$COOT_PREFIX
+
+SYMINFO=$COOT_PREFIX/share/coot/syminfo.lib
+COOT_SCHEME_DIR=$COOT_PREFIX/share/coot/scheme
+COOT_STANDARD_RESIDUES=$COOT_PREFIX/share/coot/standard-residues.pdb
+COOT_PIXMAPS_DIR=$COOT_PREFIX/share/coot/pixmaps
+COOT_DATA_DIR=$COOT_PREFIX/share/coot
+COOT_RESOURCES_FILE=$COOT_PREFIX/share/coot/cootrc
+COOT_REF_STRUCTS=$COOT_PREFIX/share/coot/reference-structures
+COOT_PYTHON_DIR=
+COOT_REFMAC_LIB_DIR=
+LC_ALL=C
+
+PYTHONPATH=${PYTHONPATH:+"${PYTHONPATH}:"}$COOT_PYTHON_DIR
+
+GUILE_WARN_DEPRECATED=no
+
+if [ -n "$LOCAL_GUILE_LOAD_PATH_EXTRAS" ] ; then
+    GUILE_LOAD_PATH=${LOCAL_GUILE_LOAD_PATH_EXTRAS}:$GUILE_LOAD_PATH
+    export GUILE_LOAD_PATH
+fi
+
+# echo GUILE_LOAD_PATH is now $GUILE_LOAD_PATH
+
+export SYMINFO
+export COOT_PREFIX
+export COOT_STANDARD_RESIDUES
+export COOT_REFMAC_LIB_DIR
+export COOT_PYTHON_DIR
+export PYTHONPATH
+export COOT_SCHEME_DIR
+export COOT_REF_STRUCTS
+export COOT_RESOURCES_FILE
+export COOT_PIXMAPS_DIR
+export COOT_DATA_DIR
+
+export LC_ALL
+
+echo $coot_real $*
+$coot_real $*
+status=$?
+
+if [ $status != 0 ] ; then
+    /usr/bin/guile1.8 -s $COOT_PREFIX/share/coot/scheme/coot-crash-catcher.scm $coot_real
+fi