FinkPorts

ccp4 stable port information

Package: ccp4
Version: 6.2.0
Revision: 102
GCC: 4.0
UseMaxBuildJobs: false
#
Source: ftp://ftp.%n.ac.uk/%n/%v/%n-%v-core-src.tar.gz
Source-MD5: 1a087d3310d70501ac370804a11f341d
SourceDirectory: %n-%v
#
Source2: http://www.chem.ucsc.edu/~wgscott/xtal/xtalfink/XCCPJiffy-custom.gz
Source2-MD5: 21568dd2475505929573a3fd452c538f
#
Source3: ftp://ftp.%n.ac.uk/%n/%v/%n-%v-phaser-cctbx-src.tar.gz
Source3-MD5: 15ef58deb26eaacc2bacf7f4ae38d391
#
Source4: ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.6.1.tar.gz
Source4-MD5: 6a2cc719e4e5a018e336375aac47288c
Source4ExtractDir: %n-%v/src/pointless
#
PatchFile: ccp4.patch
PatchFile-MD5: 30a2ecc69f0030fe33cf7c9e76d83878
#
DescPort: <<
CCP4 is designed to compile with gfortran on OS X >= 10.4 by default.
Jack Howarth has provided multiple improvements in the patch file to
address several bugs and to permit optimization with gfortran at -O3.

Users typically install all of the ccp4 files into /xtal/ccp4-%v or
into /usr/local/xtal/ccp4-%v. In the present case, these files are
installed into %p/share/xtal/ccp4-%v. The library files are installed
into the directory %p/lib/ccp4-%v and this directory is symbolically
linked to %p/share/xtal/ccp4-%v/lib which is the canonical location.
Dynamic libraries are provided in the ccp4-shlibs splitoff package, and
static libraries are provided in the ccp4-dev splitoff package. The
configure files are patched so that the full path to the dynamic
libraries is hard-coded, per fink policy. This obviates the need to
set the DYLD_LIBRARY_PATH environment variable, which should remain
unset. The appropriate shell startup files are automatically sourced
when %p/bin/init.(c)sh is invoked upon shell startup; there is no
need to do so manually. The actual files are located (not my choice)
in $CCP4/include.

The ccp4i mail utility by default will only work on machines that run
a unix mail server. As a workaround, a public domain perl script called
osx_ccp4_mail is installed that glues the ccp4i mail button to the
Apple OS X Mail.app.

Further adaptations are commented in place in the patch, configure and
install scripts below. Relevant patches specific to this version that
are issued by CCP4 are now downloaded and applied individually, helping
to keep the ccp4.patch file from growing metastatically and also to
permit the user to verify that the latest patches have been applied.
These start, when present, with Source2 (above) and are applied
individually at the end of the PatchScript field.

Clipper libraries are not behaving properly when linked to fink fftw
so we return to the option of having ccp4 build its own private fftw.
Yes, I hate it too, but now all the examples pass the run-all test.

64-bit version prior to OS X 10.7 appears to require ccp4\'s own
blas/lapak to avoid run-time errors. I use that in all versions now,
but plan to get rid of this as soon as possible.
<<
Depends: x11, tcltk, blt, gcc46-shlibs, %N-shlibs (= %v-%r)
BuildDepends: gcc46, tcltk-dev, x11-dev, xmkmf (>= 1.0.2-3), fink (>= 0.24.12)
BuildDependsOnly: False
BuildConflicts: gpp4-dev, gpp4, ssm, ssm-dev, mmdb, mmdb-dev, clipper, clipper-bin, clipper-dev, ccp4-onlylibs-dev, python
Replaces: phaser (<= 2.3.0-1), pointless (<= 1.2.18-1), mosflm (<= 7.0.3-3), mosflm-small (<= 7.0.3-3), imosflm (<= 1:1.0.4-4), imosflm-aqua (<= 1:1.0.4-4), refmac (<= 5.5.0070-1), bundle-ccp4-intel, clipper-bin, ccp4-gfortran, ccp4-gfortran-dev, bundle-ccp4-powerpc
Conflicts: <<
mosflm (<= 7.0.3-3),
mosflm-small (<= 7.0.3-3),
imosflm (<= 1:1.0.4-4),
imosflm-aqua (<= 1:1.0.4-4),
refmac (<= 5.5.0070-1),
bundle-ccp4-intel,
bundle-ccp4-powerpc,
ccp4-gfortran,
ccp4-gfortran-dev,
phaser (<= 2.3.0-1),
pointless (<= 1.2.18-1)
<<
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
#
################################################################################
PatchScript: <<
#!/bin/zsh -efv
#
umask 0022

# Now apply the primary patch
sed 's|@PREFIX@|%p|g' <%{PatchFile} | patch -p1

# setup script for tcsh, zsh and bash users
export TEMPXTAL=$PWD:h
#
perl -pi.bak -e 's|-traditional-cpp||g' src/harvest_app_/pdb_extract/etc/*.platform*
perl -pi.bak -e 's|/xtal|\$TEMPXTAL|g' include/ccp4.setup-csh # build prefix (changed in install)
perl -pi.bak -e 's|/prefix|%p|g' include/ccp4.setup* # location of tcktk, blt
perl -pi.bak -e 's|/usr/local/bin|%p/bin|g' include/ccp4.setup* # same
perl -pi.bak -e 's|limit stacksize 65536|limit stacksize unlimited|g' include/ccp4.setup* # same
perl -pi.bak -e 's|ccp4_first_in_path=1|ccp4_first_in_path=0|g' include/ccp4.setup*
perl -pi.bak -e 's|ccp4_first_in_path\ =\ 1|ccp4_first_in_path\ =\ 0|g' include/ccp4.setup*
perl -pi.bak -e 's|setenv GFORTRAN_UNBUFFERED_ALL Y|# setenv GFORTRAN_UNBUFFERED_ALL Y|g' include/ccp4.setup*
perl -pi.bak -e 's|export GFORTRAN_UNBUFFERED_ALL|# export GFORTRAN_UNBUFFERED_ALL|g' include/ccp4.setup*
perl -pi -e 's|Please get the person who installed CCP4i to run it|Please issue the command \\\"sudo -E ccp4i\\\"|g' ccp4i/src/system.tcl
if [[ $(sw_vers -productVersion) < 10.6 ]]; then
true
else
/usr/bin/grep -v "char \*strcat( char \*, const char \*);" x-windows/Mosflm/src/dps/index/ind_gen_direct.c >| x-windows/Mosflm/src/dps/index/ind_gen_direct.tmp
/bin/cp x-windows/Mosflm/src/dps/index/ind_gen_direct.tmp x-windows/Mosflm/src/dps/index/ind_gen_direct.c
/bin/rm -f x-windows/Mosflm/src/dps/index/ind_gen_direct.tmp
fi
#
/bin/cp include/ccp4.setup-dist include/ccp4.setup
rm -f include/ccp4.setup-sh
#
# Set up XCCPJiffy wrapper scripts in $CCP4/etc
# These are small wrapper scripts for xplot84driver and xloggraph generated by the patch
chmod a+x etc/x*
# Fix the dylib install path in configure
perl -pi.bak -e 's|\$rpath|%p/lib/ccp4-%v|g' **/configure
#
perl -pi.bak -e 's|import sys|import sys\nsys.path.append(\"%p/share/xtal/%n-%v/share/python\")|g' src/buccaneer_pipeline.py
#
/bin/rm -f *.bak **/configure*.bak src/buccaneer_pipeline*.bak include/*.bak
<<
################################################################################
CompileScript: <<
#!/bin/bash -efv
umask 0022
# These are required for the build environment
TEMPXTAL=$(dirname $PWD)
export TEMPXTAL
export CCP4_VERSION=""
export CCP4_MASTER=""
export BLTWISHPREFIX=""
export CCP4=""
# Fix for problem reported with 10.4
if [[ $(sw_vers -productVersion) < 10.5 ]]; then
cp $PWD/include/ccp4.setup-bash $PWD/include/ccp4.setup-bash-10.4
export CURRENT_MASTER=$( dirname $PWD )
perl -pi -e "s|export CCP4_MASTER|export CCP4_MASTER=$CURRENT_MASTER|g" $PWD/include/ccp4.setup-bash-10.4
source $PWD/include/ccp4.setup-bash-10.4
else
source $PWD/include/ccp4.setup-bash
fi
#
echo $PWD should be the same as $CCP4
[[ $CCP4 == $PWD ]] || exit 1
set +x
export DYLD_LIBRARY_PATH=$CLIB
export GFORTRAN_UNBUFFERED_ALL="Y"
export rpath=%p/lib/ccp4-%v
export RPATH=%p/lib/ccp4-%v
export PATH=%p/lib/xmkmf/bin:$PATH
export IMAKEINCLUDE=-I%p/lib/X11/config
export FC="gfortran"
export libdir="$PWD/lib"
#
# Uncomment the following line only for testing purposes. The ccp4 restrictive/commercial
# license forbid disabling the interactive check in this way for the end-user
#
# touch .agree2ccp4v6
#
#
#if [[ $(sw_vers -productVersion) < 10.7 ]]; then
F_LIBS="-L%p/lib/gcc4.6/lib -lgfortran " \
./configure --with-netlib-lapack --with-shared-libs --with-x Darwin
#else
# F_LIBS="-L%p/lib/gcc4.6/lib -lgfortran " \
# ./configure --with-shared-libs --with-x Darwin
#fi
#
# fix some post-configure bugs by getting rid of -lg2c
/usr/bin/perl -pi.bak -e "s|-lg2c||g" deprecated/src/beast_/beast_MPI/Makefile x-windows/XCCPJIFFY/Imakefile
( cd x-windows/XCCPJIFFY; perl -pi.bak -e 's|-lgfortran|-lgfortran -L%p/lib/gcc4.6/lib |g' *akefile* ) || exit 1
if [[ $(sw_vers -productVersion) < 10.5 ]]; then
perl -pi.bak -e 's| -flat_namespace -undefined suppress| -twolevel_namespace -undefined dynamic_lookup|g' lib/src/Makefile
fi
perl -pi.bak -e "s|-lcrt1.10.6.o||g" Makefile ccp4i/Makefile deprecated/src/Makefile lib/data/Makefile lib/src/Makefile share/Makefile src/Makefile
perl -pi.bak -e "s|-lcrt1.10.6.o||g" src/ccp4mapwish_/Makefile unsupported/src/Makefile x-windows/Makefile x-windows/Mosflm/mosflm/Makefile x-windows/Rotgen/Makefile

perl -pi.bak -e "s|-lcrt1.10.5.o||g" Makefile ccp4i/Makefile deprecated/src/Makefile lib/data/Makefile lib/src/Makefile share/Makefile src/Makefile
perl -pi.bak -e "s|-lcrt1.10.5.o||g" src/ccp4mapwish_/Makefile unsupported/src/Makefile x-windows/Makefile x-windows/Mosflm/mosflm/Makefile x-windows/Rotgen/Makefile

perl -pi.bak -e "s|-lcrt1.o||g" Makefile ccp4i/Makefile deprecated/src/Makefile lib/data/Makefile lib/src/Makefile share/Makefile src/Makefile
perl -pi.bak -e "s|-lcrt1.o||g" src/ccp4mapwish_/Makefile unsupported/src/Makefile x-windows/Makefile x-windows/Mosflm/mosflm/Makefile x-windows/Rotgen/Makefile

# Fix for pointless, bp3 etc to prevent linking to gcc4.6 libraries as this creates a run-time error
perl -pi.mod -e 's|-O2|-O3|g' src/pointless/Makefile
grep -v "gcc4.6" src/pointless/Makefile.mod > src/pointless/Makefile


# Fix newly indtroduced X11 library error
perl -pi.bak -e 's|/usr/X11R6/lib64|/usr/X11R6/lib|g' Makefile ccp4i/Makefile deprecated/src/Makefile lib/data/Makefile lib/src/Makefile share/Makefile src/Makefile src/ccp4mapwish_/Makefile unsupported/src/Makefile x-windows/Makefile

# Fix newly intdroduced ccif error

perl -pi.bak -e 's|LD_LIBRARY_PATH|DYLD_LIBRARY_PATH|g' lib/ccif/Makefile


#################
#################
cd $CCP4
make
make install
#################
#################

# xloggraph may fail, but we will link it with gfortran below
#
# Make wrappers for xplot84driver and xloggraph, so rename the executables
cd x-windows/XCCPJIFFY
if [[ "%m" != "x86_64" ]]; then
make msg_box.o ZDr2d.o EditString.o hardcopy_ctrl.o xloggraph.o log_file.o tom_fortran_interface.o bits_and_pieces.o graphics.o CFLAGS="-m32" FFLAGS="-m32"
else
make msg_box.o ZDr2d.o EditString.o hardcopy_ctrl.o xloggraph.o log_file.o tom_fortran_interface.o bits_and_pieces.o graphics.o CFLAGS="-m64" FFLAGS="-m64"
fi
gcc -o xplot84driver xplot84driver.o plot84_file.o msg_box.o ZDr2d.o EditString.o hardcopy_ctrl.o -Os -I/usr/include/X11R6 -L/usr/X11R6/lib -lXaw -lXmu -lXt -lSM -lICE -lXpm -lXp -lXext -lX11 -lm -L%p/lib/gcc4.6/lib -lgfortran
cp xplot84driver $CBIN/xplot84driver.exe
if [[ -x $CBIN/xplot84driver ]];then
/bin/rm -f $CBIN/xplot84driver
fi
make xccpjiffy2idraw
cp xccpjiffy2idraw $CBIN/.
cd ..
make xdlmapman xdldataman
cp xdlmapman $CBIN/.
cp xdldataman $CBIN/.
# Manually link xloggraph with gfortran (fails in make)
echo ""
echo "**********************************************************************"
echo "Re-linking xloggraph with gfortran. Ignore previous error messages."
echo "**********************************************************************"
echo ""
#
cd XCCPJIFFY
# Check to see if it really did fail before we try again.
if [[ -x $CBIN/xloggraph ]];then
true
else
gfortran -o xloggraph msg_box.o ZDr2d.o EditString.o hardcopy_ctrl.o xloggraph.o log_file.o tom_fortran_interface.o bits_and_pieces.o graphics.o -g -Os -I/usr/include/X11R6 -L/usr/X11R6/lib -lXaw -lXmu -lXt -lSM -lICE -lXpm -lXext -lX11 -lm -lgfortran -L%p/lib/gcc4.6/lib
fi
#
sleep 10
#
cp xloggraph $CBIN/xloggraph.exe
if [[ -x $CBIN/xloggraph ]];then
/bin/rm -f $CBIN/xloggraph
fi
cd ../..
#
# Cleanup:

# Get rid of the corrupting influence of ccp4's own xml2-config:
if [[ -x $CBIN/xml2-config ]];then
/bin/rm -f $CBIN/xml2-config
fi
# Do the rest in the InstallScript to take advantage of zsh.
<<
################################################################################
InstallScript: <<
#!/bin/zsh -efv

umask 0022
export TEMPXTAL=$PWD:h
source $PWD/include/ccp4.setup-zsh
export DYLD_LIBRARY_PATH=$CLIB
ORIGDIR=$(dirname $PWD)

export PATH=%p/lib/xmkmf/bin:$PATH
export IMAKEINCLUDE=-I%p/lib/X11/config

# Cleanup is much easier with zsh recursive globbing
# several requests made from users to leave
# source code in place
/bin/rm -f **/*.o
/bin/rm -f **/*.bak
# remove redundant library junk
/bin/rm -Rf lib/cctbx
/bin/rm -Rf lib/**/.libs
/bin/rm -Rf src/leiden/bp3lib/src/.libs
/bin/rm -Rf src/Prodrg/.libs
/bin/rm -f lib/ccif/libccif.dylib
/bin/rm -f lib/src/libccp4c.dylib
/bin/rm -f lib/src/libmmdb.dylib
/bin/rm -R testcomp*
/bin/rm -R BINARY*


# Change environment scripts to match final installation
perl -pi -e 's|\$TEMPXTAL|%p/share/xtal|g' include/ccp4.setup* # install prefix
#
# Bugzilla number : #3593
perl -pi -e "s|$PWD|%p/share/xtal/%n-%v|g" share/pisa/pisa.cfg
#
#
cp ../XCCPJiffy-custom.gz XCCPJiffy.gz ; gunzip XCCPJiffy.gz; chmod a+x XCCPJiffy
perl -pi -e 's|5.0.1|%v|g' XCCPJiffy
mv -f XCCPJiffy lib/X11/app-defaults/XCCPJiffy
#
perl -pi.bak -e 's|/src/fink.build/ccp4-%v-%r|/share/xtal|g' bin/clipper-config
rm -f bin/clipper-config.bak
perl -pi.bak -e 's|lclipper |lclipper-core |g' bin/clipper-config
rm -f bin/clipper-config.bak
perl -pi.bak -e 's|lib/lib -lrfftw -lfftw |lib/ccp4-%v -lsrfftw -lsfftw |g' bin/clipper-config
rm -f bin/clipper-config.bak
#
# Fix path in libfoo.la libtool files:
#
perl -pi.bak -e 's|/src/fink.build/ccp4-%v-%r/ccp4-%v/lib|/lib/ccp4-%v|g' lib/**/*.la
/bin/rm -f lib/python*/site-packages/libxml2mod.la
/bin/rm -f lib/**/*.la.bak
#######


# make and install the leiden stuff. It has to go here.

cd $CCP4/src/leiden
make clean
perl -pi -e 's|LAPACK_LIBS = -framework vecLib -L%p/lib/gcc4.6/lib -lgfortran|LAPACK_LIBS = -L$CLIB/lapack|g' **/Makefile
perl -pi -e 's|FCLIBS = -L%p/lib/gcc4.6/lib/gcc/x86_64-apple-darwin11.0.0/4.6.1 -L%p/lib/gcc4.6/lib/gcc/x86_64-apple-darwin11.0.0/4.6.1/../../.. -lgfortran -lquadmath -lm||g' **/Makefile
perl -pi -e 's|-L%p/lib/gcc4.6/lib -lgfortran||g' **/Makefile
make -i
make -i install
cd $CCP4
#################
# More cleanup:
/bin/rm -Rf src/leiden/bp3lib/src/.libs
/bin/rm -f **/*.o
perl -pi.bak -e 's|/src/fink.build/ccp4-%v-%r/ccp4-%v/lib|/lib/ccp4-%v|g' lib/**/*.la
# Remove duplicate header files
/bin/rm -f include/**/*.h

######
#
# Now install:
#
mkdir -p %i/lib
cp -R lib %i/lib/ccp4-%v
mkdir -p %i/bin
#
mkdir -p %i/share/xtal/ccp4-%v/help
mkdir -p %i/share/man/man1
# set up man pages in a fink-compliant manner
cd $PWD/doc
mv rasmol.doc eightbit_rasmol.doc
foreach docfilepage ( *.doc )
cp ${docfilepage} %i/share/man/man1/${docfilepage:r}.1
cp ${docfilepage} %i/share/xtal/ccp4-%v/help/${docfilepage:r}
end
# back to build directory
cd ..
#
/bin/rm -rf lib
cp -R * %i/share/xtal/ccp4-%v/.
ln -s %p/lib/ccp4-%v %i/share/xtal/ccp4-%v/lib
#
# making scripts for %p/etc/profile.d
mkdir -p %i/etc/profile.d
#
echo "source %p/share/xtal/ccp4-%v/include/ccp4.setup" > %i/etc/profile.d/ccp4.csh
echo "setenv CLIB %p/lib/ccp4-%v " >> %i/etc/profile.d/ccp4.csh
#

echo "if [ -z \$ZSH_NAME ];then " > %i/etc/profile.d/ccp4.sh
echo " source %p/share/xtal/ccp4-%v/include/ccp4.setup-bash " >> %i/etc/profile.d/ccp4.sh
echo "else " >> %i/etc/profile.d/ccp4.sh
echo " source %p/share/xtal/ccp4-%v/include/ccp4.setup-zsh" >> %i/etc/profile.d/ccp4.sh
echo "fi " >> %i/etc/profile.d/ccp4.sh
echo "export CLIB=%p/lib/ccp4-%v " >> %i/etc/profile.d/ccp4.sh
#
chmod a+x %i/etc/profile.d/ccp4.*
#
chmod a+x %i/share/xtal/ccp4-%v/ccp4i/etc/osx_ccp4_mail
#
chmod a+r,a+x %i/share/xtal/ccp4-%v/etc/*
chmod a+r,a+x %i/share/xtal/ccp4-%v/bin/*
chmod a+r,a+x %i/share/xtal/ccp4-%v/ccp4i/bin/*
chmod a+r,a+x %i/share/xtal/ccp4-%v/share/dbccp4i/bin/*
chmod a+r,a+x %i/share/xtal/ccp4-6.2.0/ccp4i/imosflm/src/*
#
# chmod a+x %i/share/xtal/ccp4-%v/etc/ccp4help
#
ranlib %i/lib/ccp4-%v/*.a
ranlib %i/lib/ccp4-%v/**/*.a
#
perl -pi -e 's|%p/share/%p/share|%p/share|g' %i/share/xtal/ccp4-%v/include/ccp4.setup* # fix

# remove build path from .la files
# perl -pi -e "s, \-L[^ ']*/%n-%v-%r/%n-%v/src/rapper/libxml2/.libs, \-L %p/lib,g" %i/lib/%n-%v/python*/site-packages/**/*.la

# don't package these .la files
/usr/bin/find %i/share/xtal/%n-%v/src/rapper -name '*.la' -delete
/usr/bin/find %i/share/xtal/%n-%v/x-windows -name '*.la' -delete
/usr/bin/find %i/share/xtal/%n-%v/src/leiden/bp3lib/src -name '*.la' -delete
/usr/bin/find %i/share/xtal/%n-%v/src/Prodrg -name '*.la' -delete

# hand install these shared libraries for now
mv %i/share/xtal/ccp4-%v/src/phaser/phaser-2.3.0/build/mac-osx/lib/libboost_python.dylib %i/lib/ccp4-%v
install_name_tool -id %p/lib/ccp4-%v/libboost_python.dylib %i/lib/ccp4-%v/libboost_python.dylib
mv %i/share/xtal/ccp4-%v/x-windows/libjwc/libjwc_c/.libs/libjwc_c.0.1.1.dylib %i/lib/ccp4-%v
install_name_tool -id %p/lib/ccp4-6.2.0/libjwc_c.0.dylib %i/lib/ccp4-%v/libjwc_c.0.1.1.dylib
mv %i/share/xtal/ccp4-%v/x-windows/xdl_view/src/.libs/libxdl_view.2.0.0.dylib %i/lib/ccp4-%v
install_name_tool -id %p/lib/ccp4-%v/libxdl_view.2.dylib %i/lib/ccp4-%v/libxdl_view.2.0.0.dylib
mv %i/share/xtal/ccp4-%v/x-windows/xdl_view/src/.libs/libxdl_viewextra.0.0.0.dylib %i/lib/ccp4-%v
install_name_tool -id %p/lib/ccp4-%v/libxdl_viewextra.0.dylib %i/lib/ccp4-%v/libxdl_viewextra.0.0.0.dylib

# don't package .pyc files generated in the buildroot
/usr/bin/find %i/share/xtal/%n-%v/src/phaser/phaser-2.3.0 -name '*.pyc' -delete



<<
################################################################################
PreRmScript: <<
[[ -d %p/share/xtal/%n-%v/src/phaser/phaser-2.3.0 ]] && /usr/bin/find %p/share/xtal/%n-%v/src/phaser/phaser-2.3.0 -name '*.pyo' -delete
<<
################################################################################
PostInstScript: <<

PyVers=$( /usr/bin/python --version 2>&1 | awk '{print $NF}' )

if [[ $PyVers:r == 2.6 ]]; then
/usr/bin/python -O /usr/lib/python2.6/compileall.py -q %p/share/xtal/%n-%v/src/phaser/phaser-2.3.0
elif [[ $PyVers:r == 2.5 ]]; then
/usr/bin/python -O /usr/lib/python2.5/compileall.py -q %p/share/xtal/%n-%v/src/phaser/phaser-2.3.0
elif [[ $PyVers:r == 2.4 ]]; then
/usr/bin/python -O /usr/lib/python2.4/compileall.py -q %p/share/xtal/%n-%v/src/phaser/phaser-2.3.0
fi

# Make the user read the license conditions
more %p/share/xtal/ccp4-%v/conditions.txt
<<
################################################################################
################################################################################
SplitOff: <<
Package: %N-shlibs
Description: CCP4 dynamic libraries
Files:<<
lib/ccp4-%v/*.*.dylib
lib/ccp4-%v/libccif.dylib
lib/ccp4-%v/libccp4c.dylib
lib/ccp4-%v/libmmdb.dylib
lib/ccp4-%v/libboost_python.dylib
<<
Shlibs: <<
%p/lib/ccp4-%v/libDiffractionImage.0.dylib 1.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/lib_DiffractionImage.0.dylib 1.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libccif.dylib 0.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libccp4c.dylib 0.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libclipper-ccp4.2.dylib 3.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libclipper-cif.2.dylib 3.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libclipper-cns.0.dylib 1.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libclipper-contrib.2.dylib 3.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libclipper-core.2.dylib 3.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libclipper-minimol.2.dylib 3.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libclipper-mmdb.2.dylib 3.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libclipper-phs.2.dylib 3.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libjwc_c.0.dylib 2.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libmmdb.dylib 0.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libssm.0.dylib 1.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libxdl_view.2.dylib 3.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libxdl_viewextra.0.dylib 1.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libfftw.2.dylib 3.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/librfftw.2.dylib 3.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libboost_python.dylib 0.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libbp3.1.dylib 2.0.0 %n (>= 6.2.0-1)
%p/lib/ccp4-%v/libprodrg.0.dylib 1.0.0 %n (>= 6.2.0-1)
<<
DocFiles: CHANGES COPYING INSTALL INSTALL.html INSTALL.ps README PROBLEMS academic_software_licence.pdf
<<
################################################################################
################################################################################
SplitOff2: <<
Package: %N-dev
BuildDependsOnly: true
Conflicts: gpp4-dev, ssm-dev, mmdb-dev, clipper-dev, ccp4-onlylibs-dev
Replaces: gpp4-dev, ssm-dev, mmdb-dev, clipper-dev, ccp4-onlylibs-dev
Description: CCP4 static libraries and libtool files
Files:<<
lib/ccp4-%v/*.a
lib/ccp4-%v/*.la
<<
DocFiles: CHANGES COPYING INSTALL INSTALL.html INSTALL.ps README PROBLEMS academic_software_licence.pdf
<<
################################################################################
Description: Macromolecular crystallography package
DescDetail: <<
The CCP4 macromolecular crystallography suite has approximately
200 programs and utilities. This version includes the Clipper
libraries. Current phaser and cctbx programs are available as
separate fink packages.

Type "ccp4help" for a summary listing of all ccp4 programs.
Type "ccp4help foo" for a detailed description of program "foo."

Invoke optional ccp4i gui for the first run using "sudo ccp4i"
on 10.4, or "sudo -E ccp4i" on 10.5 and above to permit global
configuration. Thereafter, you can invoke ccp4i without sudo.

This version compiles with the Apple Lapack/Blas framework.
License agreement is part of configure file -- print out form and mail in,
additional comments at http://sage.ucsc.edu/xtal/ccp4.html

CCP4 files will be installed under /sw/share/xtal/ccp4-6.2.0
This revision includes all available CCP4 patches,
and new bash and zsh command completions specific to ccp4.

The ccp4-associated molecular graphics display program coot is also
available as a fink package. It builds against the GPL gpp4 libraries
rather than those of this package.

Thanks to Jack Howarth for many helpful improvements.
<<
DocFiles: <<
README CHANGES COPYING PROBLEMS INSTALL INSTALL.html INSTALL.ps
ccp4i_installation.html academic_software_licence.pdf
academic_software_licence.ps.gz academic_software_licence.rtf
<<
Homepage: http://www.ccp4.ac.uk
License: Commercial
Maintainer: W. G. Scott

ccp4 stable port .patch

diff -ruN ccp4-6.2.0-dist/ccp4i/bin/imosflm ccp4-6.2.0/ccp4i/bin/imosflm
--- ccp4-6.2.0-dist/ccp4i/bin/imosflm 2009-04-21 05:46:23.000000000 -0700
+++ ccp4-6.2.0/ccp4i/bin/imosflm 2010-12-17 20:33:01.000000000 -0800
@@ -1,3 +1,14 @@
#!/bin/sh
# Start iMosflm interface
+if [[ $(uname) == Darwin ]];then
+
+ CCP4_BROWSER=""
+ export CCP4_BROWSER="Safari"
+
+ if [[ $(sw_vers -productVersion) < 10.6 ]]; then
+ true
+ else
+ export MOSFLM_WISH=/usr/bin/wish8.4
+ fi
+fi
exec $CCP4I_TOP/imosflm/src/imosflm
diff -ruN ccp4-6.2.0-dist/ccp4i/etc/configure.def.dist ccp4-6.2.0/ccp4i/etc/configure.def.dist
--- ccp4-6.2.0-dist/ccp4i/etc/configure.def.dist 2010-09-08 07:02:56.000000000 -0700
+++ ccp4-6.2.0/ccp4i/etc/configure.def.dist 2010-12-17 20:34:22.000000000 -0800
@@ -61,8 +61,8 @@
MESSAGE _text ""
BLT_LIBRARY _text ""
MENU_LENGTH _positiveint 25
-HYPERTEXT_VIEWER _text firefox
-START_NETSCAPE _text netscape
+HYPERTEXT_VIEWER _text safari
+START_NETSCAPE _text open
O_MAPMAN _text mapman
MAPMAN_MAXSIZE _positiveint 4194304
QUANTA_MBKALL _text mbkall
diff -ruN ccp4-6.2.0-dist/ccp4i/etc/osx_ccp4_mail ccp4-6.2.0/ccp4i/etc/osx_ccp4_mail
--- ccp4-6.2.0-dist/ccp4i/etc/osx_ccp4_mail 1969-12-31 16:00:00.000000000 -0800
+++ ccp4-6.2.0/ccp4i/etc/osx_ccp4_mail 2010-12-17 20:34:59.000000000 -0800
@@ -0,0 +1,164 @@
+#!/usr/bin/perl
+# Drop-in replacement for /usr/bin/mail that uses Mail.app (via an
+# applescript) rather than sendmail to send mail. Unlike /usr/bin/mail,
+# you can't use it for reading mail.
+#
+# usage: mail []
+# options:
+# -v be verbose
+# -g activate Mail.app to approve the message
+# -F specify the From: address
+# -b specify Bcc: recipients in a comma-separated list
+# -c specify Cc: recipients in a comma-separated list
+# -s specify the message subject
+#
+# The body of the message is read from standard input.
+#
+# Author: Nathaniel Nystrom
+# This software is in the public domain.
+#
+# Version 1.0, 21 Aug 2003 -- initial version
+# Version 1.0.1, 22 Aug 2003 -- fixes some quoting problems
+# Version 1.0.2, 23 Aug 2003 -- removed -R option; |reply to|
+# is a property of _incoming_ messages
+# Version 1.0.3, 17 Sep 2003 -- fixed escaping of \ in message body;
+# escape the subject too
+
+use strict;
+$|++;
+
+my ($verbose, $gui);
+my ($from, @to, @cc, @bcc, $subject, $body);
+my $prog;
+($prog = $0) =~ s|.*/||;
+
+while (@ARGV) {
+ my $arg = shift @ARGV;
+
+ if ($arg eq '-v') {
+ $verbose++;
+ }
+ elsif ($arg eq '-g') {
+ $gui++;
+ }
+ elsif ($arg eq '-F') {
+ $from = shift @ARGV || &usage("missing sender");
+ }
+ elsif ($arg eq '-i' || $arg eq '-l' || $arg eq '-n') {
+ # ignore; for /usr/bin/mail compatibility
+ }
+ elsif ($arg eq '-N' || $arg eq '-f' || $arg eq '-u') {
+ &usage("invalid option $arg; $prog cannot be used for reading mail");
+ }
+ elsif ($arg eq '-s') {
+ $subject = shift @ARGV || &usage("missing subject");
+ }
+ elsif ($arg eq '-c') {
+ my $list = shift @ARGV || &usage("missing Cc list");
+ @cc = split /\s*,\s*/, $list;
+ }
+ elsif ($arg eq '-b') {
+ my $list = shift @ARGV || &usage("missing Bcc list");
+ @bcc = split /\s*,\s*/, $list;
+ }
+ elsif ($arg =~ /^-/) {
+ &usage("invalid option $arg");
+ }
+ else {
+ @to = ($arg, @ARGV);
+ last;
+ }
+}
+
+&usage("missing recipients") unless @to;
+
+unless (defined $subject) {
+ print "Subject: ";
+ $subject = || '';
+ chomp $subject;
+}
+
+$body = '';
+
+while () {
+ $body .= $_;
+}
+
+$body = &escape($body);
+$subject = &escape($subject);
+
+my $script = <<"EOS";
+tell application "Mail"
+ set newMessage to make new outgoing message
+ tell newMessage
+ set subject to "$subject"
+ set content to "$body"
+EOS
+
+for (@to) { $script .= &recipient('to', $_); }
+for (@cc) { $script .= &recipient('cc', $_); }
+for (@bcc) { $script .= &recipient('bcc', $_); }
+
+my $visible = $gui ? "true" : "false";
+my $activate = $gui ? "activate" : "send newMessage";
+my $fromln = $from ? "set sender to \"$from\"" : "";
+
+$script .= <<"EOS";
+ $fromln
+ set visible to $visible
+ end tell
+ $activate
+end tell
+EOS
+
+if ($verbose >= 1) {
+ print "From: $from\n" if $from;
+ print "To: ", join(',', @to), "\n" if @to;
+ print "Cc: ", join(',', @cc), "\n" if @cc;
+ print "Bcc: ", join(',', @bcc), "\n" if @bcc;
+
+ if ($verbose >= 2) {
+ print "Script >>>\n";
+ print $script;
+ print "<<<\n";
+ print "\n";
+ print $body;
+ }
+}
+
+open(SCRIPT, "| osascript > /dev/null") || die "Couldn't fork osascript: $!\n";
+print SCRIPT $script;
+close SCRIPT;
+
+exit 0;
+
+sub escape {
+ my $x = shift;
+ $x =~ s/\\/\\\\/gm;
+ $x =~ s/"/\\"/gm;
+ $x =~ s/\n/\\n/gm;
+ $x;
+}
+
+sub recipient {
+ my ($type,$addr) = @_;
+ return <<"EOS"
+ make new $type recipient at end of $type recipients with properties {address: "$addr"}
+EOS
+}
+
+sub usage {
+ my $error = shift;
+ print STDERR "Error: $error\n" if $error;
+ print STDERR <<"EOS";
+usage: $prog []
+ options:
+ -v be verbose
+ -g activate Mail.app to approve the message
+ -F specify the From: address
+ -b specify Bcc: recipients in a comma-separated list
+ -c specify Cc: recipients in a comma-separated list
+ -s specify the message subject
+EOS
+ exit 1;
+}
diff -ruN ccp4-6.2.0-dist/ccp4i/src/local.tcl ccp4-6.2.0/ccp4i/src/local.tcl
--- ccp4-6.2.0-dist/ccp4i/src/local.tcl 2009-03-09 09:41:06.000000000 -0700
+++ ccp4-6.2.0/ccp4i/src/local.tcl 2010-12-17 20:36:07.000000000 -0800
@@ -34,7 +34,7 @@
#d_arg mail_address Mail addressee

return [expr {1 - [catch \
- "exec Mail -s \"$subject\" $mail_address < $tmp_file" ]}]
+ "exec osx_ccp4_mail -s \"$subject\" $mail_address < $tmp_file" ]}]
}

#d_index_title Interaction with Netscape
diff -ruN ccp4-6.2.0-dist/configure ccp4-6.2.0/configure
--- ccp4-6.2.0-dist/configure 2010-12-13 06:50:09.000000000 -0800
+++ ccp4-6.2.0/configure 2010-12-17 20:39:38.000000000 -0800
@@ -2458,8 +2458,8 @@
XMKMF="IMAKECPP=/usr/bin/cpp xmkmf"
if test "$shared_lib" = yes; then
SHARED_LIB_CFLAGS=${SHARED_LIB_CFLAGS:-'-fPIC -fno-common'}
- SHARE_LIB='${CC} -dynamiclib -flat_namespace -undefined suppress ${SHARED_LIB_CFLAGS} -install_name ${libdir}/libmmdb.dylib -o libmmdb.dylib $(MMDBOBJS) -lstdc++; ${CC} -dynamiclib -flat_namespace -undefined suppress ${SHARED_LIB_CFLAGS} -install_name ${libdir}/libccp4c.dylib -o libccp4c.dylib $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS)'
- SHARE_INST='${INSTALL_DATA} `pwd`/libmmdb.dylib ${libdir}/libmmdb.dylib; ${INSTALL_DATA} `pwd`/libccp4c.dylib ${libdir}/libccp4c.dylib'
+ SHARE_LIB='${CC} -dynamiclib -flat_namespace -undefined suppress ${SHARED_LIB_CFLAGS} -install_name ${rpath}/libmmdb.dylib -o libmmdb.dylib ${MMDBOBJS} -lstdc++; ${CC} -dynamiclib -flat_namespace -undefined suppress ${SHARED_LIB_CFLAGS} -install_name ${rpath}/libccp4c.dylib -o libccp4c.dylib ${CORELIBOBJS} ${CGENERALOBJS} ${CUCOBJS} ${CMTZOBJS} ${CMAPOBJS} ${CSYMOBJS}'
+ SHARE_INST='${INSTALL_DATA} `pwd`/libmmdb.dylib ${libdir}/libmmdb.dylib; ${INSTALL_DATA} `pwd`/libccp4c.dylib ${libdir}/libccp4c.dylib'
fi
#need -lcc_dynamic to get restFP and saveFP for g77 3.4 under darwin 7
case `$FC --version` in
@@ -2591,8 +2591,8 @@
if test "$shared_lib" = yes; then
LD=${LD:-"ld"}
XLDFLAGS="-limf -lirc"
- SHARE_LIB=${SHARE_LIB:-'${LD} -dylib -dynamic -flat_namespace -undefined suppress -dylib_install_name ${libdir}/libmmdb.dylib -o libmmdb.dylib $(MMDBOBJS) ${CXX_LIBS} -limf -ldylib1.o; ${LD} -dylib -dynamic -flat_namespace -undefined suppress -dylib_install_name ${libdir}/libccp4c.dylib -o libccp4c.dylib $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) -ldylib1.o;'}
- SHARE_INST='$(INSTALL_DATA) `pwd`/libmmdb.dylib $(libdir)/libmmdb.dylib; $(INSTALL_DATA) `pwd`/libccp4c.dylib $(libdir)/libccp4c.dylib;'
+ SHARE_LIB=${SHARE_LIB:-'${LD} -dylib -dynamic -flat_namespace -undefined suppress -dylib_install_name ${rpath}/libmmdb.dylib -o libmmdb.dylib ${MMDBOBJS} -lirc -limf -ldylib1.o; ${LD} -dylib -dynamic -flat_namespace -undefined suppress -dylib_install_name ${rpath}/libccp4c.dylib -o libccp4c.dylib ${CORELIBOBJS} ${CGENERALOBJS} ${CUCOBJS} ${CMTZOBJS} ${CMAPOBJS} ${CSYMOBJS} -ldylib1.o;'}
+ SHARE_INST='$(INSTALL_DATA) `pwd`/libmmdb.dylib $(libdir)/libmmdb.dylib; $(INSTALL_DATA) `pwd`/libccp4c.dylib $(libdir)/libccp4c.dylib;'
LDCXXFLAGS="-lccp4c -lmmdb \$(XCIF_LIB) \$(XLAPACK_LIB) \$(C_LIBS) \$(XLDFLAGS) -lstdc++"
fi

@@ -4117,7 +4117,8 @@
CFLAGS="${COPTIM} ${XCFLAGS}"
FFTW_LIBS="-L${prefix}/lib -lrfftw -lfftw"
FFTW_CXXFLAGS="-I${prefix}/lib/fftw/fftw -I${prefix}/lib/fftw/rfftw -I${prefix}/include"
- export CFLAGS
+ FLIBS="-L@PREFIX@/lib/gcc4.6/lib -lgfortran"
+ export CFLAGS FLIBS
# must use --enable-float
xopts="--enable-float"
if test "$shared_lib" = yes; then
diff -ruN ccp4-6.2.0-dist/etc/xloggraph ccp4-6.2.0/etc/xloggraph
--- ccp4-6.2.0-dist/etc/xloggraph 1969-12-31 16:00:00.000000000 -0800
+++ ccp4-6.2.0/etc/xloggraph 2010-12-17 20:40:20.000000000 -0800
@@ -0,0 +1,6 @@
+#!/bin/zsh
+export XUSERFILESEARCHPATH=$CLIB/X11/app-defaults/XCCPJiffy
+xloggraph.exe "$@" &
+export XUSERFILESEARCHPATH=""
+print "Plot button sends pdf to Preview. Print or save pdf in Preview window."
+exit 0
diff -ruN ccp4-6.2.0-dist/etc/xplot84 ccp4-6.2.0/etc/xplot84
--- ccp4-6.2.0-dist/etc/xplot84 1969-12-31 16:00:00.000000000 -0800
+++ ccp4-6.2.0/etc/xplot84 2010-12-17 20:40:39.000000000 -0800
@@ -0,0 +1,6 @@
+#!/bin/zsh
+export XUSERFILESEARCHPATH=$CLIB/X11/app-defaults/XCCPJiffy
+xplot84driver.exe "$@" &
+export XUSERFILESEARCHPATH=""
+print "Plot button sends pdf to Preview. Print or save pdf in Preview window."
+exit 0
diff -ruN ccp4-6.2.0-dist/etc/xplot84driver ccp4-6.2.0/etc/xplot84driver
--- ccp4-6.2.0-dist/etc/xplot84driver 1969-12-31 16:00:00.000000000 -0800
+++ ccp4-6.2.0/etc/xplot84driver 2010-12-17 20:40:39.000000000 -0800
@@ -0,0 +1,6 @@
+#!/bin/zsh
+export XUSERFILESEARCHPATH=$CLIB/X11/app-defaults/XCCPJiffy
+xplot84driver.exe "$@" &
+export XUSERFILESEARCHPATH=""
+print "Plot button sends pdf to Preview. Print or save pdf in Preview window."
+exit 0
diff -ruN ccp4-6.2.0-dist/include/ccp4.setup-bash ccp4-6.2.0/include/ccp4.setup-bash
--- ccp4-6.2.0-dist/include/ccp4.setup-bash 1969-12-31 16:00:00.000000000 -0800
+++ ccp4-6.2.0/include/ccp4.setup-bash 2010-12-17 20:47:05.000000000 -0800
@@ -0,0 +1,466 @@
+#!/bin/bash
+# [The above is just for emacs -- this file should not be executed.]
+
+# CCP4 setup file for bash users. -*- shell-script -*-
+# $Id: ccp4.setup-bash,v 1.91.2.3 2008/06/09 08:51:17 ccb Exp $
+
+###############################################################################
+
+# Edit this for the current version of ccp4:
+ # if [[ -z $CCP4_VERSION ]];then
+ CCP4_VERSION="ccp4-6.2.0"
+ # fi
+
+###############################################################################
+
+# NOTE: You should not need to edit the rest of this file unless you want to over-ride the
+# following assignments of $CCP4_MASTER and $BLTWISHPREFIX
+
+# NOTE: If you have installed ccp4 on OS X with fink, you should not need to
+# change this file or to source it (fink takes care of sourcing it for you).
+
+ # CCP4_MASTER is the location of the top-level directory containing `ccp4'.
+ # Set it manually by uncommenting and editing the following line:
+
+ # export CCP4_MASTER="@PREFIX@/share/xtal"
+
+ # or discover it from the source command if we have a current version of the bash shell
+
+ # if [[ -z "$CCP4_MASTER" ]];then
+ if [[ ${BASH_VERSION} > 3 ]];then
+ CCP4_MASTER="$(dirname $(dirname $(dirname ${BASH_SOURCE} )))"
+ else
+ # Attempt to this the hard way for older versions of bash
+ if [[ -d "@PREFIX@/share/xtal/${CCP4_VERSION}" ]]; then
+ CCP4_MASTER="@PREFIX@/share/xtal"
+ elif [[ -d "@PREFIX@/share/xtal/${CCP4_VERSION}" ]]; then
+ CCP4_MASTER="@PREFIX@/share/xtal"
+ elif [[ -d "/usr/local/${CCP4_VERSION}" ]]; then
+ CCP4_MASTER="/usr/local"
+ elif [[ -d "/usr/local/ccp4/${CCP4_VERSION}" ]]; then
+ CCP4_MASTER="/usr/local/ccp4"
+ elif [[ -d "@PREFIX@/share/xtal/ccp4/${CCP4_VERSION}" ]]; then
+ CCP4_MASTER="@PREFIX@/share/xtal/ccp4"
+ else
+ CCP4_MASTER="@PREFIX@/share/xtal"
+ fi
+ fi
+ # fi
+
+ export CCP4_MASTER
+
+
+ # Discover where bltwish executable is located
+
+ if [[ -z $BLTWISHPREFIX && -x $(which bltwish) ]];then
+ BLTWISHPREFIX=$( dirname $( which bltwish ) )
+ fi
+
+###############################################################################
+
+
+
+# This file is site specific and may also contain machine-specifics. The CCP4
+# administrator will have to edit this file and then have anyone who wants to
+# use CCP4 source it from their .login file. They will require the full path
+# name since no environment variables relevant to CCP4 are known until this is
+# executed.
+
+# For sites with more than one machine, it is recommended that the suite is
+# installed on a single machine and other machines access the source code, and
+# shareable files (such as this one) via shared file systems with NFS, RFS
+# etc. Non-shareable files reside in $CBIN and $CLIB (see below).
+
+# Copy this file to ccp4.setup and customise it for your needs. There are
+# three sections. You MUST check the first section. You may want to check
+# the second. You don't need to look at the third.
+
+
+################### THIS SECTION MUST BE EDITED #####################
+
+# CCP4_MASTER is the location of the top-level directory containing `ccp4-'
+# This is usually the directory in which you ran the tar command to unpack the
+# code, and is assumed to be shared between machines at a multi-machine site.
+
+# CCP4_MASTER="@PREFIX@/share/xtal"; export CCP4_MASTER
+# CCP4="$CCP4_MASTER/ccp4-6.2.0" ; export CCP4
+
+# Check for existence of CCP4_MASTER
+if [[ ! -d $CCP4_MASTER ]] ; then
+ echo "********************* WARNING **********************"
+ echo "The directory $CCP4_MASTER"
+ echo "(assigned to CCP4_MASTER) does not exist."
+ echo "The CCP4 programs will not run correctly, and any"
+ echo "installation attempt will have errors or will fail."
+ echo "********************* WARNING **********************"
+else
+ if [[ -d "$CCP4_MASTER/$CCP4_VERSION" ]];then
+ CCP4="$CCP4_MASTER/$CCP4_VERSION" ; export CCP4
+ else
+ echo "The directory "$CCP4_MASTER/$CCP4_VERSION" cannot be found."
+ echo " Please check that "$CCP4_VERSION" is the right ccp4 version. "
+ fi
+fi
+
+
+# CCP4_SCR: a per-user directory for run-time-generated scratch
+# files. A dedicated scratch filesystem is probably better than (/usr)/tmp
+# BINSORT_SCR: a scratch directory for binsort's use; normally same as CCP4_SCR
+
+export CCP4_SCR="/tmp/$USER"
+# check to see if this exists and if not try to make it
+test -d $CCP4_SCR || mkdir $CCP4_SCR
+test -d $CCP4_SCR || \
+ echo "Unable to make CCP4_SCR. CCP4 progs will not run correctly."
+
+export BINSORT_SCR="$CCP4_SCR"
+
+### CCP4i setup - you may need to edit CCP4I_TCLTK ###
+# CCP4I_TOP - the top directory of the interface
+export CCP4I_TOP="${CCP4}/ccp4i"
+# CCP4I_TCLTK - directory containing tclsh,wish and bltwish executables
+# as used in $CCP4I_TOP/bin/ccp4i,ccp4ish,loggraph
+# For 'standard' installations this is @PREFIX@/bin
+# but note the SGI distributed version of Tcl/Tk is not
+# appropriate version
+# export CCP4I_TCLTK="@PREFIX@/bin"
+if [[ -d "$BLTWISHPREFIX" && -x "$BLTWISHPREFIX/bltwish" ]]; then
+ export CCP4I_TCLTK="$BLTWISHPREFIX"
+else
+ echo " Cannot find bltwish executable. Please make sure it is in your \$PATH "
+fi
+
+
+# CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help
+export CCP4I_HELP="${CCP4I_TOP}/help"
+
+### Optional - setting http_proxy environment
+# The commented out 'export' line below may have to be declared to download
+# and edit protein sequences using the new "Import/Edit Protein Sequences"
+# (This may also be required for remote job submission in arp/warp.)
+# task. If so, uncomment this line and replace the example proxy URL with your
+# relevant URL
+
+#export HTTP_PROXY wwwblah.blah.ac.uk:xxxx/blah.blah
+
+################### NOVICE USERS STOP HERE #####################
+
+################### OPTIONS TO CUSTOMISE CCP4 #####################
+
+# By default, CCP4 directories are prepended to the beginning of paths (PATH,
+# LD_LIBRARY_PATH, and DYLD_LIBRARY_PATH). If ccp4_first_in_path is set
+# to 0, then they will be appended to the end of paths.
+# When deciding local policy, bear in mind the possible existence of
+# other CCP4 installations, and the possibility of non-CCP4 programs
+# with conflicting names.
+ccp4_first_in_path=0
+
+# The following checks the CCP4 server for available updates, and reports back.
+# Comment this line out if you find it annoying.
+# eval python -V >& /dev/null && python $CCP4/etc/ccp4_updates.py -l
+
+# Set GFORTRAN_UNBUFFERED_ALL to either 1 or Y to ensure that the logfile
+# output from programs compiled with Gfortran is in the correct order.
+# Note that there will be some performance penalty for this.
+# # # # # export GFORTRAN_UNBUFFERED_ALL="Y"
+
+# The commented-out switch statement below provides an example of how
+# to use this file for several machines/architectures sharing $CCP4_MASTER.
+# If necessary, uncomment and edit this. Otherwise, if you're only supporting
+# a single system alter the uncommented part as necessary.
+#
+# The significance of the environment variables is as follows:
+# CBIN: location of the executables -- must be on your path (see below);
+# CLIB: location of (binary) library files such as libccp4.a and libccp4.so;
+# MANPATH: set this if your system's `man' looks at such an environment
+# variable to determine where to look for man pages. By adding
+# $CCP4/man to the normal path you get the CCP4 man pages
+# with keyword searching as system ones.
+# MCTYPE: used for LAUE make -- see LAUE documentation
+# CCP4_BROWSER: set this if you intend to use the html documentation
+# (recommended). It should have the path and name of a html browser eg
+# /usr/bin/X11/mozilla or @PREFIX@/bin/lynx. The browser will be
+# started with the alias ccp4help and will open the file
+# $CHTML/INDEX.html.
+
+
+ export CBIN="$CCP4/bin"
+ export CLIB="$CCP4/lib"
+
+ CCP4_BROWSER=""; export CCP4_BROWSER="Safari"
+
+ if test "$MANPATH"; then
+ if [[ $ccp4_first_in_path -eq 1 ]]; then
+ export MANPATH="${CCP4}/man:${MANPATH}"
+ else
+ export MANPATH="${MANPATH}:${CCP4}/man"
+ fi
+ else
+ if [ $ccp4_first_in_path -eq 1 ]; then
+ export MANPATH="${CCP4}/man:/usr/share/man"
+ else
+ export MANPATH="/usr/share/man:${CCP4}/man"
+ fi
+ fi
+ export MCTYPE="unix" # (only for Laue)
+
+
+ if [[ $(uname) == Darwin && $(sw_vers -productVersion) < 10.5 ]];then
+ ulimit -s 65536
+ fi
+
+
+# The following are for all systems
+export CCP4_LIB="$CLIB"
+export CCP4_BIN="$CBIN"
+
+# CLASSPATH for Java
+if test "$CLASSPATH"; then
+ if [[ $ccp4_first_in_path -eq 1 ]]; then
+ export CLASSPATH="${CBIN}:${CLASSPATH}"
+ else
+ export CLASSPATH="${CLASSPATH}:${CBIN}"
+ fi
+else
+ if [ $ccp4_first_in_path -eq 1 ]; then
+ export CLASSPATH="${CBIN}:."
+ else
+ export CLASSPATH=".:${CBIN}"
+ fi
+fi
+
+### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
+export PLOT_COMMAND='lp -s -dmicrolaser'
+export PRINT_COMMAND='lp -s -denscript'
+
+# HARVESTHOME specifies location of harvesting files (defaults to $HOME)
+#export HARVESTHOME
+
+### CCP4_OPEN ###
+# CCP4_OPEN may be set to 'UNKNOWN' to stop open failures for files opened
+# as NEW that already exist. Novices should use 'NEW' to avoid inadvertant
+# over-writing of existing files, which is then treated as a fatal error.
+
+export CCP4_OPEN="UNKNOWN"
+
+### BINSORT_MEM ###
+# BINSORT_MEM is workspace used by the binsort program. In principle this
+# value is machine-dependent. It may benefit from being enlarged, but values
+# higher than 2M have been reported to cause excessive paging on some systems.
+# You might like to experiment with a program such as fft with different
+# values -- 102400 (bytes) is the default. csh's `time' command can tell you
+# about paging.
+#
+# export BINSORT_MEM="8388608"
+
+# LD_LIBRARY_PATH specifies where to find dynamic libraries (e.g. libccp4.so)
+# at runtime
+##### if test "$LD_LIBRARY_PATH"; then
+##### if [[ $ccp4_first_in_path -eq 1 ]]; then
+##### export LD_LIBRARY_PATH="${CLIB}:${LD_LIBRARY_PATH}"
+##### else
+##### export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${CLIB}"
+##### fi
+##### else
+##### export LD_LIBRARY_PATH="${CLIB}"
+##### fi
+#####
+##### # DYLD_LIBRARY_PATH specifies where to find dynamic libraries (e.g. libccp4.dylib)
+##### # at runtime (used on Mac OS X)
+##### if test "$DYLD_LIBRARY_PATH"; then
+##### if [[ $ccp4_first_in_path -eq 1 ]]; then
+##### export DYLD_LIBRARY_PATH="${CLIB}:${DYLD_LIBRARY_PATH}"
+##### else
+##### export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}:${CLIB}"
+##### fi
+##### else
+##### export DYLD_LIBRARY_PATH="${CLIB}"
+##### fi
+#####
+##### ### XAPPLRESDIR ###
+#####
+##### # If you want to use xloggraph/xplot84driver, you need to get the application
+##### # defaults picked up somehow. As distributed, the file can't just live in an
+##### # application defaults directory since it requires reading by xrdb to sort out
+##### # the differences for monochrome displays. At Daresbury a version of the file
+##### # assuming a monochrome display is kept in the directory
+##### # $CCP4_LIB/X11/app-defaults and this is picked up through the
+##### # XUSERFILESEARCHPATH environment variable. That means you only see black and
+##### # white on a colour display. Alternatively you might make sure that it is
+##### # read by xrdb on startup of the X Windows system or delegate the
+##### # responsibility to users to run it. There are disadvantages to putting an
+##### # invocation of xrdb in here, one being that the correct value of DISPLAY may
+##### # not be set at the time this file is read. Thus edit this part as
+##### # appropriate. (SunOS will normally want to use /usr/openwin or $OPENWINHOME
+##### # instead of /usr; others may want /usr/local/lib or some such):
+##### if test "$XUSERFILESEARCHPATH"; then
+##### export XUSERFILESEARCHPATH="$CCP4_LIB/X11/app-defaults/%N:$XUSERFILESEARCHPATH"
+##### else
+##### export XUSERFILESEARCHPATH="$CCP4_LIB/X11/app-defaults/%N:/usr/lib/X11/app-defaults"
+##### fi
+#####
+##### ### TRAPPFE ###
+##### # TRAPFPE is set to ensure (in collaboration with -lfpe) an abort on floating
+##### # point exceptions under IRIX. It shouldn't cause harm on other systems, but
+##### # edit this to comment it out if necessary.
+##### export TRAP_FPE="OVERFL=ABORT" ; export DIVZERO="ABORT" ; export INVALID="ABORT"
+#####
+##### # The following can be used to put a message of the day to announce news about
+##### # CCP4 or whatever to CCP4 users. You might also want to edit this part to
+##### # have machine-specific messages dependent on `hostname`.
+##### [[ -f "$CCP4/include/ccp4.msg" ]] && cat "$CCP4/include/ccp4.msg"
+
+################### EXPERIENCED USERS STOP HERE #####################
+
+################### THE REST SHOULDN'T NEED EDITING #####################
+
+### dbCCP4i database handler setup ###
+
+export DBCCP4I_TOP="${CCP4}/share/dbccp4i"
+
+### IMOSFLM environment is now defined here
+
+export MOSFLM_EXEC="${CBIN}/ipmosflm"
+export MOSFLM_WISH="${CCP4I_TCLTK}/wish"
+export IMOSFLM_VERSION="0.6.1"
+
+
+### MMCIFDIC is now defined here. cif_mmdic.lib is a binary file ===
+# so on multiple installs it need to be unique and not in $CLIBD
+
+export MMCIFDIC="$CLIB/cif_mmdic.lib"
+
+### MOLREPLIB Point to the location of the files bs-zeros.dat ps.resource symlib.blc
+# They are distributed with CCP4 in $CLIBD. This env must have the trailing \ or /
+
+export MOLREPLIB="$CCP4/lib/data/monomers/"
+
+### CRANK points to location of Crank automation suite within ccp4i
+
+export CRANK="$CCP4/ccp4i/crank"
+export CCP4_CRANK="1"
+
+# ### XIA2 setup
+# # XIAROOT directory (default is under the share folder)
+#
+# if [[ -f "$CCP4/share/XIAROOT/setup.sh" ]]; then
+# source "$CCP4/share/XIAROOT/setup.sh"
+# fi
+#
+# Note: The PATH is updated with the xia2 Applications directory in the
+# construct below.
+
+### PISA_CONF_FILE is the config file needed to run the stand-alone PISA,
+# though this can be set on the command line too.
+
+export PISA_CONF_FILE="$CCP4/share/pisa/pisa.cfg"
+
+### CLIBD_MON Point to the location of the dictionary files for REFMAC5
+# They are distributed with CCP4 in $CLIBD/monomers. This env must have
+# the trailing \ or /
+
+export CLIBD_MON="$CCP4/lib/data/monomers/"
+
+### PUBLIC_FONT84, CCP4_HELPDIR, HELPDIR, MOSHELPFILE ###
+# (essential for the relevant programs)
+export PUBLIC_FONT84="$CLIB/font84.dat" # plot84 fonts [used by plot84lib]
+
+# location of VMS-style help files required for mosflm [used by hlplib, chelp,
+# chlp, (ip)mosflm]:
+export CCP4_HELPDIR="$CCP4/help/" # NB trailing /
+
+# Rasmol path. Needed for prog. to find rasmol.hlp
+export RASMOLPATH="$CCP4/x-windows/RasMol/src"
+
+if [[ $ZSH_NAME != "zsh" ]];then
+
+ # This is specific to bash, so protect it from zsh users
+
+ # CCP4 executables and scripts live in $CBIN and $CETC respectively; put them
+ # on the path in an appropriate order for scripts to be used as wrappers for
+ # binaries of the same name. Put ccp4 stuff after the current path to avoid
+ # confusion with `.' or whatever in the path:
+ #
+ # This construct prevents the path getting longer each time ccp4.setup is
+ # executed (A. Perrakis)
+ #
+ ccp4pathlist="${CCP4}/etc ${CBIN} ${CCP4I_TOP}/bin ${DBCCP4I_TOP}/bin ${CCP4}/share/XIAROOT/xia2/Applications"
+ #
+ for dir in ${ccp4pathlist}; do
+ if [[ `expr ":${PATH}:" : ".*:${dir}:"` -eq 0 ]]; then
+ if [[ $ccp4_first_in_path -eq 1 ]]; then
+ export PATH="${dir}:${PATH}"
+ else
+ export PATH="${PATH}:${dir}"
+ fi
+ fi
+ done
+
+fi
+
+# Optional (useful) additional environment variables
+ #export CCP4="$CCP4"
+ export CDOC="$CCP4/doc"
+ export CHTML="$CCP4/html"
+ export CETC="$CCP4/etc"
+ export CEXAM="$CCP4/examples"
+ export CINCL="$CCP4/include"
+ export CLIBD="$CCP4/lib/data"
+ export CLIBS="$CCP4/lib/src"
+ export CPROG="$CCP4/src"
+
+if [[ "`basename $SHELL`" != "ksh" ]]; then
+# useful aliases, at least for developers
+ alias ccp4='pushd $CCP4>/dev/null'
+ alias xtal='pushd $CCP4_MASTER>/dev/null'
+ alias cbin='pushd $CBIN>/dev/null'
+ alias cetc='pushd $CETC>/dev/null'
+ alias cprog='pushd $CPROG>/dev/null'
+ alias cincl='pushd $CINCL>/dev/null'
+ alias clib='pushd $CLIB>/dev/null'
+ alias clibd='pushd $CLIBD>/dev/null'
+ alias clibs='pushd $CLIBS>/dev/null'
+ alias cbin='pushd $CBIN>/dev/null'
+ alias cexam='pushd $CEXAM>/dev/null'
+ alias cdoc='pushd $CDOC>/dev/null'
+ alias chtml='pushd $CHTML>/dev/null'
+ alias ccp4help='$CCP4_BROWSER $CHTML/INDEX.html \&'
+
+### laue, lget, linkimages ###
+# Essential aliases for the Laue software suite
+ alias laue='$CCP4_MASTER/laue/cmd/laue.cmd'
+ alias lget='$CCP4_MASTER/laue/cmd/lget.cmd'
+ alias linkimages='$CCP4_MASTER/laue/cmd/linkimages.cmd'
+
+# additional useful aliases for Laue directories
+ alias llaue='pushd $CCP4_MASTER/laue'
+ alias lsrc='pushd $CCP4_MASTER/laue/src>/dev/null'
+ alias llib='pushd $CCP4_MASTER/laue/lib>/dev/null'
+ alias llibs='pushd $CCP4_MASTER/laue/lib/src>/dev/null'
+ alias ldoc='pushd $CCP4_MASTER/laue/doc>/dev/null'
+ alias lmak='pushd $CCP4_MASTER/laue/make>/dev/null'
+ alias lutils='pushd $CCP4_MASTER/laue/utils>/dev/null'
+ alias lcmd='pushd $CCP4_MASTER/laue/cmd>/dev/null'
+ alias ldl='pushd $CCP4_MASTER/laue/dl>/dev/null'
+ alias ltestd='pushd $CCP4_MASTER/laue/testdata>/dev/null'
+ alias lxdl='pushd $CCP4_MASTER/laue/xdl_view>/dev/null'
+ alias lxdls='pushd $CCP4_MASTER/laue/xdl_view/src>/dev/null'
+ alias lgnom='pushd $CCP4_MASTER/laue/gnom>/dev/null'
+ alias lgnoms='pushd $CCP4_MASTER/laue/gnom/src>/dev/null'
+ alias lbin='pushd $CBIN>/dev/null'
+
+fi # ksh test
+
+#### # Set-up cctbx environment
+#### [[ -f "$CCP4/lib/cctbx/cctbx_build/setpaths.sh" ]] && source "$CCP4/lib/cctbx/cctbx_build/setpaths.sh"
+####
+#### # Set-up phaser environment
+#### if [[ -d $CCP4/src/phaser ]] ; then
+#### export phaser_mtype=`$CCP4/src/phaser/bin/machine_type`
+#### export phaser_version=`grep PHASER_VERSION $CCP4/src/phaser/conf/version | awk '{print $3}'`
+#### export phaser_setup_file="${CCP4}/src/phaser/phaser-${phaser_version}/build/${phaser_mtype}/setpaths.sh"
+#### [[ -f "$phaser_setup_file" ]] && source "$phaser_setup_file"
+#### fi
+####
+#BALBES root configuration
+export BALBES_ROOT="$CCP4/share/balbes/BALBES_0.0.1"
diff -ruN ccp4-6.2.0-dist/include/ccp4.setup-dist ccp4-6.2.0/include/ccp4.setup-dist
--- ccp4-6.2.0-dist/include/ccp4.setup-dist 1969-12-31 16:00:00.000000000 -0800
+++ ccp4-6.2.0/include/ccp4.setup-dist 2010-12-17 20:47:18.000000000 -0800
@@ -0,0 +1,431 @@
+#!/bin/csh
+# CCP4 setup file for C-shell (or tcsh) users. -*- shell-script -*-
+
+# $Id: ccp4.setup-dist,v 1.116.2.3 2008/11/20 15:19:24 rmk65 Exp $
+
+# This file is site specific and may also contain machine-specifics. The CCP4
+# administrator will have to edit this file and then have anyone who wants to
+# use CCP4 source it from their .login file. They will require the full path
+# name since no environment variables relevant to CCP4 are known until this is
+# executed.
+
+# For sites with more than one machine, it is recommended that the suite is
+# installed on a single machine and other machines access the source code, and
+# shareable files (such as this one) via shared file systems with NFS, RFS
+# etc. Non-shareable files reside in $CBIN and $CLIB (see below).
+
+# Copy this file to ccp4.setup and customise it for your needs. There are
+# three sections. You MUST check the first section. You may want to check
+# the second. You don't need to look at the third.
+
+################### THIS SECTION MUST BE EDITED #####################
+
+# CCP4_MASTER is the location of the top-level directory containing `ccp4-'
+# This is usually the directory in which you ran the tar command to unpack the
+# code, and is assumed to be shared between machines at a multi-machine site.
+
+setenv CCP4_MASTER @PREFIX@/share/xtal
+setenv CCP4 $CCP4_MASTER/ccp4-6.2.0
+
+# Check for existence of CCP4_MASTER
+if (! -e $CCP4_MASTER) then
+ echo "********************* WARNING **********************"
+ echo "The directory $CCP4_MASTER"
+ echo "(assigned to CCP4_MASTER) does not exist."
+ echo "The CCP4 programs will not run correctly, and any"
+ echo "installation attempt will have errors or will fail."
+ echo "********************* WARNING **********************"
+endif
+
+# CCP4_SCR: a per-user directory for run-time-generated scratch
+# files. A dedicated scratch filesystem is probably better than (/usr)/tmp
+# BINSORT_SCR: a scratch directory for binsort's use; normally same as CCP4_SCR
+
+setenv CCP4_SCR /tmp/$USER
+# check to see if this exists and if not try to make it
+if (! -e $CCP4_SCR) mkdir $CCP4_SCR
+if (! -e $CCP4_SCR) \
+ echo "Unable to make CCP4_SCR. CCP4 progs will not run correctly."
+
+setenv BINSORT_SCR $CCP4_SCR
+
+### CCP4i setup - you may need to edit CCP4I_TCLTK ###
+# CCP4I_TOP - the top directory of the interface
+setenv CCP4I_TOP ${CCP4}/ccp4i
+# CCP4I_TCLTK - directory containing tclsh,wish and bltwish executables
+# as used in $CCP4I_TOP/bin/ccp4i,ccp4ish,loggraph
+# For 'standard' installations this is @PREFIX@/bin
+# but note the SGI distributed version of Tcl/Tk is not
+# appropriate version
+setenv CCP4I_TCLTK @PREFIX@/bin
+# CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help
+setenv CCP4I_HELP ${CCP4I_TOP}/help
+
+### Optional - setting http_proxy environment
+# The commented out 'setenv' line below may have to be declared to download
+# and edit protein sequences using the new "Import/Edit Protein Sequences"
+# (This may also be required for remote job submission in arp/warp.)
+# task. If so, uncomment this line and replace the example proxy URL with your
+# relevant URL
+
+#setenv HTTP_PROXY wwwblah.blah.ac.uk:xxxx/blah.blah
+
+################### NOVICE USERS STOP HERE #####################
+
+################### OPTIONS TO CUSTOMISE CCP4 #####################
+
+# By default, CCP4 directories are prepended to the beginning of paths (PATH,
+# LD_LIBRARY_PATH, and DYLD_LIBRARY_PATH). If ccp4_first_in_path is set
+# to 0, then they will be appended to the end of paths.
+# When deciding local policy, bear in mind the possible existence of
+# other CCP4 installations, and the possibility of non-CCP4 programs
+# with conflicting names.
+set ccp4_first_in_path = 0
+
+# The following checks the CCP4 server for available updates, and reports back.
+# Uncomment this line if you want to know about available updates.
+
+#eval python -V >& /dev/null && python $CCP4/etc/ccp4_updates.py -l
+
+# Set GFORTRAN_UNBUFFERED_ALL to either 1 or Y to ensure that the logfile
+# output from programs compiled with Gfortran is in the correct order.
+# Note that there will be some performance penalty for this.
+# # # # setenv GFORTRAN_UNBUFFERED_ALL Y
+
+# The commented-out switch statement below provides an example of how
+# to use this file for several machines/architectures sharing $CCP4_MASTER.
+# If necessary, uncomment and edit this. Otherwise, if you're only supporting
+# a single system alter the uncommented part as necessary.
+#
+# The significance of the environment variables is as follows:
+# CBIN: location of the executables -- must be on your path (see below);
+# CLIB: location of (binary) library files such as libccp4.a and libccp4.so;
+# MANPATH: set this if your system's `man' looks at such an environment
+# variable to determine where to look for man pages. By adding
+# $CCP4/man to the normal path you get the CCP4 man pages
+# with keyword searching as system ones.
+# MCTYPE: used for LAUE make -- see LAUE documentation
+# CCP4_BROWSER: set this if you intend to use the html documentation
+# (recommended). It should have the path and name of a html browser eg
+# /usr/bin/X11/mozilla or @PREFIX@/bin/lynx. The browser will be
+# started with the alias ccp4help and will open the file
+# $CHTML/INDEX.html.
+
+# switch (`hostname`) # edit this switch statement if used
+# # for multiple systems
+# case 'foo':
+ setenv CBIN $CCP4/bin
+ setenv CLIB $CCP4/lib
+
+ setenv CCP4_BROWSER Safari
+
+ if (${?MANPATH}) then
+ if ($ccp4_first_in_path) then
+ setenv MANPATH ${CCP4}/man:${MANPATH}
+ else
+ setenv MANPATH ${MANPATH}:${CCP4}/man
+ endif
+ else
+ if ($ccp4_first_in_path) then
+ setenv MANPATH ${CCP4}/man:/usr/share/man
+ else
+ setenv MANPATH /usr/share/man:${CCP4}/man
+ endif
+ endif
+ if (-d $CCP4_MASTER/laue) then
+ setenv MCTYPE unix # (only for Laue)
+ endif
+# breaksw
+# default:
+# echo "CCP4 not implemented on this system"
+# exit 1
+# breaksw
+# endsw
+
+switch (`uname`)
+case 'Darwin':
+ limit stacksize unlimited
+ breaksw
+default:
+ breaksw
+endsw
+
+# The following are for all systems
+setenv CCP4_LIB $CLIB
+setenv CCP4_BIN $CBIN
+
+# CLASSPATH for Java
+if (${?CLASSPATH}) then
+ if ($ccp4_first_in_path) then
+ setenv CLASSPATH ${CBIN}:${CLASSPATH}
+ else
+ setenv CLASSPATH ${CLASSPATH}:${CBIN}
+ endif
+else
+ if ($ccp4_first_in_path) then
+ setenv CLASSPATH ${CBIN}:.
+ else
+ setenv CLASSPATH .:${CBIN}
+ endif
+endif
+
+# #Python path for the subprocess fixed module
+# if (${?PYTHONPATH}) then
+# if ($ccp4_first_in_path) then
+# setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
+# else
+# setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
+# endif
+# else
+# setenv PYTHONPATH ${CCP4}/share/python
+# endif
+
+### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
+setenv PLOT_COMMAND 'lpr'
+setenv PRINT_COMMAND 'lpr'
+
+# HARVESTHOME specifies location of harvesting files (defaults to $HOME)
+#setenv HARVESTHOME
+
+### CCP4_OPEN ###
+# CCP4_OPEN may be set to 'UNKNOWN' to stop open failures for files opened
+# as NEW that already exist. Novices should use 'NEW' to avoid inadvertant
+# over-writing of existing files, which is then treated as a fatal error.
+
+setenv CCP4_OPEN UNKNOWN
+
+### BINSORT_MEM ###
+# BINSORT_MEM is workspace used by the binsort program. In principle this
+# value is machine-dependent. It may benefit from being enlarged, but values
+# higher than 2M have been reported to cause excessive paging on some systems.
+# You might like to experiment with a program such as fft with different
+# values -- 102400 (bytes) is the default. csh's `time' command can tell you
+# about paging.
+#
+# setenv BINSORT_MEM 8388608
+
+# # LD_LIBRARY_PATH specifies where to find dynamic libraries (e.g. libccp4.so)
+# # at runtime
+# if (${?LD_LIBRARY_PATH}) then
+# if ($ccp4_first_in_path) then
+# setenv LD_LIBRARY_PATH ${CLIB}:${LD_LIBRARY_PATH}
+# else
+# setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${CLIB}
+# endif
+# else
+# setenv LD_LIBRARY_PATH ${CLIB}
+# endif
+#
+# # DYLD_LIBRARY_PATH specifies where to find dynamic libraries (e.g. libccp4.dylib)
+# # at runtime (used on Mac OS X)
+# if (${?DYLD_LIBRARY_PATH}) then
+# if ($ccp4_first_in_path) then
+# setenv DYLD_LIBRARY_PATH ${CLIB}:${DYLD_LIBRARY_PATH}
+# else
+# setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:${CLIB}
+# endif
+# else
+# setenv DYLD_LIBRARY_PATH ${CLIB}
+# endif
+#
+### XAPPLRESDIR ###
+
+# If you want to use xloggraph/xplot84driver, you need to get the application
+# defaults picked up somehow. As distributed, the file can't just live in an
+# application defaults directory since it requires reading by xrdb to sort out
+# the differences for monochrome displays. At Daresbury a version of the file
+# assuming a monochrome display is kept in the directory
+# $CCP4_LIB/X11/app-defaults and this is picked up through the
+# XUSERFILESEARCHPATH environment variable. That means you only see black and
+# white on a colour display. Alternatively you might make sure that it is
+# read by xrdb on startup of the X Windows system or delegate the
+# responsibility to users to run it. There are disadvantages to putting an
+# invocation of xrdb in here, one being that the correct value of DISPLAY may
+# not be set at the time this file is read. Thus edit this part as
+# appropriate. (SunOS will normally want to use /usr/openwin or $OPENWINHOME
+# instead of /usr; others may want /usr/local/lib or some such):
+# if (-d $CCP4_LIB/X11/app-defaults) then
+# if ($?XUSERFILESEARCHPATH) then
+# setenv XUSERFILESEARCHPATH $CCP4_LIB/X11/app-defaults/%N:$XUSERFILESEARCHPATH
+# else
+# setenv XUSERFILESEARCHPATH $CCP4_LIB/X11/app-defaults/%N:/usr/lib/X11/app-defaults
+# endif
+# endif
+
+### TRAPPFE ###
+# TRAPFPE is set to ensure (in collaboration with -lfpe) an abort on floating
+# point exceptions under IRIX. It shouldn't cause harm on other systems, but
+# edit this to comment it out if necessary.
+
+switch (`uname`)
+case '*IRIX*':
+ setenv TRAP_FPE "OVERFL=ABORT; DIVZERO=ABORT; INVALID=ABORT"
+ breaksw
+default:
+ breaksw
+endsw
+
+# The following can be used to put a message of the day to announce news about
+# CCP4 or whatever to CCP4 users. You might also want to edit this part to
+# have machine-specific messages dependent on `hostname`.
+if (-e $CCP4/include/ccp4.msg) cat $CCP4/include/ccp4.msg
+
+################### EXPERIENCED USERS STOP HERE #####################
+
+################### THE REST SHOULDN'T NEED EDITING #####################
+
+### dbCCP4i database handler setup ###
+
+setenv DBCCP4I_TOP ${CCP4}/share/dbccp4i
+
+### IMOSFLM environment is now defined here
+
+setenv MOSFLM_EXEC ${CBIN}/ipmosflm
+setenv MOSFLM_WISH ${CCP4I_TCLTK}/wish
+setenv IMOSFLM_VERSION "0.6.1"
+
+### MMCIFDIC is now defined here. cif_mmdic.lib is a binary file ===
+# so on multiple installs it need to be unique and not in $CLIBD
+
+setenv MMCIFDIC $CLIB/cif_mmdic.lib
+
+### MOLREPLIB Point to the location of the files bs-zeros.dat ps.resource symlib.blc
+# They are distributed with CCP4 in $CLIBD. This env must have the trailing \ or /
+
+setenv MOLREPLIB $CCP4/lib/data/monomers/
+
+### CRANK points to location of Crank automation suite within ccp4i
+
+setenv CRANK $CCP4/ccp4i/crank
+setenv CCP4_CRANK 1
+#
+# ### XIA2 setup
+# # XIAROOT directory (default is under the share folder)
+#
+# if (-e $CCP4/share/XIAROOT/setup.csh) then
+# source $CCP4/share/XIAROOT/setup.csh
+# endif
+
+# Note: The PATH is updated with the xia2 Applications directory in the
+# construct below.
+
+### PISA_CONF_FILE is the config file needed to run the stand-alone PISA,
+# though this can be set on the command line too.
+
+if (-e $CCP4/share/pisa/pisa.cfg) then
+ setenv PISA_CONF_FILE $CCP4/share/pisa/pisa.cfg
+endif
+
+### CLIBD_MON Point to the location of the dictionary files for REFMAC5
+# They are distributed with CCP4 in $CLIBD/monomers. This env must have
+# the trailing \ or /
+
+setenv CLIBD_MON $CCP4/lib/data/monomers/
+
+### PUBLIC_FONT84, CCP4_HELPDIR, HELPDIR, MOSHELPFILE ###
+# (essential for the relevant programs)
+setenv PUBLIC_FONT84 $CLIB/font84.dat # plot84 fonts [used by plot84lib]
+
+# location of VMS-style help files required for mosflm [used by hlplib, chelp,
+# chlp, (ip)mosflm]:
+setenv CCP4_HELPDIR $CCP4/help/ # NB trailing /
+
+# Rasmol path. Needed for prog. to find rasmol.hlp
+setenv RASMOLPATH $CCP4/x-windows/RasMol/src
+
+# CCP4 executables and scripts live in $CBIN and $CETC respectively; put them
+# on the path in an appropriate order for scripts to be used as wrappers for
+# binaries of the same name. Put ccp4 stuff after the current path to avoid
+# confusion with `.' or whatever in the path:
+#
+# This construct prevents the path getting longer each time ccp4.setup is
+# executed (A. Perrakis)
+set ccp4pathlist = "${CCP4}/etc ${CBIN} ${CCP4I_TOP}/bin ${DBCCP4I_TOP}/bin ${CCP4}/share/XIAROOT/xia2/Applications"
+#
+foreach dir ( ${ccp4pathlist} )
+ if ( ${?PATH} ) then
+ if ( :${PATH}: !~ *:${dir}:* ) then
+ if ($ccp4_first_in_path) then
+ setenv PATH ${dir}:${PATH}
+ else
+ setenv PATH ${PATH}:${dir}
+ endif
+ endif
+ else
+ setenv PATH ${dir}
+ endif
+end
+
+# Optional (useful) additional environment variables
+ setenv CCP4 $CCP4
+ setenv CDOC $CCP4/doc
+ setenv CHTML $CCP4/html
+ setenv CETC $CCP4/etc
+ setenv CEXAM $CCP4/examples
+ setenv CINCL $CCP4/include
+ setenv CLIBD $CCP4/lib/data
+ setenv CLIBS $CCP4/lib/src
+ setenv CPROG $CCP4/src
+
+# useful aliases, at least for developers
+ alias ccp4 'pushd $CCP4>/dev/null'
+ alias xtal 'pushd $CCP4_MASTER>/dev/null'
+ alias cbin 'pushd $CBIN>/dev/null'
+ alias cetc 'pushd $CETC>/dev/null'
+ alias cprog 'pushd $CPROG>/dev/null'
+ alias cincl 'pushd $CINCL>/dev/null'
+ alias clib 'pushd $CLIB>/dev/null'
+ alias clibd 'pushd $CLIBD>/dev/null'
+ alias clibs 'pushd $CLIBS>/dev/null'
+ alias cbin 'pushd $CBIN>/dev/null'
+ alias cexam 'pushd $CEXAM>/dev/null'
+ alias cdoc 'pushd $CDOC>/dev/null'
+ alias chtml 'pushd $CHTML>/dev/null'
+ alias ccp4help '$CCP4_BROWSER $CHTML/INDEX.html &'
+
+### laue, lget, linkimages ###
+
+### only if we have the Laue software suite...
+
+ if (-d $CCP4_MASTER/laue) then
+
+# Essential aliases for the Laue software suite
+ alias laue '$CCP4_MASTER/laue/cmd/laue.cmd'
+ alias lget '$CCP4_MASTER/laue/cmd/lget.cmd'
+ alias linkimages '$CCP4_MASTER/laue/cmd/linkimages.cmd'
+
+# additional useful aliases for Laue directories
+ alias llaue 'pushd $CCP4_MASTER/laue'
+ alias lsrc 'pushd $CCP4_MASTER/laue/src>/dev/null'
+ alias llib 'pushd $CCP4_MASTER/laue/lib>/dev/null'
+ alias llibs 'pushd $CCP4_MASTER/laue/lib/src>/dev/null'
+ alias ldoc 'pushd $CCP4_MASTER/laue/doc>/dev/null'
+ alias lmak 'pushd $CCP4_MASTER/laue/make>/dev/null'
+ alias lutils 'pushd $CCP4_MASTER/laue/utils>/dev/null'
+ alias lcmd 'pushd $CCP4_MASTER/laue/cmd>/dev/null'
+ alias ldl 'pushd $CCP4_MASTER/laue/dl>/dev/null'
+ alias ltestd 'pushd $CCP4_MASTER/laue/testdata>/dev/null'
+ alias lxdl 'pushd $CCP4_MASTER/laue/xdl_view>/dev/null'
+ alias lxdls 'pushd $CCP4_MASTER/laue/xdl_view/src>/dev/null'
+ alias lgnom 'pushd $CCP4_MASTER/laue/gnom>/dev/null'
+ alias lgnoms 'pushd $CCP4_MASTER/laue/gnom/src>/dev/null'
+ alias lbin 'pushd $CBIN>/dev/null'
+#
+
+ endif
+
+# Set-up cctbx environment
+# if (-e $CCP4/lib/cctbx/cctbx_build/setpaths.csh) source $CCP4/lib/cctbx/cctbx_build/setpaths.csh
+
+# # Set-up phaser environment
+# if (-d $CCP4/src/phaser) then
+# set phaser_mtype = `$CCP4/src/phaser/bin/machine_type`
+# set phaser_version = `grep PHASER_VERSION $CCP4/src/phaser/conf/version | awk '{print $3}'`
+# set phaser_setup_file = "${CCP4}/src/phaser/phaser-${phaser_version}/build/${phaser_mtype}/setpaths.csh"
+# if (-e $phaser_setup_file) source $phaser_setup_file
+# endif
+#
+# #BALBES root configuration
+ if ( -d $CCP4/share/balbes/BALBES_0.0.1) then
+ setenv BALBES_ROOT $CCP4/share/balbes/BALBES_0.0.1
+ endif
diff -ruN ccp4-6.2.0-dist/include/ccp4.setup-sh ccp4-6.2.0/include/ccp4.setup-sh
--- ccp4-6.2.0-dist/include/ccp4.setup-sh 2010-10-19 06:16:18.000000000 -0700
+++ ccp4-6.2.0/include/ccp4.setup-sh 2010-12-17 20:47:15.000000000 -0800
@@ -195,7 +195,7 @@
# appropriate. (SunOS will normally want to use /usr/openwin or $OPENWINHOME
# instead of /usr; others may want /usr/local/lib or somw such):

-# export XAPPLRESDIR=/sw/etc/app-defaults/
+# export XAPPLRESDIR=@PREFIX@/etc/app-defaults/

if test -d $CCP4_LIB/X11/app-defaults ; then
if test "$XUSERFILESEARCHPATH"; then
diff -ruN ccp4-6.2.0-dist/include/ccp4.setup-zsh ccp4-6.2.0/include/ccp4.setup-zsh
--- ccp4-6.2.0-dist/include/ccp4.setup-zsh 1969-12-31 16:00:00.000000000 -0800
+++ ccp4-6.2.0/include/ccp4.setup-zsh 2010-12-17 20:47:11.000000000 -0800
@@ -0,0 +1,427 @@
+#! /bin/zsh -f
+# [The above is just for emacs -- this file should not be executed.]
+# $Id: ccp4.setup-zsh,v 1.30.2.3 2008/06/09 08:51:18 ccb Exp $
+
+###############################################################################
+
+# Edit this for the current version of ccp4:
+ # if [[ -z $CCP4_VERSION ]];then
+ CCP4_VERSION="ccp4-6.2.0"
+ # fi
+
+###############################################################################
+
+# NOTE: You should not need to edit the rest of this file unless you want to over-ride the
+# following assignments of $CCP4_MASTER and $BLTWISHPREFIX
+
+# NOTE: If you have installed ccp4 on OS X with fink, you should not need to
+# change this file or to source it (fink takes care of sourcing it for you).
+
+ # CCP4_MASTER is the location of the top-level directory containing `ccp4'.
+ # Set it manually by uncommenting and editing the following line:
+
+ # export CCP4_MASTER="@PREFIX@/share/xtal"
+
+ # or discover it from the source command
+
+ # if [[ -z "$CCP4_MASTER" ]];then
+ CCP4_MASTER="$(dirname $(dirname $(dirname $0)))"
+ # fi
+
+ export CCP4_MASTER
+
+
+ # Discover where bltwish executable is located
+ if [[ -z $BLTWISHPREFIX && -x $(which bltwish) ]];then
+ BLTWISHPREFIX=$( dirname $( which bltwish ) )
+ fi
+
+###############################################################################
+
+# CCP4 setup file for zsh users.
+
+# Also contains a few zsh-specific functions and command-completions.
+
+# This file is site specific and may also contain machine-specifics. The CCP4
+# administrator will have to edit this file and then have anyone who wants to
+# use CCP4 source it from their .login file. They will require the full path
+# name since no environment variables relevant to CCP4 are known until this is
+# executed.
+
+# For sites with more than one machine, it is recommended that the suite is
+# installed on a single machine and other machines access the source code, and
+# shareable files (such as this one) via shared file systems with NFS, RFS
+# etc. Non-shareable files reside in $CBIN and $CLIB (see below).
+
+# Copy this file to ccp4.setup-zsh and customise it for your needs. There are
+# three sections. You MUST check the first section. You may want to check
+# the second. You don't need to look at the third.
+
+###############################################################################
+
+
+if [[ -d "$CCP4_MASTER/$CCP4_VERSION" ]];then
+ CCP4="$CCP4_MASTER/$CCP4_VERSION" ; export CCP4
+else
+ print ""
+ print "\e[1m The directory "$CCP4_MASTER/$CCP4_VERSION" cannot be found."
+ print " Please check that "$CCP4_VERSION" is the right ccp4 version. "
+ print " Edit the file \e[0m $0 \e[1m accordingly. \e[0m"
+ print ""
+fi
+
+# CCP4_SCR: a per-user directory for run-time-generated scratch
+# files. A dedicated scratch filesystem is probably better than (/usr)/tmp
+# BINSORT_SCR: a scratch directory for binsort's use; normally same as CCP4_SCR
+
+export CCP4_SCR="/tmp/$USER"
+
+# check to see if this exists and if not try to make it
+
+if [[ ! -d "$CCP4_SCR" ]];then
+ mkdir -p "$CCP4_SCR"
+fi
+
+if [[ ! -d "$CCP4_SCR" ]];then
+ echo "Unable to assign CCP4_SCR. This will cause probs."
+fi
+
+export BINSORT_SCR="$CCP4_SCR"
+
+### CCP4i setup - you may need to edit CCP4I_TCLTK ###
+# CCP4I_TOP - the top directory of the interface
+export CCP4I_TOP="$CCP4/ccp4i"
+
+# CCP4I_TCLTK - directory containing tclsh,wish and bltwish executables
+# as used in $CCP4I_TOP/bin/ccp4i,ccp4ish,loggraph
+# For 'standard' installations this is @PREFIX@/bin
+# but note the SGI distributed version of Tcl/Tk is not
+# appropriate version
+
+if [[ -d "$BLTWISHPREFIX" && -x "$BLTWISHPREFIX/bltwish" ]]; then
+ export CCP4I_TCLTK="$BLTWISHPREFIX"
+else
+ print "\e[1m Cannot find bltwish executable. Please make sure it is in your \$PATH \e[0m"
+fi
+
+# CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help
+export CCP4I_HELP=$CCP4I_TOP/help
+
+###Optional - setting http_proxy environment
+#The commented out 'export' line below may have to be declared to download
+#and edit protein sequences using the new "Import/Edit protein sequences"
+#task. If so, uncomment this line and replace example proxy URL with your
+#relevant URL
+
+#export HTTP_PROXY wwwblah.blah.ac.uk:xxxx/blah.blah
+
+################### NOVICE USERS STOP HERE #####################
+
+################### OPTIONS TO CUSTOMISE CCP4 #####################
+
+# By default, CCP4 directories are prepended to the beginning of paths (PATH,
+# LD_LIBRARY_PATH, and DYLD_LIBRARY_PATH). If ccp4_first_in_path is set
+# to 0, then they will be appended to the end of paths.
+# When deciding local policy, bear in mind the possible existence of
+# other CCP4 installations, and the possibility of non-CCP4 programs
+# with conflicting names.
+ccp4_first_in_path=0
+
+# Set GFORTRAN_UNBUFFERED_ALL to either 1 or Y to ensure that the logfile
+# output from programs compiled with Gfortran is in the correct order.
+# Note that there will be some performance penalty for this.
+# # # # # export GFORTRAN_UNBUFFERED_ALL=Y
+
+# The following checks the CCP4 server for available updates, and reports back.
+# Comment this line out if you find it annoying.
+# eval python -V >& /dev/null && python $CCP4/etc/ccp4_updates.py -l
+
+# The commented-out switch statement below provides an example of how
+# to use this file for several machines/architectures sharing $CCP4_MASTER.
+# If necessary, uncomment and edit this. Otherwise, if you're only supporting
+# a single system alter the uncommented part as necessary.
+#
+# The significance of the environment variables is as follows:
+# CBIN: location of the executables -- must be on your path (see below);
+# CLIB: location of (binary) library files such as libccp4.a and libccp4.so;
+# MANPATH: set this if your system's `man' looks at such an environment
+# variable to determine where to look for man pages. By adding
+# $CCP4/man to the normal path you get the CCP4 man pages
+# with keyword searching as system ones.
+# MCTYPE: used for LAUE make -- see LAUE documentation
+# CCP4_BROWSER: set this if you intend to use the html documentation
+# (recommended). It should have the path and name of a html browser eg
+# /usr/bin/X11/mozilla or @PREFIX@/bin/lynx. The browser will be
+# started with the alias ccp4help and will open the file
+# $CHTML/INDEX.html.
+
+ export CBIN=$CCP4/bin
+ export CLIB=$CCP4/lib
+
+ CCP4_BROWSER=""
+ if [[ $(uname) == Darwin ]]; then
+ export CCP4_BROWSER="Safari"
+ elif [[ -x $(which firefox) ]]; then
+ export CCP4_BROWSER="firefox"
+ else
+ export CCP4_BROWSER="mozilla"
+ fi
+
+ MANPATH=$CCP4/man:$MANPATH # edit this if necessary
+ export MANPATH
+ export MCTYPE=unix # (only for Laue)
+
+
+# The following are for all systems
+
+export CCP4_LIB=$CLIB
+export CCP4_BIN=$CBIN
+
+# CLASSPATH for Java
+CLASSPATH=$CBIN:$CLASSPATH # edit this if necessary
+export CLASSPATH
+
+### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
+export PLOT_COMMAND='lpr'
+export PRINT_COMMAND='lpr'
+
+# HARVESTHOME specifies location of harvesting files (defaults to $HOME)
+export HARVESTHOME=$HOME
+
+### CCP4_OPEN ###
+# CCP4_OPEN may be set to 'UNKNOWN' to stop open failures for files opened
+# as NEW that already exist. Novices should use 'NEW' to avoid inadvertant
+# over-writing of existing files, which is then treated as a fatal error.
+
+export CCP4_OPEN=UNKNOWN
+
+### BINSORT_MEM ###
+# BINSORT_MEM is workspace used by the binsort program. In principle this
+# value is machine-dependent. It may benefit from being enlarged, but values
+# higher than 2M have been reported to cause excessive paging on some systems.
+# You might like to experiment with a program such as fft with different
+# values -- 102400 (bytes) is the default. csh's `time' command can tell you
+# about paging.
+#
+# export BINSORT_MEM=8388608
+
+
+################### EXPERIENCED USERS STOP HERE #####################
+
+################### THE REST SHOULDN'T NEED EDITING #####################
+
+### dbCCP4i database handler setup ###
+
+export DBCCP4I_TOP="${CCP4}/share/dbccp4i"
+
+### IMOSFLM environment is now defined here
+
+export MOSFLM_EXEC="${CBIN}/ipmosflm"
+export MOSFLM_WISH="${CCP4I_TCLTK}/wish"
+export IMOSFLM_VERSION="0.6.1"
+
+### MMCIFDIC is now defined here. cif_mmdic.lib is a binary file ===
+# so on multiple installs it need to be unique and not in $CLIBD
+
+export MMCIFDIC="$CLIB/cif_mmdic.lib"
+
+### MOLREPLIB Point to the location of the files bs-zeros.dat ps.resource symlib.blc
+# They are distributed with CCP4 in $CLIBD. This env must have the trailing \ or /
+
+export MOLREPLIB="$CCP4/lib/data/monomers/"
+
+### CRANK points to location of Crank automation suite within ccp4i
+
+export CRANK="$CCP4/ccp4i/crank"
+export CCP4_CRANK="1"
+
+# ### XIA2 setup
+# # XIAROOT directory (default is under the share folder)
+#
+# if [[ -f "$CCP4/share/XIAROOT/setup.sh" ]]; then
+# # source "$CCP4/share/XIAROOT/setup.sh" #has bad zsh syntax
+# # so let us just do this here instead.
+# export XIA2_HOME=${CCP4}/share/XIAROOT
+#
+# export XIA2CORE_ROOT=${XIA2_HOME}/xia2core
+# export XIA2_ROOT=${XIA2_HOME}/xia2
+# export XIA2_CCP4_61=1
+# # add the test programs to the path
+# if [[ $ccp4_first_in_path == 1 ]]; then
+# PATH=${XIA2CORE_ROOT}/Test:${PATH}
+# else
+# PATH=${PATH}:${XIA2CORE_ROOT}/Test
+# fi
+# # check now according to platform
+# if [[ "$(uname)" = "Darwin" ]]; then
+# if [[ "$(uname -p)" == "powerpc" ]]; then
+# if [[ $ccp4_first_in_path == 1 ]]; then
+# PATH=${XIA2_ROOT}/binaries/mac_ppc:${XIA2CORE_ROOT}/Test/Compiled/mac_ppc:${PATH}
+# else
+# PATH=${PATH}:${XIA2_ROOT}/binaries/mac_ppc:${XIA2CORE_ROOT}/Test/Compiled/mac_ppc
+# fi
+# if [[ -z $SWPREFIX || $CCP4_MASTER != @PREFIX@/share/xtal ]];then
+# DYLD_LIBRARY_PATH=${XIA2_ROOT}/binaries/mac_ppc:${DYLD_LIBRARY_PATH}
+# export DYLD_LIBRARY_PATH
+# fi
+# elif [[ "$(uname -p)" == "i386" ]]; then
+# if [[ $ccp4_first_in_path == 1 ]]; then
+# PATH=${XIA2_ROOT}/binaries/mac_386:${XIA2CORE_ROOT}/Test/Compiled/mac_386:${PATH}
+# else
+# PATH=${PATH}:${XIA2_ROOT}/binaries/mac_386:${XIA2CORE_ROOT}/Test/Compiled/mac_386
+# fi
+# if [[ -z $SWPREFIX || $CCP4_MASTER != @PREFIX@/share/xtal ]];then
+# DYLD_LIBRARY_PATH=${XIA2_ROOT}/binaries/mac_386:${DYLD_LIBRARY_PATH}
+# export DYLD_LIBRARY_PATH
+# fi
+# fi
+# elif [[ "$(uname)" = "Linux" ]]; then
+# if [[ $ccp4_first_in_path == 1 ]]; then
+# PATH=${XIA2_ROOT}/binaries/linux_386:${XIA2CORE_ROOT}/Test/Compiled/linux_386:${PATH}
+# else
+# PATH=${PATH}:${XIA2_ROOT}/binaries/linux_386:${XIA2CORE_ROOT}/Test/Compiled/linux_386
+# fi
+# fi
+# fi
+
+# Note: The PATH is updated with the xia2 Applications directory in the
+# construct below.
+
+### PISA_CONF_FILE is the config file needed to run the stand-alone PISA,
+# though this can be set on the command line too.
+
+export PISA_CONF_FILE=$CCP4/share/pisa/pisa.cfg
+
+### CLIBD_MON Point to the location of the dictionary files for REFMAC5
+# They are distributed with CCP4 in $CLIBD/monomers. This env must have
+# the trailing \ or /
+
+export CLIBD_MON="$CCP4/lib/data/monomers/"
+
+### PUBLIC_FONT84, CCP4_HELPDIR, HELPDIR, MOSHELPFILE ###
+# (essential for the relevant programs)
+export PUBLIC_FONT84="$CLIB/font84.dat" # plot84 fonts [used by plot84lib]
+
+# location of VMS-style help files required for mosflm [used by hlplib, chelp,
+# chlp, (ip)mosflm]:
+export CCP4_HELPDIR="$CCP4/help/" # NB trailing /
+
+# Rasmol path. Needed for prog. to find rasmol.hlp
+export RASMOLPATH="$CCP4/x-windows/RasMol"
+
+# CCP4 executables and scripts live in $CBIN and $CETC respectively; put them
+# on the path in an appropriate order for scripts to be used as wrappers for
+# binaries of the same name. Prepend ccp4 stuff to the current path to avoid
+# confusion with `.' or whatever in the path:
+#
+
+if [[ $ccp4_first_in_path == 1 ]]; then
+ PATH=${CCP4}/etc:${CBIN}:${CCP4I_TOP}/bin:${DBCCP4I_TOP}/bin:${CCP4}/share/XIAROOT/xia2/Applications:$PATH
+else
+ PATH=$PATH:${CCP4}/etc:${CBIN}:${CCP4I_TOP}/bin:${DBCCP4I_TOP}/bin:${CCP4}/share/XIAROOT/xia2/Applications
+fi
+typeset -U path # This construct prevents the path getting longer each time
+ # ccp4.setup is executed in zsh.
+export PATH
+
+# Optional (useful) additional environment variables
+ export CCP4=$CCP4
+ export CDOC=$CCP4/doc
+ export CHTML=$CCP4/html
+ export CETC=$CCP4/etc
+ export CEXAM=$CCP4/examples
+ export CINCL=$CCP4/include
+ export CLIBD=$CCP4/lib/data
+ export CLIBS=$CCP4/lib/src
+ export CPROG=$CCP4/src
+
+# useful aliases, at least for developers
+ alias ccp4='pushd $CCP4>/dev/null'
+ alias xtal='pushd $CCP4_MASTER>/dev/null'
+ alias cbin='pushd $CBIN>/dev/null'
+ alias cetc='pushd $CETC>/dev/null'
+ alias cprog='pushd $CPROG>/dev/null'
+ alias cincl='pushd $CINCL>/dev/null'
+ alias clib='pushd $CLIB>/dev/null'
+ alias clibd='pushd $CLIBD>/dev/null'
+ alias clibs='pushd $CLIBS>/dev/null'
+ alias cbin='pushd $CBIN>/dev/null'
+ alias cexam='pushd $CEXAM>/dev/null'
+ alias cdoc='pushd $CDOC>/dev/null'
+ alias chtml='pushd $CHTML>/dev/null'
+ alias ccp4help='$CCP4_BROWSER $CHTML/INDEX.html'
+
+### laue, lget, linkimages ###
+# Essential aliases for the Laue software suite
+ alias laue='$CCP4_MASTER/laue/cmd/laue.cmd'
+ alias lget='$CCP4_MASTER/laue/cmd/lget.cmd'
+ alias linkimages='$CCP4_MASTER/laue/cmd/linkimages.cmd'
+
+# additional useful aliases for Laue directories
+ alias llaue='pushd $CCP4_MASTER/laue'
+ alias lsrc='pushd $CCP4_MASTER/laue/src>/dev/null'
+ alias llib='pushd $CCP4_MASTER/laue/lib>/dev/null'
+ alias llibs='pushd $CCP4_MASTER/laue/lib/src>/dev/null'
+ alias ldoc='pushd $CCP4_MASTER/laue/doc>/dev/null'
+ alias lmak='pushd $CCP4_MASTER/laue/make>/dev/null'
+ alias lutils='pushd $CCP4_MASTER/laue/utils>/dev/null'
+ alias lcmd='pushd $CCP4_MASTER/laue/cmd>/dev/null'
+ alias ldl='pushd $CCP4_MASTER/laue/dl>/dev/null'
+ alias ltestd='pushd $CCP4_MASTER/laue/testdata>/dev/null'
+ alias lxdl='pushd $CCP4_MASTER/laue/xdl_view>/dev/null'
+ alias lxdls='pushd $CCP4_MASTER/laue/xdl_view/src>/dev/null'
+ alias lgnom='pushd $CCP4_MASTER/laue/gnom>/dev/null'
+ alias lgnoms='pushd $CCP4_MASTER/laue/gnom/src>/dev/null'
+ alias lbin='pushd $CBIN>/dev/null'
+
+# Get rid of the ccp4help alias and make a more useful function
+
+ alias ccp4help="" ; unalias ccp4help
+
+ function ccp4help {
+ if [[ $# = 0 ]]; then
+ $CCP4_BROWSER $CHTML/INDEX.html
+ else
+ $CCP4_BROWSER $CHTML/$1.html
+ fi
+ }
+
+
+# zsh specific completions:
+
+ function getccp4progs {
+ foreach progpage ($CHTML/*.html)
+ print $progpage:t:r
+ end
+ }
+
+ compctl -g "$(getccp4progs)" ccp4help
+
+ compctl -g '*.mtz' mtzdmp
+
+ compctl -g '*.plt' xplot84
+ compctl -g '*.plt' xplot84driver
+
+ # Remove any instances of multiple colons
+ PATH=${PATH/::/:}
+
+ # Avoid repeats in the path
+
+ typeset -U path
+ typeset -U manpath
+ typeset -U classpath
+
+#### # Set up cctbx environment
+#### [[ -f "$CCP4/lib/cctbx/cctbx_build/setpaths.sh" ]] && source "$CCP4/lib/cctbx/cctbx_build/setpaths.sh"
+####
+#### # Set up phaser environment
+#### if [[ -f $CCP4/src/phaser ]] ; then
+#### phaser_mtype=$( $CCP4/src/phaser/bin/machine_type )
+#### phaser_version=$(grep PHASER_VERSION $CCP4/src/phaser/conf/version | awk '{print $3}')
+#### phaser_setup_file="${CCP4}/src/phaser/phaser-${phaser_version}/build/${phaser_mtype}/setpaths.sh"
+#### [[ -f "$phaser_setup_file" ]] && source "$phaser_setup_file"
+#### fi
+
+#BALBES root configuration
+export BALBES_ROOT="$CCP4/share/balbes/BALBES_0.0.1"
+
diff -ruN ccp4-6.2.0-dist/lib/ccif/configure ccp4-6.2.0/lib/ccif/configure
--- ccp4-6.2.0-dist/lib/ccif/configure 2010-09-10 08:03:13.000000000 -0700
+++ ccp4-6.2.0/lib/ccif/configure 2010-12-17 20:48:48.000000000 -0800
@@ -5684,8 +5684,8 @@
else
SHARED_LIB_PATH='LD_LIBRARY_PATH=`pwd`'
fi
- SHARED_LIB_CMD='$(CC) $(SHARED_LIB_CFLAGS) -dynamiclib -flat_namespace -undefined suppress -install_name $(SHARED_LIB_NAME) -all_load $L -o $(SHARED_LIB_NAME)'
- SHARED_LIB_EXPORTS_CMD=''
+ SHARED_LIB_CMD='$(CC) $(SHARED_LIB_CFLAGS) -dynamiclib -flat_namespace -undefined suppress -install_name ${rpath}/$(SHARED_LIB_NAME) -all_load $L -o $(SHARED_LIB_NAME)'
+ SHARED_LIB_EXPORTS_CMD=''
;;
esac
fi
diff -ruN ccp4-6.2.0-dist/src/rapper/gc7.0/Makefile.in ccp4-6.2.0/src/rapper/gc7.0/Makefile.in
--- ccp4-6.2.0-dist/src/rapper/gc7.0/Makefile.in 2008-01-24 05:52:42.000000000 -0800
+++ ccp4-6.2.0/src/rapper/gc7.0/Makefile.in 2010-12-17 20:49:48.000000000 -0800
@@ -295,7 +295,7 @@
CYGPATH_W = @CYGPATH_W@
DARWIN_THREADS_FALSE = @DARWIN_THREADS_FALSE@
DARWIN_THREADS_TRUE = @DARWIN_THREADS_TRUE@
-DEFS = @DEFS@
+DEFS = @DEFS@ -D_XOPEN_SOURCE
DEPDIR = @DEPDIR@
ECHO = @ECHO@
ECHO_C = @ECHO_C@
diff -ruN ccp4-6.2.0-dist/src/rapper/libxml2/threads.c ccp4-6.2.0/src/rapper/libxml2/threads.c
--- ccp4-6.2.0-dist/src/rapper/libxml2/threads.c 2006-12-19 03:39:24.000000000 -0800
+++ ccp4-6.2.0/src/rapper/libxml2/threads.c 2010-12-17 20:50:56.000000000 -0800
@@ -619,7 +619,7 @@
#ifdef HAVE_PTHREAD_H
if (libxml_is_threaded == 0)
return(0);
- return((int) pthread_self());
+ return((int)(uintptr_t) pthread_self());
#elif defined HAVE_WIN32_THREADS
return GetCurrentThreadId();
#elif defined HAVE_BEOS_THREADS
diff -ruN ccp4-6.2.0-dist/x-windows/Mosflm/src/dps/util/filec/namfil.c ccp4-6.2.0/x-windows/Mosflm/src/dps/util/filec/namfil.c
--- ccp4-6.2.0-dist/x-windows/Mosflm/src/dps/util/filec/namfil.c 2003-03-10 05:38:21.000000000 -0800
+++ ccp4-6.2.0/x-windows/Mosflm/src/dps/util/filec/namfil.c 2010-12-17 20:52:13.000000000 -0800
@@ -78,7 +78,7 @@
* Find first hash in FILNAM, it will hold sign if NUM is negative and
* there is room for it.
*/
- fsthsh = (int) strchr(filnam, '#')- (int) filnam;
+ fsthsh = (int)(uintptr_t) strchr(filnam, '#')- (int)(uintptr_t) filnam;
if (fsthsh > 0)
{
for (i = len-1; i>=fsthsh; i--)
diff -ruN ccp4-6.2.0-dist/x-windows/Mosflm/src/dps/util/filec/rdbinary.c ccp4-6.2.0/x-windows/Mosflm/src/dps/util/filec/rdbinary.c
--- ccp4-6.2.0-dist/x-windows/Mosflm/src/dps/util/filec/rdbinary.c 2003-07-25 04:14:53.000000000 -0700
+++ ccp4-6.2.0/x-windows/Mosflm/src/dps/util/filec/rdbinary.c 2010-12-17 20:53:13.000000000 -0800
@@ -84,7 +84,7 @@

if ( global_debug )
printf ("Allocated %d bytes at location %d\n",
- *filesize, (int) a);
+ *filesize, (int)(uintptr_t) a);

j = strlen(filename);
dskbor_ ( &lun, filename, &j, &istat);
diff -ruN ccp4-6.2.0-dist/x-windows/Mosflm/src/dps/util/filec/wrfile.c ccp4-6.2.0/x-windows/Mosflm/src/dps/util/filec/wrfile.c
--- ccp4-6.2.0-dist/x-windows/Mosflm/src/dps/util/filec/wrfile.c 2003-03-10 05:38:21.000000000 -0800
+++ ccp4-6.2.0/x-windows/Mosflm/src/dps/util/filec/wrfile.c 2010-12-17 20:54:31.000000000 -0800
@@ -15,6 +15,7 @@
****************************************************************/
#include
#include
+#include
#include "filec.h"

int wrfile (char* filename, char* head, char* array,
@@ -35,7 +36,7 @@
{
printf("Filename : %s\n", filename);
printf("Header : \n%s - printf("Array address : %d\n", (int) array);
+ printf("Array address : %d\n", (int)(uintptr_t) array);
printf("Array dim : %d\n", naxis);
for (i=0; i printf(" : %d\n", axis[i]);
diff -ruN ccp4-6.2.0-dist/x-windows/Mosflm/src/dps/util/filec/wrmad.c ccp4-6.2.0/x-windows/Mosflm/src/dps/util/filec/wrmad.c
--- ccp4-6.2.0-dist/x-windows/Mosflm/src/dps/util/filec/wrmad.c 2003-03-10 05:38:22.000000000 -0800
+++ ccp4-6.2.0/x-windows/Mosflm/src/dps/util/filec/wrmad.c 2010-12-17 20:55:19.000000000 -0800
@@ -47,7 +47,7 @@
{
printf("Filename : %s\n", filename);
printf("Header : \n%s - printf("Array address : %d\n", (int) array);
+ printf("Array address : %d\n", (int)(uintptr_t) array);
printf("Array size : %d %d\n", as1, as2);
printf("Image size : %d %d\n", is1, is2);
}
diff -ruN ccp4-6.2.0-dist/x-windows/XCCPJIFFY/EditString.c ccp4-6.2.0/x-windows/XCCPJIFFY/EditString.c
--- ccp4-6.2.0-dist/x-windows/XCCPJIFFY/EditString.c 2003-11-19 01:46:38.000000000 -0800
+++ ccp4-6.2.0/x-windows/XCCPJIFFY/EditString.c 2010-12-17 20:56:34.000000000 -0800
@@ -256,10 +256,10 @@
WidgetClass editStringWidgetClass = (WidgetClass)&editStringClassRec;


-static char space_char [] = {' ',NULL};
+static char space_char [] = {' ',(uintptr_t)NULL};
static XawTextBlock new_input,
- no_input = {0, 0, NULL, NULL},
- space_input = {0, 1, space_char, NULL};
+ no_input = {0, 0, NULL, (uintptr_t)NULL},
+ space_input = {0, 1, space_char, (uintptr_t)NULL};

/***********************************************************/
static void
diff -ruN ccp4-6.2.0-dist/x-windows/XCCPJIFFY/ZDr2d.c ccp4-6.2.0/x-windows/XCCPJIFFY/ZDr2d.c
--- ccp4-6.2.0-dist/x-windows/XCCPJIFFY/ZDr2d.c 2003-07-01 09:57:00.000000000 -0700
+++ ccp4-6.2.0/x-windows/XCCPJIFFY/ZDr2d.c 2010-12-18 01:50:57.000000000 -0800
@@ -1007,7 +1007,7 @@
return("Object alredy exists");

gobj = XtNew(GR_OBJECT);
- memset((void *)gobj, NULL, sizeof(GR_OBJECT));
+ memset((void *)gobj, (uintptr_t)NULL, sizeof(GR_OBJECT));
gobj->objid = obj_id;

if (!parent_obj_id) { /* object attached directly to scene */
@@ -1200,7 +1200,7 @@

ppart = &(w->zDr2d);
instr = XtNew(INSTRUCTION);
- memset((void *)instr, NULL, sizeof(INSTRUCTION));
+ memset((void *)instr, (uintptr_t)NULL, sizeof(INSTRUCTION));
instr->instruction_type = instruction_type;

if (ppart->current_instr)
diff -ruN ccp4-6.2.0-dist/x-windows/XCCPJIFFY/log_file.c ccp4-6.2.0/x-windows/XCCPJIFFY/log_file.c
--- ccp4-6.2.0-dist/x-windows/XCCPJIFFY/log_file.c 2004-12-08 09:57:45.000000000 -0800
+++ ccp4-6.2.0/x-windows/XCCPJIFFY/log_file.c 2010-12-17 21:00:47.000000000 -0800
@@ -214,27 +214,27 @@

log_file_tabs =
(LOG_FILE_TABLE *)malloc(sizeof(LOG_FILE_TABLE) * (ntables+1));
- memset((void *)log_file_tabs, NULL,
+ memset((void *)log_file_tabs, (uintptr_t)NULL,
(size_t)sizeof(LOG_FILE_TABLE) * (ntables+1));
table_list = (char **)XtMalloc(sizeof(char *) * (ntables + 1));
table_list [ntables] = (char *)NULL;

log_file_keytxts =
(LOG_FILE_KEYTEXT *)malloc(sizeof(LOG_FILE_KEYTEXT) * (nkeytexts+1));
- memset((void *)log_file_keytxts, NULL,
+ memset((void *)log_file_keytxts, (uintptr_t)NULL,
(size_t)sizeof(LOG_FILE_KEYTEXT) * (nkeytexts+1));
keytext_list = (char **)XtMalloc(sizeof(char *) * (nkeytexts + 1));
keytext_list [nkeytexts] = (char *)NULL;

log_file_txts = (LOG_FILE_TEXT *)malloc(sizeof(LOG_FILE_TEXT) * (ntexts+1));
- memset((void *)log_file_txts, NULL,
+ memset((void *)log_file_txts, (uintptr_t)NULL,
(size_t)sizeof(LOG_FILE_TEXT) * (ntexts+1));
text_list = (char **)XtMalloc(sizeof(char *) * (ntexts + 1));
text_list [ntexts] = (char *)NULL;

log_file_summs =
(LOG_FILE_SUMMARY *)malloc(sizeof(LOG_FILE_SUMMARY) * (nsumms+1));
- memset((void *)log_file_summs, NULL,
+ memset((void *)log_file_summs, (uintptr_t)NULL,
(size_t)sizeof(LOG_FILE_SUMMARY) * (nsumms+1));
summary_list = (char **)XtMalloc(sizeof(char *) * (nsumms + 1));
summary_list [nsumms] = (char *)NULL;
@@ -568,7 +568,7 @@

/*** Play with absolute/relative scale ***/

- memset((void *)(&scene), (int)NULL, sizeof(scene));
+ memset((void *)(uintptr_t)(&scene), (int)(uintptr_t)NULL, sizeof(scene));

scale = 1.0; /* scaling done in plot widget */

@@ -756,7 +756,7 @@
/*** Allocate entry & chain it ***/

pgraph = XtNew(LOG_FILE_GRAPH);
- memset((void *)pgraph, NULL, (size_t)sizeof(LOG_FILE_GRAPH));
+ memset((void *)pgraph, (uintptr_t)NULL, (size_t)sizeof(LOG_FILE_GRAPH));
if (!table->graphs)
table->graphs = pgraph;
else {
diff -ruN ccp4-6.2.0-dist/x-windows/XCCPJIFFY/plot84_file.c ccp4-6.2.0/x-windows/XCCPJIFFY/plot84_file.c
--- ccp4-6.2.0-dist/x-windows/XCCPJIFFY/plot84_file.c 2004-07-08 08:29:48.000000000 -0700
+++ ccp4-6.2.0/x-windows/XCCPJIFFY/plot84_file.c 2010-12-17 21:01:34.000000000 -0800
@@ -148,7 +148,7 @@
return("I/O error on plot84 file");
}

- memset((void *)(&scene), (int)NULL, sizeof(scene));
+ memset((void *)(uintptr_t)(&scene), (int)(uintptr_t)NULL, sizeof(scene));

scale = 0.1; /* 10 dots per mm plot 84 convention */

--- ccp4-6.1.13.orig/configure 2011-05-13 22:52:40.000000000 -0400
+++ ccp4-6.1.13/configure 2011-05-13 22:53:28.000000000 -0400
@@ -2711,7 +2711,7 @@
#get CXX_LIBS in general manner
if test x"$CXX_LIBS" = x ; then
cat >> conftest.cc << _EOF
-main ()
+int main ()
{

;
--- ccp4-6.1.13.orig/x-windows/xdl_view/src/xdl_eg_c.c 2011-05-14 20:21:50.000000000 -0400
+++ ccp4-6.1.13/x-windows/xdl_view/src/xdl_eg_c.c 2011-05-14 20:26:38.000000000 -0400
@@ -1,12 +1,12 @@
#include "xdl_view.h"

/* Dummy data processing routines */
-void rd_data (filnam, a) char *filnam; float a;
+void rd_data (filnam, a) char *filnam; float a[];
{ printf ("\nOpen file %s and read data into 'a'", filnam); return;}
-void wr_data (filnam, a) char *filnam; float a;
+void wr_data (filnam, a) char *filnam; float a[];
{ printf ("\nOpen file %s and write data from 'a'", filnam); return;}
-void trans_a (a) float a; {printf ("Transformation A\n"); return;}
-void trans_b (a) float a; {printf ("Transformation B\n"); return;}
+void trans_a (a) float a[]; {printf ("Transformation A\n"); return;}
+void trans_b (a) float a[]; {printf ("Transformation B\n"); return;}

main()
{
--- ccp4-6.1.13.orig/x-windows/XCCPJIFFY/xloggraph.c 2011-05-14 20:20:40.000000000 -0400
+++ ccp4-6.1.13/x-windows/XCCPJIFFY/xloggraph.c 2011-05-14 20:20:52.000000000 -0400
@@ -487,7 +487,7 @@
/***************************************************************/

main(
- Cardinal argc,
+ int argc,
char *argv[])
{
Display *display;
--- ccp4-6.1.13.orig/x-windows/XCCPJIFFY/xplot84driver.c 2011-05-14 20:18:54.000000000 -0400
+++ ccp4-6.1.13/x-windows/XCCPJIFFY/xplot84driver.c 2011-05-14 20:20:05.000000000 -0400
@@ -228,7 +228,7 @@
/***************************************************************/

main(
- Cardinal argc,
+ int argc,
char *argv[])
{
Display *display;
--- ccp4-6.1.13.orig/src/harvest_app_/pdb_extract/common-v4.5/include/mapped_vector.h 2011-05-14 23:16:22.000000000 -0400
+++ ccp4-6.1.13/src/harvest_app_/pdb_extract/common-v4.5/include/mapped_vector.h 2011-05-14 23:16:40.000000000 -0400
@@ -11,6 +11,7 @@
#include
#include

ccp4 _unstable_ port .patch

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