Installation

Installing Clipper and dependencies

On Linux systems you will need at least gcc 3.0.

Clipper has the following dependencies:

• The 'fftw' FFT library: http://www.fftw.org/
• (Alternatively, a kiss-fft overlay is available).

It may optionally be used with:

• The CCP4v6.1 and mmdb libraries: ftp://ftp.ccp4.ac.uk/ccp4/6.1.1/ccp4-6.1.1-core-src.tar.gz
• The 'cctbx' Crystallographic toolbox: http://cctbx.sourceforge.net/

The following instructions should download and install Clipper and all its dependencies on a properly configured Linux machine.

#!/bin/csh -f
wget ftp://ftp.ccp4.ac.uk/ccp4/6.1.1/ccp4-6.1.1-core-src.tar.gz
wget http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper21.latest.tar.gz
#wget http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper-kiss.latest.tar.gz
tar xvfz ccp4-6.1.1-core-src.tar.gz
setenv CCP4_MASTER      $PWD/
setenv CCP4             $CCP4_MASTER/ccp4-6.1.1/
setenv CCP4_SCR         /tmp/$USER
setenv BINSORT_SCR      $CCP4_SCR
setenv CCP4_OPEN        UNKNOWN
setenv CLIB             $CCP4/lib
setenv CLIBD            $CCP4/lib/data
setenv CLIBS            $CCP4/lib/src
setenv CINCL            $CCP4/include
setenv PUBLIC_FONT84    $CLIB/font84.dat
cd $CCP4
sed -i.orig 's#^\(.*passwd_struct.*\)$#//\1#' lib/src/library_utils.c 
./configure --enable-fftw --disable-clipper --disable-ccif --disable-lapack --disable-ssm --disable-pdb_extract --disable-cctbx --disable-diffractionImg --onlylib
gmake -k install

cd $CCP4_MASTER
mkdir clipper
cd clipper
tar xvfz ../clipper21.latest.tar.gz
#tar xvfz ../clipper-kiss.latest.tar.gz
setenv OPT -O1
./configure --ccp4dir=$CCP4
gmake examples

This file is available as a shell script from the Clipper homepage.

Problems

Likely problems may include:

• Failure to agree to CCP4 v6 license agreement. If you have not installed CCP4 v6 before, you should read the agreement at http://www.ccp4.ac.uk/ and then use the following before attempting the install:

  echo $user `date` "V5.0" > ${HOME}/.agree2ccp4v6
  

• Non-Linux platforms: Change the CCP4 configure line to have the name of your platform, instead of 'linux', on the end. The fortran example will fail.
• 'wget' fails: Your firewall may block wget. In which case, fetch the tar files by hand and then run the rest of the script.
• If you haven't installed cctbx, the cctbx example will fail.