Installing PyMOL and cctbx

Getting PyMOL to play nicely with cctbx can sometimes be a chore. In order to get the two projects to use the same version of python, you need to install both of them from source.

I install cctbx from source, although you could use one of the self-extracting binary distributions:

CCTBX installation instructions

Download the self-extracting source from the cctbx downloads page
put the file self_bundle.selfx in new directory, e.g. /usr/local/cctbx, and then
run the command perl self_bundle.selfx
Note the creation of the file: cctbx_build/setpath.sh and cctbx_build/setpath.csh. You will need to run one of these, depending on whether you use a bash-like or csh-like shell, to allow subsequent python commands to see the newly installed cctbx modules.

I personally use PyMOL installed from the SVN source to have the latest and greatest features.

PyMOL installation instructions

Download (or update) PyMOL via SVN. I use a little script that looks like this:


  #! /bin/sh

  usage() {
    echo -e "\nsvn_update.sh [options]"
    echo      "where [options] could be:"
    echo      "     --backup|--back   Make backup copy"
  }

  svnbackup() {
    echo "Making backup copy (in case something goes wrong ...)"
    cd pymol && tar cf - . | ( cd ../old_pymol && tar xf - )
    cd ../
  }

  svnupdate () {
    svn checkout https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol
  }

  if [[ "$#argv" < 1 ]] ; then
    svnupdate
  else
    if [[ "$1" == "-h" || "$1" == "--help" ]]; then
      usage
  # don't do backup unless "back" flag is given
    elif [[ "$1" == "--back" || "$1" == "--backup" ]]; then
      svnbackup
      svnupdate
    else
      svnupdate
    fi
  fi

This will download the pymol source into the "pymol" directory.

Now you just need to run a few commands:
```
  python setup.py build
  python setup.py install
  python setup2.py install
  
```
Optionally, you can specify an installation location with the "prefix" option to the setup.py install command. For example, I store all of our software on an NFS accessible disk that is mounted as "/software" and the python libraries for our Linux computers are installed in /software/Linux/lib/python2.5/site-packages so I do this as:
```
  python setup.py install prefix=/software/Linux
    
```

After installing these and sourcing the setpaths.(c)sh script for cctbx, executing the pymol command should start a version of PyMOL that can use the cctbx modules.