Hi James, On Sun, 25 Apr 2010 15:41:32 -0700, James Stroud <xtald...@gmail.com> wrote:
> cctbx is cool in principle, but I would be very happy to know how to > use it with a pre-existing python like most other packages are capable > of. I'm starting to lose patience reverse-engineering the install > scripts to figure out how to do it. I can't seem to find instructions > on the web page. > > What am I missing? Is it that I must migrate my entire python > environment to cctbx.python? Isn't it better to add cctbx to a current > environment rather than the other way around? If every package > required the user's migrating his python environment to the package's > environment, then we wouldn't be able to use more than one package > with a given python install. > > It seems ridiculous. I don't have a problem doing this (at least with Linux). I simply download the "Self-extracting cctbx sources for Unix" and put it somewhere appropriate and run the installation command "perl cctbx_bundle.selfx". After it finishes installing I modify my login shell script according to the installers instructions. Actually I modify a large setup script that allows me and all the users to set up any particular program. This will add the cctbx/cctbx_build/bin directory to the beginning of the PATH variable. In order for cctbx to work with any python script then I simply add a link in the cctbx/cctbx_build/bin directory so that "python" points at cctbx.python: i.e. cd cctbx_build/bin ln -s cctbx.python python Any other python scripts that call cctbx then start with #! /usr/bin/env python rather than #! /usr/bin/python In order to have cctbx play nice with PyMOL, then I also install PyMOL from the SVN sources (also not too difficult). Then I make sure that my PyMOL start up script uses "python" and not "/usr/bin/python" and then I can use both PyMOL and cctbx with the system's python. Perhaps this still sounds ridiculous to you, but I don't have a problem with it. Once the initial set up is done there isn't much to it. Of course I have left myself little instruction files in my installation directories to remind myself what I need to do. > It doesn't make sense, so I must be missing something fundamental. I > think this is the reason I have never used cctbx before. I last tried > about 4 years and I thought that it was because the package was > immature. There is also a new PyMOL script in the PyMOL wiki called "supercell" http://pymolwiki.org/index.php/Supercell that will build a unit cell, or a block of multiple unit cells. I think this should work in a script to PyMOL, hence not needing the graphics nor any interactive work. I haven't tried it that way, though. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
