pymol for Debian
----------------

Community-maintained documentation for pymol is available at
http://www.pymolwiki.org/.

 -- Michael Banck <mbanck@debian.org>, Thu, 05 Jul 2007 11:43:55 +0200
 
Notes on example scripts which were not installed to pymol-data package
-----------------------------------------------------------------------
Many example scripts accompanying pymol can be run with 'pymol -c <scriptname>'
command, but some of scripts from examples/ directory are not listed in 
`debian/pymol-data.install` and not installed.

Some of them can be installed with minor fixes.

Scripts inside examples/devel/ upstream's directory
 - start_pymol.py - this script is outdated.
 - povray01.py:
 This script can be run with 'pymol -c povray01.py' command, still it produces 
 povray-related error, which is not fixed for now. 
 Requires `povray` package to be installed.

Scripts inside examples/cookbook/ upstream's directory, which are skipped
- dali.py - requires dali.txt to be located at the same directory (which is not
  present and probably won't be found);
- density.pml - requires 1DN2.pdb and 2fofc.xplor to be located at the same 
  directory [*]; command "fetch 1dn2, type=2fofc,async=0" couldn't locate 
  any electron density map.
- groel_es.pml - requires 1AON.pdb to be located at the same directory [*], 
  `molscript` and `molauto` commands to be available to run;
- ribosome.pml - requires 1FFK.pdb to be located at the same directory [*];
  It also uses identifiers like (pkchain), which produce 'Selector-Error': 
  http://pymol.sourceforge.net/newman/user/S0350advmouse.html
  
[*]: .pdb files with corresponding identifiers can be found at 
  [Protein Data Bank](http://www.rcsb.org/pdb/home/home.do), and probably 
  they'll make these scripts work correctly from the directory they are located at.
  Pdb files can be loaded by changing load to fetch in corresponding script.
  However, I couldn't locate 2fofc.xplor, and fetch can't locate it for structure 
  with identifier `1dn2`.

In autopkgtest scripts one file is installed, but skipped in autopkgtest tests -
/usr/share/pymol/examples/cookbook/multiclip_ray.pml.
It can be run by hand by executing (as mentioned in README.test)
   
     pymol /usr/share/pymol/examples/cookbook/multiclip_ray.pml
   
Note that it requires display to be installed and can't be run with Xvfb-run,
because at final step it actually displays image, and this is blocking operation.
This is why command

    xvfb-run -s '-screen 0 700x500x24' pymol /usr/share/pymol/examples/cookbook/multiclip_ray.pml

 - won't terminate. That's the reason why it's skipped in autopkgtest.

Other skipped files from examples/cookbook, which can be run by hand, are 
described in Debian.test.

 -- Tatiana Malygina <merlettaia@gmail.com>, Tue, 16 Aug 2016 14:06:15 +0300