[Debichem-devel] Bug#459644: pymol: script (command-line) mode appears broken...

Daniel Freedman freedman at physics.cornell.edu
Mon Jan 7 20:30:10 UTC 2008

Subject: pymol: script (command-line) mode appears broken...
Package: pymol
Version: 0.98+0.99rc6-2
Severity: important

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I've newly encountered a problem with pymol on etch that didn't exist
with pymol on sarge, namely it's inability to run in
script/batch/command-line mode (ie using pymol's "pml" files).

According to the manual, I should be able to invoke pymol as:

  pymol -c foo.pml
And have the pymol interpreter evoke the appropriate script (render,
etc.) without necessity of GUI and with greater speed and smaller
memory footprint, etc.

Instead, though, I'm getting a python IndexError, even though the
exact same files work fine with the older version of pymol (from
sarge), and works fine in normal GUI mode.

freedman at littlebird:~$ cat foo.pml
load foo.pdb
show spheres
png foo
freedman at littlebird:~$ cat foo.pdb
ATOM    1   Sr STO     1        0.000    0.000    0.000
freedman at littlebird:~$ pymol foo.pml

 PyMOL(TM) Molecular Graphics System, Version 0.99rc6.


 PyMOL: normal program termination.
freedman at littlebird:~$ pymol -c foo.pml
Traceback (most recent call last):
  File "/var/lib/python-support/python2.4/pymol//__init__.py", line 364, in ?
  File "/var/lib/python-support/python2.4/pymol/invocation.py", line 199, in parse_args
    options.internal_feedback = int(av.pop())
IndexError: pop from empty list
freedman at littlebird:~$ 

Conversely, the same scenario works just fine on my workstation
running sarge:

freedman at dft:~$ pymol -c foo.pml

 PyMOL(TM) Molecular Graphics System, Version 0.97.


 PyMOL: normal program termination.
freedman at dft:~$ 

Any ideas?  I listed this with severity=important as it makes pymol
unusable for all the batch rendering jobs I run on our HPC compute
nodes (and likely for others in similar situations).

Thanks for all of your work on pymol.  Hope you had a happy New Year!

Take care,

-- System Information:
Debian Release: 4.0
  APT prefers stable
  APT policy: (500, 'stable')
Architecture: i386 (i686)
Shell:  /bin/sh linked to /bin/bash
Kernel: Linux 2.6.18-5-686
Locale: LANG=C, LC_CTYPE=C (charmap=ANSI_X3.4-1968)

Versions of packages pymol depends on:
ii  freeglut3              2.4.0-5           OpenGL Utility Toolkit
ii  libc6                  2.3.6.ds1-13etch2 GNU C Library: Shared libraries
ii  libfreetype6           2.2.1-5+etch1     FreeType 2 font engine, shared lib
ii  libgl1-mesa-glx [libgl 6.5.1-0.6         A free implementation of the OpenG
ii  libglu1-mesa [libglu1] 6.5.1-0.6         The OpenGL utility library (GLU)
ii  libpng12-0             1.2.15~beta5-1    PNG library - runtime
ii  python                 2.4.4-2           An interactive high-level object-o
ii  python-pmw             1.2-5             Pmw -- Python MegaWidgets
ii  python-support         0.5.6             automated rebuilding support for p
ii  python-tk              2.4.4-1           Tkinter - Writing Tk applications 
ii  zlib1g                 1:1.2.3-13        compression library - runtime

Versions of packages pymol recommends:
ii  apbs                          0.4.0-2    Adaptive Poisson Boltzmann Solver

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