Subject: pymol: script (command-line) mode appears broken... Package: pymol Version: 0.98+0.99rc6-2 Severity: important
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Hi,
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.
[EMAIL PROTECTED]:~$ cat foo.pml
load foo.pdb
show spheres
png foo
quit
[EMAIL PROTECTED]:~$ cat foo.pdb
ATOM 1 Sr STO 1 0.000 0.000 0.000
[EMAIL PROTECTED]:~$ pymol foo.pml
PyMOL(TM) Molecular Graphics System, Version 0.99rc6.
<snip>
PyMOL: normal program termination.
[EMAIL PROTECTED]:~$ pymol -c foo.pml
Traceback (most recent call last):
File "/var/lib/python-support/python2.4/pymol//__init__.py", line 364, in ?
invocation.parse_args(pymol_argv)
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
[EMAIL PROTECTED]:~$
Conversely, the same scenario works just fine on my workstation
running sarge:
[EMAIL PROTECTED]:~$ pymol -c foo.pml
PyMOL(TM) Molecular Graphics System, Version 0.97.
<snip>
PyMOL: normal program termination.
[EMAIL PROTECTED]:~$
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,
Daniel
-- 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
-- no debconf information
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