Dear Folks (perhaps especially Warren!), I'm trying to write a script for python that happens to use the Computational Crystallography Toolbox (cctbx) and its python interface. I keep getting dumped out of pymol with no error message whatsoever.
The script, test_cell.py, is an abbreviated script to try to sort out
the problem when I was running something larger. All it contains is
#### test_cell.py
from cctbx import uctbx, sgtbx
a = 31.1
b = 52.5
c = 85.3
alpha = 90.
beta = 100.
gamma = 90.
sg = 'P21'
Unitcell_obj = uctbx.UnitCell((a,b,c,alpha,beta,gamma))
Here is an exact transcript from the terminal window:
% pymol
PyMOL(TM) Molecular Graphics System, Version 0.78.
Copyright (C) 1998-2002 by DeLano Scientific.
All Rights Reserved.
Created by Warren L. DeLano, Ph.D.
Other Major Authors and Contributors:
Ralf W. Grosse-Kunstleve, Ph.D.
This software is open source and freely available.
Updates can be found at "http://www.pymol.org";.
Is PyMOL a free and open-source project worthy of your support?
Then visit the home page to learn what you can do to contribute!
Also, please cite PyMOL in publications and presentations:
Warren L. DeLano "The PyMOL Molecular Graphics System."
DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org
Enter "help release" for release notes (PLEASE READ!).
Enter "help commands" for a list of commands.
Enter "help <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
OpenGL based graphics front end:
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: RIVA TNT2/PCI/SSE
GL_VERSION: 1.3.0
PyMOL>set bg_rgb, .5 .5 .5
Setting: bg_rgb set to [ 0.50000, 0.50000, 0.50000 ].
PyMOL>viewport 800, 600
PyMOL>set cgo_line_radius, 0.05
Setting: cgo_line_radius set to 0.05000.
PyMOL>set line_width, 2
Setting: line_width set to 2.00000.
PyMOL>set cgo_line_width, 2
Setting: cgo_line_width set to 2.00000.
PyMOL>run test_cell.py
[134]%
The '134' in brackets above is the value of the $status variable that
gets set by the shell on the exit from pymol. (This is the only clue
to the problem that I can think of, but I don't know what it means.)
I have verified that the unwanted exit happens when the 'Unitcell_obj'
instance gets created in the line:
Unitcell_obj = uctbx.UnitCell((a,b,c,alpha,beta,gamma))
by typing it alone (with it commented out of the script). I've tried a
different call to the sgtbx class:
sgsymb = sgtbx.SpaceGroupSymbols(sg)
and it has exactly the same effect.
Anybody have a clue that they'd like to share, or some other test that
could be done for debugging purposes?
Cheers,
Robert
--
Robert L. Campbell, Ph.D. http://biophysics.med.jhmi.edu/rlc
Research Specialist/X-ray Facility Manager
HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
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