[PyMOL] Error when running python script that uses cctbx

[Robert C. <rl...@k2...>]

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 =3D 31.1
	b =3D 52.5
	c =3D 85.3
	alpha =3D 90.
	beta =3D 100.
	gamma =3D 90.
	sg =3D 'P21'
	Unitcell_obj =3D uctbx.UnitCell((a,b,c,alpha,beta,gamma))

Here is an exact transcript from the terminal window:

   % pymol
  =20
    PyMOL(TM) Molecular Graphics System, Version 0.78.
    Copyright (C) 1998-2002 by DeLano Scientific.
    All Rights Reserved.
   =20
       Created by Warren L. DeLano, Ph.D.=20
   =20
       Other Major Authors and Contributors:
  =20
          Ralf W. Grosse-Kunstleve, Ph.D.
   =20
       This software is open source and freely available.
       Updates can be found at "http://www.pymol.org".
   =20
       Is PyMOL a free and open-source project worthy of your support?
  =20
       Then visit the home page to learn what you can do to contribute!
  =20
       Also, please cite PyMOL in publications and presentations:
  =20
          Warren L. DeLano "The PyMOL Molecular Graphics System."
          DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org
  =20
       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.
  =20
    Hit ESC anytime to toggle between text and graphics.
  =20
    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'=20
instance gets created in the line:

   Unitcell_obj =3D 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 =3D 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
--=20
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
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2