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 PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
pgpgOfohkdu7s.pgp
Description: PGP signature