Symmetry space groups aren't recognized by sglite

Bug #349849 reported by Eric Talevich
2
Affects Status Importance Assigned to Milestone
pymol (Ubuntu)
Fix Released
Undecided
Unassigned

Bug Description

Binary package hint: pymol

The symmetry information listed in PDB files isn't read properly by the Ubuntu version of Pymol, in up-to-date installations of either Hardy or Intrepid. The example file 1m14.pdb is a valid PDB file and the free Windows version of Pymol (v0.99) performs correctly.

Steps to reproduce:
1. Download RCSB's current 1M14.pdb
2. Load the molecule in Pymol
3. Click "Actions:" (the 'A' button for object 1M14) -> "generate" -> "symmetry mates" -> "within 4 A" (or any distance)

It should display the symmetries.

Instead, we get this in the terminal:

$ pymol 1M14.pdb
 PyMOL(TM) Molecular Graphics System, Version 1.1beta3.
 Copyright (C) 2007 by DeLano Scientific LLC.
 All Rights Reserved.

    Created by Warren L. DeLano, Ph.D.

    Other Major Authors and Contributors:

       Ralf W. Grosse-Kunstleve, Ph.D.

    PyMOL is user-supported open-source software. Although some versions
    are freely available, PyMOL is not in the public domain.

    If PyMOL is helpful in your work or study, then please volunteer
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.

    More information can be found at "http://www.pymol.org".

    Enter "help" 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 graphics engine:
  GL_VENDOR: NVIDIA Corporation
  GL_RENDERER: Quadro NVS 290/PCI/SSE2
  GL_VERSION: 2.1.2 NVIDIA 177.82
 Adapting to Quadro hardware.
 Detected 8 CPU cores. Enabled multithreaded rendering.
HEADER TRANSFERASE 17-JUN-02 1M14
TITLE TYROSINE KINASE DOMAIN FROM EPIDERMAL GROWTH FACTOR RECEPTOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: EPIDERMAL GROWTH FACTOR RECEPTOR;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: TYROSINE KINASE DOMAIN (RESIDUES 671-998);
COMPND 5 SYNONYM: RECEPTOR PROTEIN-TYROSINE KINASE ERBB-1;
COMPND 6 EC: 2.7.1.112;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
Symmetry-Error: Urecognized space group symbol 'I 2 3'.
Symmetry-Error: Unable to get matrices from sglite.
 CmdLoad: "1M14.pdb" loaded as "1M14".
ExecutiveSymExp-Error: No symmetry matrices!

The space group symbol "I 2 3" is valid [1] and this problem seems to occur for all PDB files with symmetry information. The source code for SgLite looks sane [2], so maybe there's something wrong with the compilation of SgLite that clobbers the symbol table?

[1] http://www.bmsc.washington.edu/CrystaLinks/space_group_freq.html
[2] http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/contrib/sglite/sgsymbols.c?view=markup

Revision history for this message
Eric Talevich (eric-talevich) wrote :
Revision history for this message
Eric Talevich (eric-talevich) wrote :

Followup: I compiled the latest version of Pymol from source (svn trunk) and it worked properly. The listed version is 1.2b5pre and the relevant terminal output is:

 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 Symmetry: Found 24 symmetry operators.
 CmdLoad: "/home/etal/Desktop/1M14.pdb" loaded as "1M14".
 You clicked /1M14_23000000/X000/A/TYR`845/CZ
 Selector: selection "sele" defined with 12 atoms.

Revision history for this message
Daniel Leidert (dleidert-deactivatedaccount) wrote :

Should already be fixed then in 1.2r2-1.1 in Ubuntu.

Changed in pymol (Ubuntu):
status: New → Fix Released
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