[Bug 349849] [NEW] Symmetry space groups aren't recognized by sglite

[Eric Talevich]

Public bug reported:

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

** Affects: pymol (Ubuntu)
     Importance: Undecided
         Status: New

-- 
Symmetry space groups aren't recognized by sglite
https://bugs.launchpad.net/bugs/349849
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