Symmetry space groups aren't recognized by sglite
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.
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are freely available, PyMOL is not in the public domain.
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More information can be found at "http://
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
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://
[2] http://
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. etal/Desktop/ 1M14.pdb" loaded as "1M14". X000/A/ TYR`845/ CZ
ObjectMolecule: Read crystal symmetry information.
Symmetry: Found 24 symmetry operators.
CmdLoad: "/home/
You clicked /1M14_23000000/
Selector: selection "sele" defined with 12 atoms.