Difference between revisions of "SuperSym"

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(Using SuperSym)
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==Using SuperSym==
==Using SuperSym==
The SuperSym dropdown menu on the PyMOL GUI provides the following options:
The SuperSym dropdown menu options:
*Default Symmetry Partner Set
*''Default Symmetry Partner Set'': ''See Build Symmetry Partners > Cell [0,0,0] (default)''
*Draw Unit Cell
*''Draw Unit Cell''
*Build Symmetry Partners >
*''Build Symmetry Partners >''
**Cell [0,0,0] (default)
**''Cell [0,0,0] (default)''
**Cell [x,y,z] (custom)
**''Cell [x,y,z] (custom)''
**2x2x2 Block
**''2x2x2 Block''
**3x3x3 Block
**''3x3x3 Block''
*Coloring >
*''Coloring >''
**Default Rainbow
**''Default Rainbow''
**Select color for each operation
**''Select color for each operation''
**Select one color for custom set of operations
**''Select one color for custom set of operations''
*Graphics >
*''Graphics >''
**Sphere Surface (best for printing)
**''Sphere Surface (best for printing)''
**Surface (high load render)
**''Surface (high load render)''
*Symmetry Axes >
*''Symmetry Axes >''
**Build Axes
**''Build Axes''
*Move symmetry partners
*''Move symmetry partners''

Revision as of 19:22, 11 September 2009

SuperSym is a PyMOL plugin providing a large number of tools for visualization of space groups; unit cells; and symmetry axes, operators, and partners. Source code for version 1.0 is available from https://sourceforge.net/projects/supersym/ or SuperSymSource.

Dependencies, Bugs, and Acknowledgments

This plugin has only been tested for PyMOL version 1.2b6pre and 1.2r1.

Pre-v1.0 PyMOL may not display objects created by this plugin properly, even if the pse file displays normally in other versions. Use at your own risk.

SuperSym has failed to load properly in OSX 10.6 (Snow Leopard), but functions normally in OSX 10.5. Bug fixing is underway.

This plugin requires cctbx and numeric python.

Code for unit cell and symmetry axis building is borrowed from scripts created by Robert Campbell and Ralf W. Grosse-Kunstleve, available at http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/. Some of this code has been modified for use in SuperSym.

FindSurfaceResidues is utilized for some of SuperSym's graphics generation, with some modifications.

Installing SuperSym

To install SuperSym, first copy the text of source files to corresponding .py files or download them from SourceForge. Place SuperSymMenu.py in pymol/modules/pmg_tk/startup, and all other files in pymol/modules. This will make all of SuperSym's functions available through a drop-down menu in the PyMOL GUI

To use functions of SuperSym directly, without creating a drop-down menu, ignore SuperSymMenu.py and use the run command on the other files in PyMOL as you would for any other script.

Using SuperSym

The SuperSym dropdown menu options:

  • Default Symmetry Partner Set: See Build Symmetry Partners > Cell [0,0,0] (default)
  • Draw Unit Cell
  • Build Symmetry Partners >
    • Cell [0,0,0] (default)
    • Cell [x,y,z] (custom)
    • 2x2x2 Block
    • 3x3x3 Block
  • Coloring >
    • Default Rainbow
    • Select color for each operation
    • Select one color for custom set of operations
  • Graphics >
    • Lines
    • Ribbon
    • Sphere Surface (best for printing)
    • Surface (high load render)
  • Symmetry Axes >
    • Build Axes
  • Move symmetry partners
  • About
  • Help