SuperSym - Revision history

Cchem: 1 revision

2020-07-20T16:19:42Z

1 revision

2020-07-01T09:41:53Z

Infobox

2019-02-04T04:20:40Z

2 revisions

2019-01-24T10:26:24Z

See CCTBX

2019-01-24T09:14:51Z

Python distribution

2014-03-28T01:44:24Z

29 revisions

2010-06-30T17:36:48Z

/author Feedback section added

2010-01-11T20:56:46Z

Installing SuperSym: updated to reflect v1.2

2009-10-20T02:39:16Z

2009-10-19T22:58:58Z

The Menu

@@ Line 1: / Line 1: @@
 [[File:SuperSymExample.png|300px|thumb|right|Symmetry partners for 1hpv showing 6-1 screw axis]]
 [[File:SuperSymExample2.png|300px|thumb|right|Full cell of symmetry partners with symmetry axes displayed]]
-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 all versions is available from [https://sourceforge.net/projects/supersym/ https://sourceforge.net/projects/supersym/], and the most recent code is available in regular text format from [[SuperSymSource]].
+SuperSym is a PyMOL plugin providing a large number of tools for visualization of space groups; unit cells; and symmetry axes, operators, and partners.
 == Dependencies ==

@@ Line 8: / Line 8: @@
 * numpy
-PyMOL, cctbx and numpy must all be compiled with the same Python distribution!
+'''PyMOL, cctbx and numpy must all be compiled with the same Python distribution!'''
 This plugin was developed in 2010 for PyMOL version 1.2r1 and has not been updated since.

@@ Line 3: / Line 3: @@
 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 all versions is available from [https://sourceforge.net/projects/supersym/ https://sourceforge.net/projects/supersym/], and the most recent code is available in regular text format from [[SuperSymSource]].
-==Dependencies, Bugs, and Acknowledgments==
+== Dependencies ==
-This plugin has only been tested for PyMOL version 1.2b6pre and 1.2r1.
+* [[CCTBX|cctbx]]
-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.
+PyMOL, cctbx and numpy must all be compiled with the same Python distribution!
 Symmetry axes are not defined for all space groups, and do not display properly for some.
-This plugin requires cctbx and numeric python (numpy).
+== Acknowledgments ==
 Primary coding and development was done by Stuart Ballard. All comments, questions, and issues should be directed to him at srballard@wisc.edu.

← Older revision		Revision as of 17:36, 30 June 2010
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	Note: previous errors resulting from incorrect naming of the plugin file have been resolved in v1.2.		Note: previous errors resulting from incorrect naming of the plugin file have been resolved in v1.2.
		+
		+	==Feedback==
		+
		+	Please post any comments, complaints, bug fix requests, useful tricks, or cool adaptations of SuperSym here.

	==The Menu==		==The Menu==

@@ Line 21: / Line 21: @@
 ==Installing SuperSym==
-To install SuperSym v1.1, download SuperSymPlugin v1.1.py from [https://sourceforge.net/projects/supersym/ https://sourceforge.net/projects/supersym/]. In PyMOL, go to:
+To install SuperSym v1.2, download SuperSymPlugin12.py from [https://sourceforge.net/projects/supersym/ https://sourceforge.net/projects/supersym/]. In PyMOL, go to:
 *Plugin > Manage Plugins > Install...
-A file selector dialog will appear. Select SuperSymPlugin v1.1.py. PyMOL will direct you to restart, and upon doing so SuperSym will be accessible through the Plugin menu.
+A file selector dialog will appear. Select SuperSymPlugin12.py. PyMOL will direct you to restart, and upon doing so SuperSym will be accessible through the Plugin menu.
-To use functions of SuperSym directly, without creating a drop-down menu, use the run command in PyMOL on SuperSymPlugin v1.1.py.
+To use functions of SuperSym directly, without creating a drop-down menu, use the run command in PyMOL on SuperSymPlugin12.py.
 ==The Menu==

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← Older revision		Revision as of 02:39, 20 October 2009
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	This plugin requires cctbx and numeric python (numpy).		This plugin requires cctbx and numeric python (numpy).
		+
		+	Primary coding and development was done by Stuart Ballard. All comments, questions, and issues should be directed to him at srballard@wisc.edu.

	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/ http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/]. Some of this code has been modified for use in SuperSym.		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/ http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/]. Some of this code has been modified for use in SuperSym.

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 **'''3x3x3 Block'''
 ***Generates 27 sets of symmetry partners for a given object, filling lattice positions [-1,-1,-1] through [1,1,1]. This option may take a long time to execute
 *'''Coloring >'''
 **'''Default Rainbow'''
@@ Line 52: / Line 54: @@
 **'''Ribbon'''
 **Convenience function to display symmetry partners as ribbons
 **'''Sphere Surface (best for printing)'''
 ***Uses the findSurfaceResidues function and shows surface residues as spheres. If printing, this option saves at least 60% of materials relative to regular surfaces, with minimal loss in resolution