Category:Structural Biology Scripts - Revision history

Pyadmin: 11 revisions

2014-03-28T01:29:47Z

11 revisions

Jaredsampson: fixed typo in word "dependent"

2011-03-09T18:29:05Z

fixed typo in word "dependent"

Tlinnet at 22:19, 26 December 2010

2010-12-26T22:19:00Z

New page

This page is a sub-category of scripts for Structural Biology Applications.

* [[Cealign]] -- Implementation of the CE Structure Alignment algorithm as a PyMOL plugin.
* [[Kabsch]] -- Kabsch alignment of two sets of vectors. (Part 2 of a protein alignment.)
* [[LigAlign]] -- Ligand-based active site alignment and comparison.
* [[WriteSS]] -- Writes secondary structural elements, for each residues, to a file.
* [[ss]] -- Simple command to summarise the Secondary Structure as a list of "start-end type" like sses.
* [[iterate_sses]] -- Slightly more complex version of "ss" that allows the user to pass in a function to act on the sse list.
* [[Helicity_check]] -- helicity_check show the evolution of O - N distances over an amino acid sequence
* [[Measure Distance]] -- Measures the distance between two atoms (Python script).
* [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X
* [[motif]] -- Designed for easy display of backbone motifs (nests, catgrips, etc).
* [[Show NMR constrains]] -- This script will display the NMR constrains used for a structure calculation atop a structure. Usage: Save this as "NMRcnstr.py" load your protein in PyMOL, and run the script. type upl('fname') or cns('fname') where fname is the filename with the NMR constrains you want to display.
* [[CreateSecondaryStructure]] -- Grow a helix,strand or loop from ends of proteins
* [[DynoPlot]] -- Generic dynamic plotting utility; Interactive Ramachandran Plots.
* [[Rotamer Toggle]] -- Toggle through the most common side chain rotamers and/or color by rotamer probability (Dunbrack's Backbone-depenedent library)
* [[DisplacementMap]] -- Finds the best residue pair for FRET and EPR measurements. Given and open and closed form of a protein (and after pymol alignment), it returns
a data-matrix for displacement between residues and a gnuplot plot file. It returns best positive and negative delta displacement suggestions. The suggestions can be mutated into cysteines and labelled for FRET/EPR measurements.

[[Category:Script_Library]]

Aheifets: Added link to LigAlign. Alphabetized script descriptions.

2008-10-03T22:43:18Z

Added link to LigAlign. Alphabetized script descriptions.

Tmwsiy at 02:13, 9 September 2005

2005-09-09T02:13:22Z

Tmwsiy at 13:26, 29 August 2005

2005-08-29T13:26:46Z

Tmwsiy at 13:09, 29 August 2005

2005-08-29T13:09:58Z

Tmwsiy at 02:29, 17 August 2005

2005-08-17T02:29:59Z

Tmwsiy at 22:01, 11 May 2005

2005-05-11T22:01:22Z

Tmwsiy at 21:13, 11 May 2005

2005-05-11T21:13:37Z

New page

This page is a sub-category of scripts for Structural Biology Applications.

* [[Rotamer Toggle]] -- Toggle through the most common side chain rotamers

[[Category:Script_Library]]

@@ Line 1: / Line 1: @@
 This page is a sub-category of scripts for Structural Biology Applications.
-* [[Rotamer Toggle]] -- Toggle through the most common side chain rotamers (Backbone-depenedent library)
+* [[Rotamer Toggle]] -- Toggle through the most common side chain rotamers (Dunbrack's Backbone-depenedent library)
 [[Category:Script_Library]]

← Older revision	Revision as of 01:29, 28 March 2014
(No difference)

@@ Line 14: / Line 14: @@
 * [[CreateSecondaryStructure]] -- Grow a helix,strand or loop from ends of proteins
 * [[DynoPlot]]  -- Generic dynamic plotting utility; Interactive Ramachandran Plots.
-* [[Rotamer Toggle]] -- Toggle through the most common side chain rotamers and/or color by rotamer probability (Dunbrack's Backbone-depenedent library)
+* [[Rotamer Toggle]] -- Toggle through the most common side chain rotamers and/or color by rotamer probability (Dunbrack's Backbone-dependent library)
 * [[DisplacementMap]]  -- Finds the best residue pair for FRET and EPR measurements. Given and open and closed form of a protein (and after pymol alignment), it returns
 a data-matrix for displacement between residues and a gnuplot plot file. It returns best positive and negative delta displacement suggestions. The suggestions can be mutated into cysteines and labelled for FRET/EPR measurements.
 [[Category:Script_Library]]