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Difference between revisions of "Category:Structural Biology Scripts"

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

Latest revision as of 01:29, 28 March 2014

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-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.