View source for Category:Structural Biology Scripts

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.

[[Category:Script_Library]]