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.