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News & Updates
Official Release PyMOL, AxPyMOL, and JyMO v1.7 have all been released today, January 14, 2014.
New Plugin Bondpack is a collection of PyMOL plugins for easy visualization of atomic bonds.
New Plugin MOLE 2.0 is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
3D using Geforce PyMOL can now be visualized in 3D using Nvidia GeForce video cards (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
New Plugin GROMACS_Plugin is a new plugin that ties together PyMOL and GROMACS.
New Software CMPyMOL is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
New Script cgo_arrow draws an arrow between two picked atoms.
Tips & Tricks Instructions for generating movie PDFs using .mpg movies from PyMOL.
Older News See Older News.
Did you know...

Cluster Count

= Overview =

This script calculates statistics on the B-values for all atoms in the selected object, prints the information on screen and appends it to a file called "cluster_count.txt".


Usage

cluster_count object


Example

cluster_count 1ubq
 
#output on screen:
 
Number of atoms in ' 1ubq ':  602
Minimum and Maximum B-values:  2.0 42.75
Average B-value:  13.4131063029
Standard deviation of the B-values:  8.70767140923
This data will be appended to cluster_count.txt
 
#output in file cluster_count.txt; the format is:
#objectname N minB maxB aveB stdevB
1ubq            602    2.000   42.750   13.413    8.708


The Code

# Script: cluster_count.py
# Copyleft 2010 Martin Christen
 
from pymol import cmd,stored
def cluster_count(selection):
 
        """
 AUTHOR
 
 Martin Christen
 
 DESCRIPTION
 
 This script calculates statistics on the B-values for all atoms in
 the selected object, prints the information on screen and appends
 it to the  [[Cluster Count|..→]]
A Random PyMOL-generated Cover. See Covers.


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