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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...

Expand To Surface

= Overview =

This little script will color the surface of your protein the same color as the b-factors from the alpha carbons of each amino acid. This script is useful when you want to color a protein by the b-factor column, but all you have in the b-factor for each alpha carbon. If you try to color a surface based only on the alpha carbon b-factors, then the surface isn't rendered as you typically want.

Note: This script, once run in PyMOL, is called e2s. See examples, below.

Example

# in PyMOL type the following
 
# fetch 1cll
fetch 1cll
 
# load your b-factor column; for "1cll" you can simulate fake data
# by writing 144 random integers to /tmp/bb.  If you have some real
# data, then put that there.  1 row for each alpha carbon.
f = open('/tmp/bb', 'r').readlines();
 
# alter the alpha carbon coords
alter *,b=0
alter n. CA, b=f.pop(0)
 
# color the surface
e2s 1cll

You can make fake data in a shell by quickly executing:

# in a BASH shell, type the  [[Expand To Surface|..→]]
A Random PyMOL-generated Cover. See Covers.


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