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 following

for ((i=0; i<144; i++)); do echo $RANDOM.$RANDOM >> /tmp/bb; done

The Code

##########################################################
#
# Expand_to_surface (e2s): Expands alpha-carbon-only 
# b-factor coloring to an entire surface of the protein
# of your choice.
#
# AUTHOR: Jason Vertrees -- Python code; Warren DeLano,
#         the original code.
#
# COPYRIGHT: BSDL.  Feel free to use it.
#
# DATE: 2007-12-03
#
##########################################################
from pymol import cmd
def e2s(sel):
        """
        e2s: Expand to surface

        e2s will color a surface based upon the b-factors
        from the alpha carbons in your selection.

        usage: e2s protName
        """

        cmd.create("ca_obj", sel + " and n. CA" )
        cmd.ramp_new("ramp_obj", "ca_obj", [0, 10], [-1, -1, 0] );
        cmd.set("surface_color", "ramp_obj", sel )

cmd.extend("e2s", e2s);