[Chimera-users] coloring with partial charges

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 15 09:35:50 PDT 2009

Hi Bala,
In version 1.4 (you would need to get a recent daily build, not the  
production release) there is a Coulombic Surface Coloring tool under  
Tools... Surface/Binding Analysis.  The documentation describes how it  

It will assign charges to your structure.  It doesn't matter where the  
PDB file is from, except that it should be in correct PDB format and  
have standard atom names for standard residues so that they can be  
recognized correctly by the charge assignment step.  Sometimes there  
are some format problems with PDB files created by Amber, however, so  
be sure to check in the Reply Log to see if there were problems with  
charge assignment.  If there are, you may need to manually edit the  
file to correct any format problems.

There is also an "Electrostatic Surface Coloring" tool, but it  
requires an electrostatic potential map previously calculated with  
some other program such as DelPhi, APBS, or UHBD.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 15, 2009, at 9:10 AM, Bala subramanian wrote:

> Friends,
> How to do electrostatic coloring based on partial charges. I have a  
> pdb generated from amber, i would like to assign amber charges and  
> color the surface using assigned charges.
> Bala

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