[Chimera-users] Chimera electrostatic potential

[Elaine Meng]

Dear Kate, John, et al.

Currently there is no way to calculate the electrostatic potential in 
Chimera.  The separate (not included in Chimera) programs APBS, DelPhi, 
Grasp, or UHBD can be used to calculate a potential map and write it 
out to a file, which can then be read into Chimera.  Chimera does have 
a "DelPhiController" tool that interfaces with the academic version of 
DelPhi, but you still have to get that program separately from its 
authors.

See this page for links to the Web sites for APBS, DelPhi, Grasp, and 
UHBD:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp

While I don't think there are web servers to run such calculations 
(perhaps due to their complexity and the frequent need to edit the 
structure beforehand), some of those programs are available free of 
charge for academic use.

Once you have generated an electrostatic potential file, you can open 
it and the corresponding structure (PDB file) in Chimera, show the 
surface, and use Chimera's "Electrostatic Surface Coloring" tool to 
color the surface based on the values.  You can also display 
isopotential surfaces using the "Volume Viewer" tool.

I don't know what the issue is with Pymol, but I hope this clarifies 
the Chimera situation. Best,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html


On Sep 7, 2007, at 4:46 AM, Patton, John (NIH/NIAID) wrote:

> An excellent question, one we have tried wrestling with along the way, 
> so far unsuccessfully. John
>
>  On 9/7/07 3:07 AM, "Kate Hardie" <kate at flamerock.com> wrote:
>> Hi,
>>  I've been unable to figure out how to colour the electrostatic 
>> surface of a protein red/white/blue. I'm assuming that you have to 
>> some how assign electrostatic potential before colouring but how is 
>> this done? I'm using a Mac and I've tried to use apbs with pymol but 
>> it will not recognise my pqr file generated on the pdb2pqr server or 
>> generate it itself.
>>  Thanks,
>>  Kate