[Chimera-users] Electrostatic Potentials

[Elaine Meng]

Hi Nihshanka,
It is necessary to delete atoms you don't want included in the  
calculation before initiating the calculation.  Undisplaying atoms or  
surface does not make a difference - the atoms are still there, just  
undisplayed.  Later, you could open the electrostatic potential map  
with the original full structure, if you wanted to display parts that  
had been deleted for the potential calculation.

The "Electrostatic Surface Coloring" tool does get a potential value  
at each surface point in order to do the coloring, but the values are  
not available from the user interface.  The "Values at Atom  
Positions" tool could be used to get the potential at the positions  
of atoms, but not the surface.  If you knew particular coordinates  
you wanted to look at, you could make a PDB file with fake atoms at  
those positions and use the latter tool. However, if you really did  
want all the surface point values, I must defer to others who know  
python and the under-the-hood details.

Electrostatic Surface Coloring man page:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/ 
surfcolor.html

Values at Atom Positions man page:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/density/ 
density.html

Best,
Elaine

On Aug 6, 2006, at 11:36 PM, Nihshanka Debroy wrote:

> Hi everyone,
>                   I have a couple of questions about the  
> electrostatic potentials generated in Chimera using the Delphi  
> Controller. If I have a protein with 5 chains A,B,C,D,E, and I  
> choose to show the surfaces of all chains except C (but keep the  
> wireframe of chain C's atoms) and then run Delphi using the  
> DelphiController, does that mean that the potential surface  
> generated is in the absence of chain C (which is what I want)? I'm  
> trying to generate the potential surface without taking into  
> account chain C, but would like to see C's wire frame for analysis  
> purposes.
>                   Also, is there a way to get the actual potential  
> values at each surface coordinate?
>
> Thanks a lot for the help.
> Sincerely,
> Nihshanka
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> Chimera-users at cgl.ucsf.edu
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-----
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




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