[Chimera-users] Electrostatic Potentials

Eric Pettersen pett at cgl.ucsf.edu
Mon Aug 7 16:24:58 PDT 2006

You could also select chain C, use File...Save PDB to save just the  
selected atoms (there's a check button for that in the dialog) and  
then delete chain C, run Delphi, and then read in the file you saved.


On Aug 7, 2006, at 4:15 PM, Elaine Meng wrote:

> 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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> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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