[Chimera-users] electrostatic surface coloring

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 22 10:57:03 PDT 2008

Hi James,
Currently there is no Chimera command for electrostatic surface  
coloring.  I am sure it could be done in python, but that is beyond my  
skill set.

It is my understanding that the PCE server does not output the  
electrostatic potential map - I think it only provides the PQR file  
(simply the PDB file with extra columns with atomic radii and atomic  
partial charges, essentially the input to the ESP calculation rather  
than output), images from the DINO program of different orientations  
of the protein, and PDB with ESP values at the atom positions.  I  
don't remember the format of the latter, but if the ESP values are in  
the B-factor column, you could use "Render by Attribute" in Chimera  
(under Tools... Depiction) to color by atom "bfactor" to show these  
values.  However, I think it is much less useful to show the potential  
values at the underlying atoms  rather than at the surface, especially  
if they are the same atoms used to calculate the potential in the  
first place.

The only web server I have ever found that provides ESP map outputs is
webPIPSA:  Protein Interaction Property Similarity Analysis
It is focused on performing a calculation on multiple proteins and  
comparing them (won't let you proceed until you specify at least two),  
choice of using UHBD or APBS.
webPIPSA input: upload PDB files or specify PDB IDs, email address for  
getting results
webPIPSA output: dendrogram and heat map comparing the results for the  
multiple proteins, optional download of zip file with intermediate  
results (includes map files and corresponding PDBs)
  - my first attempt with two structures and align "none" and use UHBD  
failed...I guess you are only supposed to use "none" if the proteins  
are already superimposed, which they weren't because I didn't care  
about the comparison
  - second attempt with align option "sup2pdbs" and use UHBD was  
successful.  In Chimera, should probably only view the maps along with  
the corresponding PDBs from the intermediate results since they may  
have been transformed (in the superposition step)

I last tried it in May, resulting in the notes above.

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 Aug 22, 2008, at 9:16 AM, James Fethiere wrote:

> Hi,
> 	• is there a way to use the electrostatic surface coloring from the  
> tools/surface menu, in a command file? It seems that it is only  
> available through the menu?
> 	• I have a pqr electrostatic potential file calculated from the PCE  
> server http://bioserv.rpbs.jussieu.fr/Help/PCE.html using MEAD. How  
> do I get it into chimera?
> Thanks

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