[Chimera-users] electrostatic potential based on Swiss-Model

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 5 16:25:45 PDT 2014


Hello Jingga Inlora,
It is impossible to tell  what (if anything) might be wrong with your structure from Swissmodel or the resulting phi map from DelPhi.  You can't judge just from which program built the structure (in this case Swissmodel), because it also depends on what you used as input to that program and whether similar protein structures are available to use as modeling templates.  I guess you could ask the Swissmodel developers but they would probably give a similar answer.

This is not really a Chimera question, but I will try to answer generally. If I had the problem of suspicious-looking electrostatic potential, here is what I would check:

(1) does the atomic structure itself look bad or strange?  Maybe Swissprot wasn't able to make a good model in this specific case, for example if there were no good template structures available.  There are programs that can evaluate the quality of protein structures, for example: Molprobity, PROCHECK, and probably many others.

(2) was the charge, radius parameter assignment for DelPhi successful?  Sometimes the atom names don't match what is in the DelPhi charge and radius files, resulting in a DelPhi calculation that thinks the protein has a ridiculous large negative charge.  Or maybe you didn't even add hydrogens.  Some of the charge/radius files don't require hydrogens, but many do. In my experience, depending on what DelPhi charge and radius parameter files you are using, it can be very difficult to fix up all your atom and residue names to correctly match. 

if you think the atomic structure looks reasonable (#1 is OK) and the problem is more in #2 above, you can try something easier like the "Coulombic Surface Coloring" tool in Chimera and see whether the result looks more reasonable:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html>

This tutorial includes Coulombic calculations, as well as the slightly more complicated approach with PDB2PQR and APBS (Poisson-Boltzmann calculations, more similar to DelPhi):
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>

Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 5, 2014, at 1:07 PM, Jingga Inlora <arolni at umich.edu> wrote:

> Hello,
> I am a graduate student at the University of Michigan and I am currently trying to obtain images of my proteins with electrostatic potentials for my manuscript. For one of my proteins, there is no solved protein structure (by X-ray crystallography or NMR) and I had to use SWISS-MODEL to predict the structure. I did electrostatic potential calculation using DelPhi but when I visualized it using Chimera, the electrostatic distribution is not what I expected. I did notice the electrostatic potential calculations for other previously solved protein structures took much longer and resulted in bigger files, whereas the SWISS-MODEL-predicted protein contains much smaller .phi file size.
> I was wondering if you have any idea how accurate it is to calculate the electrostatic potential based on a SWISS-MODEL predicted protein structure, and if there are ways to improve the reliability of the calculated electrostatic potentials for that protein?
> Thank you very much for your help!
> Sincerely,
> Jingga Inlora



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