[Chimera-users] visualization of electrostatic potential

[Christos Deligkaris]

Dear Chimera Users,

I am interested in visualizing the electrostatic potential calculated by
the APBS tool Chimera provides and I have several questions regarding this.

1) We have been having troubles running the PDB2PQR/APBS tools (I am not
sure if we had trouble with both, it has been a few weeks) that Chimera
provides, and I believe we fixed this by changing the version number at the
very end of the web server address. Is there anything else we could have
done to fix this?

2) I noticed that the numbers that are displayed when I visualize the
APBS-calculated potential on the MSMS are very different from the numbers
shown when I use the volume viewer (I mapped the values to atoms and then
displayed those as labels). Why are those numbers not the same? Is it
because the volume data will map the potential near the atoms and display
that, whereas the potential on the surface (or actually 1.4 Angstroms from
the surface) will display the potential value on the surface? Should I
assume that the units are the same?

3) I am interested in finding the "patches" of the molecular surface the
have fairly positive potential. I am familiar with the PatchFinderPlus
server but I am interested in finding several patches, not just the largest
one. I have not found any tool related to this in Chimera, please let me
know if I am wrong. So,I found the redarea.py script avalaible from
Chimera's website and I am thinking about modifying it in order to do this.
The script iterates over all surface pieces. Is it possible to calculate
the distance between vertices and atoms? Is it possible to obtain the
potential value at a vortex? I think this would help me get started...

Thank you very much,

Christos Deligkaris, PhD
Assistant Professor of Physics, Drury University
900 N Benton Ave, Springfield MO, 65802
Office Phone: (417) 873-7234
www2.drury.edu/christos <http://www2.drury.edu/christos/index.html>
@DeligkarisGroup <https://twitter.com/DeligkarisGroup> +ChristosDeligkaris
<http://google.com/+ChristosDeligkaris>
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