[Chimera-users] visualization of electrostatic potential

Tom Goddard goddard at sonic.net
Wed Mar 18 09:58:46 PDT 2015

Hi Christos,

  The surface coloring and volume viewer APBS map values are the same.  You will get much higher values with Values at Atom Positions than used with surface coloring because the electrostatic potential at a point charge is infinite.  You will instead get very large values because potential is sampled on a grid, so values at atom positions are interpolated from nearby grid points.

  The Chimera Python script you found red_area.py and the one Elaine mentioned surfvalues.py show you most of what you need to access the potential values on or near the surface.  One extra ingredient is to find which atom a surface point is associated with — that is given by surface.atomMap that is a dictionary mapping vertex array index to an atom object.  This is defined in your Chimera distribution file


(on Mac in Chimera.app/Contents/Resources/share/MoleculeSurface/msurf.py)


> On Mar 18, 2015, at 9:28 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Dear Christos,
> 1) It would be great if you could provide any more details about this.  In general, when you have problems you can report them to chimera-bugs at cgl.ucsf.edu.  This sounds like something we need to look at and fix for everybody, if possible.   PDB2PQR and APBS are web services provided by a separate resource and we are not always aware when they make changes.  Also, I’m not sure what you meant by “troubles” … no results at all, or error messages, or strange results?
> 2) The units are the same, but as you guessed, the evaluations are at different locations.  When you map to atoms, the evaluation is at the atom center.  When you color the surface, the default evaluation for electrostatic potential is furthermore not even at the displayed solvent-excluded surface, but 1.4 further outward (the probe radius).  So even though the coloring is displayed on the solvent-excluded surface, it reflects values at approximately the solvent-accessible surface.  This additional projection is optional.  In the Surface Color dialog, click Options and see the “surface offset” value.  
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html#options>
> Or, if you’re using the “scolor” command, it’s the “offset” option:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#volume>
> 3) You found the “redarea.py” post, which is the most similar to what you describe:
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-December/009401.html>
> See also the posts regarding “surfvalues.py” for obtaining values for surface vertices:
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2011-February/006000.html>
> I hope this helps,
> 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 Mar 18, 2015, at 7:01 AM, Christos Deligkaris <deligkaris at gmail.com> wrote:
>> 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 @DeligkarisGroup +ChristosDeligkaris
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