[chimerax-users] Coulombic surface coloring

[Elaine Meng]

Hi Gabor,
ChimeraX can color a surface by the values in any map model (density, electrostatic potential, etc.) but you would have to create the ESP map file in some other program and then read it into ChimeraX.  ChimeraX does not yet have tools to calculate the ESP directly, although it can calculate a  molecular lipophilicity potential (MLP) map.

If you have the structure open as #1 and the map open as #2, then you could use ChimeraX commands something like:

surface #1
volume #2 hide
color electrostatic #1 map #2 range -10,10

There are other options, you could use other color palettes, etc.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map>

Several other programs could be used to create the ESP map, but If you wanted to try using Chimera, below are some possible approaches.  I don’t know if they will work on your large structure.

(1) use PDB2PQR tool to convert your structure to PQR format, then use the resulting pqr model as input to the APBS tool to create an ESP map in .dx format.  These Chimera tools connect to web services.  You could also use the PDB2PQR webserver directly.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html>

(2) use Coulombic Surface Coloring tool with “Compute grid” option turned on. This will open the map as a volume in Volume Viewer, and you can save it to a file from Volume Viewer.   However, Coulombic Surface Coloring relies on the ability to calculate the surface in Chimera.  If surface calculation in Chimera doesn’t work on your structure, I’m not sure if this approach is possible.  It might be possible using the “coulombic” command with the “atoms protein” option plus any of the options that start with “g” to calculate a grid file, but I’m not sure. 
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html#volume>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 27, 2019, at 3:58 AM, Gabor PAPAI <papai at igbmc.fr> wrote:
> 
> Dear ChimeraX team,
> 
> I would like to color a protein surface by electrostatic potential. Is there a way in ChimeraX to do that? My protein is too large (more than 20 000 atoms) to create a surface in Chimera, but ChimeraX has no problem to create it.
> 
> Thank you in advance for your help!
> 
> Best regards,
> Gabor