[Chimera-users] Visualizing Electrostatic Potential of *.grd format?

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 7 09:16:40 PDT 2005

Hi Anna,
Actually, Chimera does read UHBD grids, the binary version. The older  
approach to displaying potential on a surface, DelPhiViewer, is being  
phased out in favor of the newer and more general tool, Surface Color  
(Tools... Surface/Binding Analysis... Electrostatic Surface Coloring  
or Tools... Volume Data... Surface Color both open this tool).

Surface Color can color surfaces based on any of the volume data (3D  
grid) formats that can be read by Volume Viewer (which include UHBD  

Surface Color is relatively new.  It is available in the snapshots  
1.2154 (linux, mac) and 1.2143 (windows).  It is also available in  
1.2105, but I don't recommend using that one because we have made it  
easier to use in the more recent snapshots.  Here is the man page for  
Surface Color in version 1.2154:

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 Sep 7, 2005, at 4:14 AM, Anna Feldman-Salit wrote:

> Dear All,
> I would like to ask you a question regarding the visualization of  
> electrostatic potential on msms. For this purpose, of course, I  
> need a readable format for Potential Map.
> In the past I used to work with DelPhi for potential calculations  
> and then visualize the outputted *.14 file by Chimera.
> Today I calculate potentials by using UHBD program, while output  
> files are saved in /phi/ format with .grd extension (could be  
> written either in binary or ascii form).
> Unfortunately, the Chimera doesn't recognize this format.
> Dear Chimera users, do you know the way to convert the *.grd files  
> to the *.phi ones readable by Chimera, or any other trick?
> I can't recalculate the potentials by DelPhiController, because I  
> have only one dat-file for both radii sizes and charges (it also  
> doesn't work in the simple way).
> I'd very appreciate any help of yours!
> Yours sincerely,
> Anna.
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