[Chimera-users] APBS electrostatic potential map not visible

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 10 13:01:38 PDT 2019

Hi Ahmad,
I do not understand your description, because you said that volume view does display a surface… so it IS shown.

 Maybe you mean that when it is first opened, nothing displays.  By default it might not be displayed because usually these electrostatic potential (ESP) maps are used to color some other surface, the surface of the protein.   So you would need to show the surface of the protein in the usual way (e.g. command “surface”) and then use the Surface Color (Electrostatic Surface Coloring) tool or “scolor” command to color that molecular surface by the values in the ESP map.  This tool may appear automatically when you open the ESP file (.dx or .phi).


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

> On Sep 10, 2019, at 11:15 AM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> Hello, 
> After PDB2PQR and APBS calculation, I get an .dx that I can't view (doesn't appear when I click show), let alone color. 
> I tried to launch volume viewer, it does display a surface.
> What am I doing wrong?
> Regards. 

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