[Chimera-users] [EXT] Re: Problem with electrostatic surface

Benedikt Moissl benedikt.moissl at biologie.uni-regensburg.de
Thu Mar 26 08:58:30 PDT 2020

Hi Elaine,

thank you a lot for your fast response! Your suggestion helped and my
problem is solved :-)

Best regards


-----Ursprüngliche Nachricht-----
Von: Elaine Meng <meng at cgl.ucsf.edu> 
Gesendet: Dienstag, 24. März 2020 18:27
An: Benedikt Moissl <benedikt.moissl at biologie.uni-regensburg.de>
Cc: chimera-users at cgl.ucsf.edu BB <chimera-users at cgl.ucsf.edu>
Betreff: [EXT] Re: [Chimera-users] Problem with electrostatic surface

Hi Benedikt,
You still need to show the surface of your molecule, e.g. with command
"surface #0 & protein" (or "surface #1 & protein" since they are the same
atomic coordinates).  After you do that, it will be listed in the menu of
choices of what surface to color in the Surface Color dialog.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 23, 2020, at 11:35 PM, Benedikt Moissl
<benedikt.moissl at biologie.uni-regensburg.de> wrote:
> Dear Chimera team,
> I am trying to display color the surface of my molecule according with
Poisson-Boltzmann electrostatics using Chimera 1.14. I ran the PDB2PQR tool
as described in the user guide and obtained a PDB2PQR file. With that, I ran
the APBS tool and obtained a .dx file. As described, the Surface Color panel
opens automatically, but here I am unable to choose my structure file for
"color surface" (s. attachment 1). I can only choose the .dx file, which
does not work. All three models obtained during this process are opened in
the model panel though (s. attachment 2).
> Do you have any idea on how to fix this?
> Thank you very much in advance and keep up the great work!
> Benedikt Moissl

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