[Chimera-users] APBS

[Elaine Meng]

To clarify:  you have to display the surface of the protein yourself (e.g. command: surface protein) so that it will be listed as a choice in Surface Color.

Elaine

> On Jun 11, 2019, at 8:16 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Karl,
> It’s not possible to tell what went wrong from that description, but to avoid the two most common errors:
> 
> (1) make sure to submit the pqr model as input to APBS, not the original PDB model which doesn’t have charges
> 
> (2)  in Surface Color make sure the surface is the surface of the molecule (from pqr or PDB file), not the APBS model (dx file)
> 
> Most common is #2.  I assume you actually want to color the surface of the protein, not isosurfaces of the APBS map (which would be a single color anyway). I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Jun 10, 2019, at 4:44 PM, Karl R Voigtritter <kvoigtritter at csuchico.edu> wrote:
>> 
>> Hello,
>> I am trying to display an APBS surface. 
>> I loaded a .pqr file that was generated using the http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1server. I then ran the APBS tool in the surface/binding analysis tab in Chimera. I left everything to default and clicked OK. It launched the executable and then executed it. The newly generated files came into the Surface Color window correctly. Upon trying to color the surface with the “color” nothing happens.
>> 
>> -Karl Voigtritter, Ph.D.
>> California State University, Chico
>