[Chimera-users] APBS

[Karl R Voigtritter]

Elaine,

It works now!

Thanks,
-Karl

-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu> 
Sent: Tuesday, June 11, 2019 8:20 AM
To: Karl R Voigtritter <kvoigtritter at csuchico.edu>
Cc: chimera-users at cgl.ucsf.edu BB <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] APBS

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
>