[Chimera-users] Electrostatic Potential based on Poisson-Boltzmann using APBS

Elaine Meng meng at cgl.ucsf.edu
Sat Jul 18 08:43:10 PDT 2015


Dear Leila,
Probably the PDB file you opened is model 0 in Chimera. The PQR file is automatically opened by PDB2PQR when it finishes running, and that is probably model 1 in Chimera.  

You can just close the original PDB file before you run APBS, or you can make sure to tell APBS to use the new one.  Either way, you can see which file is which model number by looking in the Model Panel (menu: Favorites… Model Panel).  You can close a model using the Model Panel or with a command, for example: close 0

If you don’t close the original PDB file, you can still tell APBS to use the new model.  In the APBS graphical interface (menu Tools… Surface/Binding Analysis… APBS), you can change the “Molecule:” setting at the top to be the new model output by PDB2PQR, or the apbs command can be something like: apbs molecule #1
(using the correct number for the PDB2PQR file, of course)

This is all mentioned in the help pages, so it would be useful to read the help for what you are doing before asking this email list.  For example, you can see the help for the apbs command by using the command: help apbs
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/apbs.html>

Also for basic familiarity with Chimera, you could try tutorials, see menu Help… Tutorials, and also the longer “getting started” tutorial at our website:
<http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 18, 2015, at 12:37 AM, leila karami <karami.leila1 at gmail.com> wrote:

> Dear Elaine,
> Very thanks for your time and consideration.
> I downloaded the daily build version of chimera.
> 
> After using PDB2PQR in command line, status line shows that output.pqr file was generated.
> 
> Then, I used APBS in command line, dx file was created. But after coloring, the colors are as black and white. 
> 
> I think chimera uses a pqr file other than output.pqr file which PDB2PQR has generated.
> 
> After using APBS in command line, pqr, in and dx files were created in following address:
> 
> C:\Users\karami\AppData\Local\Temp\tmphrfmlq
> 
> How to find output.pqr file to use that as inout for APBS?
> 
> Is my manner wrong?
> Thanks in advance,
> Leila
> _



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