[Chimera-users] chimera help

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 11 16:58:44 PDT 2009

Hi Terrance,
Chimera does not read "pqr" files, such as those created by the  
pdb2pqr server.  The "pqr" file is only input to APBS, whereas the  
APBS output (the electrostatic potential map) is what Chimera can  
read and display.  I can't help with the pdb2pqr server -- that is  
another group's server.  Were you trying to open the pqr file in  
Chimera?  If you were really opening APBS output, however, we would  
need to see the file:  you could use Help... Report a Bug in the  
Chimera menu and attach that file.

APBS is a separate program, not included with Chimera.  It is free  
but you might have to compile it yourself.  This page includes links  
to the home pages for APBS, DelPhi, and UHBD, all programs whose  
electrostatic map output Chimera can read and display:

If you would prefer not going to the effort of obtaining any of those  
programs and figuring out how to run them, there is a simpler option  
in recent versions of Chimera (need to get the daily build, version  
"Coulombic Surface Coloring" (under Tools... Surface/Binding  
Analysis).  This type of calculation is not as accurate as the  
continuum electrostatics calculations done by the programs mentioned  
above, but simpler and easier to obtain... like so many things in  
life, a trade-off.

Here is the man page:

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

On Mar 11, 2009, at 3:34 PM, Terrance Chiang wrote:

> Hi,
> I've been trying to make an electrostatic potential map for the  
> protein that I'm working on, but there seems to be some error with  
> the file when I try to open it. I was wondering if you could help  
> me with this.
> The error says: Missing "object 1 class gridpositions counts  
> <l><m><n>" header line
> I also need help with using the pdb2pqr service that can convert  
> files from pdb into apbs. Perhaps my error lies there.
> Thanks,
> Terrance Chiang

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