[Chimera-users] chimera help

Tom Goddard goddard at cgl.ucsf.edu
Wed Mar 11 16:40:51 PDT 2009

Hi Terrance,

  The Chimera error means the format of the APBS potential file you are 
opening is wrong.  Probably you are not opening the correct file or the 
file is empty.  Below is an example what the first few lines a correct 
APBS potential file looks like.

  We do not have documentation in how to use pdb2pqr or APBS.

  You may be interested in Coulombic electrostatic potential calculation 
added to Chimera 1.4, under menu Tools / Structure & Binding Analysis.  
You'll need a Chimera daily build to use this.


# Data from APBS 0.3.2
object 1 class gridpositions counts 65 97 97
origin -8.064450e+00 -4.768105e+01 -4.266980e+01
delta 3.779047e-01 0.000000e+00 0.000000e+00
delta 0.000000e+00 4.098240e-01 0.000000e+00
delta 0.000000e+00 0.000000e+00 4.099125e-01
object 2 class gridconnections counts 65 97 97
object 3 class array type double rank 0 items 611585 data follows
8.921700e-01 9.000006e-01 9.078676e-01
9.157664e-01 9.236924e-01 9.316403e-01
9.396046e-01 9.475795e-01 9.555586e-01

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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