[Chimera-users] pdb format and charges

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 6 12:32:29 PST 2008

Hi Terry,
I am guessing this is to use as input to some other program?  There  
are much better ways to save attribute values (charge,  
hydrophobicity, etc.) if you are going to be using them in Chimera.

You can tell Chimera to change the bfactor to equal the charge, then  
save a PDB file (File... Save PDB or command "write").  However, the  
bfactor column only has 2 digits after the decimal and you lose a lot  
of the actual charge data.

First add charge, then reset bfactor to equal them:
- open Attribute Calculator (under Tools... Structure Analysis)
- in that tool, Calculate attribute bfactor for atoms with the  
Formula: atom.charge

This is really twisting the intent of PDB saving in Chimera.  We  
generate only standard PDB format, so you can't write the bfactor  
column with more digits.  If you were saving the attribute values for  
later use in Chimera, you would instead save an attribute assignment  
file, which would preserve the entire values.

Names of several atom attributes are listed here:

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 6, 2008, at 12:17 PM, Terry Lang wrote:

> Hey Everyone,
>        I would like to use Chimera to write charges for a pdb file in
> the b-factor column.  I feel like this is possible but couldn't quite
> figure out how to do it.
> Sincerely,
> Terry
> -- 
> P. Therese Lang
> Post Doc
> Alber Lab, UC Berkeley
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> Chimera-users at cgl.ucsf.edu
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