[Chimera-users] Fe in chimera antechamber

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 6 14:19:35 PST 2007

Dear S,
I forgot to mention before that the label will not automatically  
change when the charge value is changed.  You have to re-label to see  
the new charge.  Just thought I would mention that first, in case  
that is the problem!

Otherwise, you only want to change the charge of one atom?  Seems  
like it would be easier to just edit the charge value in the Mol2  
file than to use Define Attribute.  Also, for one atom you could just  
use the "setattr" command.
For example, in 1a6m the iron is :hem at fe, so if you wanted  
charge=1.5, the command would be:

setattr a charge 1.5 :hem at fe

However, in case you mean FE is just an example and you might want to  
change the charges of multiple atoms, I attach an example file to use  
with Define Attribute to define the charges of all the atoms in HEM.   
This plain text file assumes your structure is open as #0 and has the  
same HEM atom names you would get by adding hydrogens to 1a6m.  You  
could edit the charge values and atom names as needed, then choose  
"Tools... Structure Analysis... Define Attribute" and then open this  
text file, which will set the charge values as specified (FE is 1.75,  

I hope this helps,
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

P.S. If you use only the FE charge from your amber data but not the  
rest of the values for the HEM residue, it might not add up to the  
correct net charge.  I'm guessing those charges were generated by  
considering FE and the rest of HEM together as one residue.  Just  
something to consider, and perhaps it is not that important for your  

P.P.S. Some details you probably don't care about but maybe others in  
the list would be interested:  I made this attribute definition file  
using the "Attribute Calculator" tool with the "Formula" set to  
atom.charge  (i.e. I didn't calculate anything, just used the tool to  
write out an existing attribute), naming the attribute "charge" and  
specifying "Save calculation results to file."   To make sure it  
worked, I text-edited the FE charge to 1.75 and reassigned the values  
with this file and "Define Attribute" as described above.

-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: defcharge.txt
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20071106/dc5ec73c/attachment.txt>
-------------- next part --------------

More information about the Chimera-users mailing list