[Chimera-users] change B factor

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 6 12:26:18 PDT 2015


Hi Caitie,
Yes, you can read in the values and change the B-factor to those values, then save to a PDB file with the new values and/or do coloring by B-factor.

However, if the main reason is for coloring (or other display mapping like worm thickness) to show the values, there is no need to overwrite B-factor.  You can just assign the values to atoms or residues and name this new “attribute” whatever you like.   Thus you could retain the original B-factors yet also have one or more user-defined attributes for each atom or residue.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef>

Either way the procedure is the same; you would need to create an atribute assignment file. This is a simple text file format described here, and several examples are provided:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile>

To overwrite B-factor you would need to specify “attribute:bfactor” and “recipient:atoms” in the file.   To create a new attribute, for example named “myvalues”, you’d specify “attribute:myvalues” in the file.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

Attribute values can also be assigned with the “setattr” command, but that would only let you specify one value per command, so it sounds like reformatting your file into the attribute assignment format is the way to go.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.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 6, 2015, at 9:45 AM, McCafferty, Caitlyn (NIH/NEI) [F] <caitlyn.mccafferty at nih.gov> wrote:
> 
> Hi, Is there a feature in Chimera that allows you to change the B-factor of the Amino Acids. I have a txt file with the values that I would like to replace the current B-factors with.
> 
> Thank you,
> Caitie




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