[Chimera-users] Assigning pre-calculated attribute to B-factor column of pdb

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 26 10:27:37 PDT 2014

Hi Oliver,
The more direct way I tried used Attribute Calculator (in menu under Tools.. Structure Analysis) to calculate attribute "bfactor" for "atoms" using the formula:


(after assignment using Ramachandran).  It currently generates an error, which seems buglike.  I could create a new atom attribute with that formula, but not overwrite "bfactor". We'll look into that .

On Aug 26, 2014, at 10:17 AM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Thanks to both Elaine and Mark for the quick replies!
> Elaine, that works very well, thank you. Would it be possible in some future version to have an option to replace the b-factor column with a custom attribute directly (or via a command), to make this process quicker and avoid having to write out, edit and read in the attribute file? 
> I find this handy for highlighting particular problem regions in coot or other programs that can color by b-factor (I could envision doing the same thing for the overlap attribute of find clashes, or some sort of rotamer probability attribute, for example).
> Cheers,
> Oliver.

More information about the Chimera-users mailing list