[Chimera-users] Average Backbone B-factor

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 17 13:55:19 PDT 2011

Hi Simon,
Chimera automatically calculates the average bfactor per residue, but it uses all atoms.  The trick is to delete all atoms other than the ones you want to average, for example with the commands:

sel @n,ca,c
del ~sel

(select those atoms, and then delete all the atoms that are not selected)
You can see a histogram of the values and save them to a file by starting Render by Attribute (under Tools... Structure Analysis), choosing attributes of "residues" and then the attribute name "average -> bfactor".  The values can be saved to a file using the File menu of the Render by Attribute tool, or you can use that tool to show the values with color, worm "fatness" etc.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 17, 2011, at 1:09 PM, Simon Sham wrote:

> Hi,
> I need to read a pdb file and calculate the average backbone (CA, C, & N) B-factor for each residue and compare it with the result some MD. 
> Is there anyway I can do it in Chimera?
> Thanks,
> Simon

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