[chimera-dev] B factor

[Elaine Meng]

On Jul 26, 2016, at 5:12 PM, Bashayer Althufairi <althufairib at mymail.vcu.edu> wrote:

> Hello
> As you know many crystallographers need to determine the ave. B factor of selected amino acids or sometimes they wanna know B factor of N-termius Vs. C-terminus of a protein. I'm working on a protein where I need to predict B factor of certain amino acids sequence as well as difference between the values for analysis. Is this possible by Chimera? If yes, I'd like to know Please the way step be step, If no, I wish you could recommend a simple way to do it by educational simple software like PyMol. 
> Thank You in Advance 
> -- 
> Bashayer Althufairi
> Medicinal Chemistry department 
> Virginia Commonwealth University 

Hello Bashayer Althufairi,
This is really a  Chimera user question so I’m CCing the chimera-users mailing list.  The chimera-dev list is for Chimera programming questions.

Chimera doesn’t predict any B-factors, but you can see the B-factors from the PDB file for a structure, e.g. in a histogram in the Render by Attribute (in menu under Tools… Structure Analysis).  This tool can color the structure to show the B-factor values.  It also automatically calculates the average B-factor per residue (over the atoms in each individual residue so that each residue can have one number).  It can also save the values to a file (see File menu of that tool) although of course the PDB file already contains the per-atom B-factor values.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>

See also the tutorial for coloring by B-factor: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html>

But maybe you mean that you want to select several residues and then calculate a single average B-factor for them. You can do that with Attribute Calculator (in menu under Tools… Structure Analysis)
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html>

For example, you could select several residues and open Attribute Calculator, turn on the options to “Restrict formula domain to current selection” and  “Show calculation results in Reply Log”, calculate a new attribute named whatever you want for “molecules” with formula: 
average(atom.bfactor).  
Click Apply to calculate a single average over all selected atoms, value reported in Reply Log.

If you have predicted B-factor values you can also read them into Chimera as a custom attribute (see file format for doing that <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile> … it is the same format as used for the saving mentioned above).  When you read in those values they are also available for use in Render by Attribute and in Attribute Calculator, and with the latter you could calculate the differences between the bfactor attribute from the PDB file and your custom attribute (the predicted values).  The differences would then be another attribute also available for coloring using Render by Attribute.

See also the attributes tutorial for examples of using Attribute Calculator and Render by Attribute:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html>

I don’t use other programs so I don’t have any advice about using them for this purpose.
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