[Chimera-users] B-factors

[Elaine Meng]

Hi Narender,
You can write out the values of any numerical attribute using the  
Attribute Calculator tool. This tool was mainly designed to create new  
attributes by combining other attributes with mathematical formulas,  
but it can also be used to write out values for attributes that already  
exist.

In fact, I'm not sure what the residue average B-factor attribute is  
actually named, so we can just use the tool to average the atomic ones  
and write the values.  Start the Attribute Calculator (under Tools,  
Structure Analysis), give the new attribute whatever name you want, and  
make it an attribute of "residues."  Enter the Formula:

average(atom.bfactor)

Depending on where you want the results, turn on "Show calculation  
results in Reply Log" and/or "Save calculation results to file."  You  
probably want the other options turned off.  Then hit Apply or OK (if  
you also want the dialog to disappear), and that will do the  
calculation and write the results.

To write out an existing attribute, use a Formula like this:

attribute-level.attribute-name

where attribute-level is atom or residue, for example

residue.kdHydrophobicity

It doesn't matter what you name the new attribute in this case, since  
you won't be using the name. The names of many attributes are listed  
here:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ 
atom_spec.html#descriptors

and here is the Attribute Calculator man page:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/ 
calculator.html

I hope this helps!
Elaine

On May 5, 2006, at 1:04 PM, Narender Singh Maan wrote:

> Dear Chimera users,
> i am looking for a way to write down the average B-factors for each  
> residue from a pdb file (which shows atomic bfactors). I tried using  
> chimera attributes which can color the protein and shows a histogram  
> for bfactors, but i am not able to get those average values in reply  
> log or some other written file.
> Please let me know if i can get any help in this.
> thanxs
> ns
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-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html