[Chimera-users] occupancy calculations

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 2 09:30:36 PDT 2012


Hi Ben,
Yes, you would have to get a daily build dated after when the change was made.  Occasionally the build will fail and there might not be a new one every single day.  You would need to wait for the next successful build for your type of computer.

There are many ways to set radii.  I'll list several; option (D) might be easiest...

An advantage of Chimera is that you don't have to use the B-factor column every time you want to assign some values to atoms.  It can read a separate "attribute definition" file, and you can have multiple custom attributes; rather than reading in multiple PDB files of the same structure with different values in the B-factor column, you could just load the structure once and then load several different attributes using separate definition file(s).  In this case, you would have to use atom atribute name "radius". That's option (A).
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile>

(B) there is also a "setattr" command to set one value at a time.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

(C) for VDW radii specifically, there is also a "vdwdef" command. 
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html> 

(D) if you already have those PDB files with B-factor field used for radius, you could just equivalence "radius" to your existing "bfactor" values using "Attribute Calculator" (under Tools... Structure Analysis). 
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html>

Start that tool, Calculate attribute "radius" (omit quotes please) for atoms.  Set Formula to
atom.bfactor, uncheck all the checkboxes except for maybe "Show calculation results in Reply Log" if you want to verify the assignments, then Apply.

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 Nov 2, 2012, at 7:51 AM, Benjamin SCHWARZ wrote:
> 
> 1. (newby question, sorry) I guess if I want to access that I'll have to download the latest night build ? 
> 2. In my case I play with fake Calpha PDB files, with radii stored in the B factor… I guess I'll have to change the radii of my fake atoms manually in chimera. How can I do that ?




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