[Chimera-users] Modification of b-factor and occupancy

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 8 17:38:29 PDT 2009

Hi Tsutomu,
If there are lots of changes (if it would require an inconvenient  
number of setattr commands) you could create a "define attribute"  
file and read it in with the "defattr" command or the Define  
Attribute tool.

Notice you can create your own new attributes named whatever you  
want, show them with colors, worms, etc., and save them to files in  
that same "define attribute" format.  At least if you will be working  
with Chimera, there is no need to use bfactor and occupancy for  
things that aren't really bfactor and occupancy.

However, if you really want them written out in a PDB file, it is  
necessary to put the values in bfactor or occupancy.  It might cause  
you to lose digits on the values because those columns are not very  

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

On Apr 8, 2009, at 5:13 PM, Tom Goddard wrote:

> Tsutomu Matsui wrote:
>> Hi Tom,
>> Is it possible to change b-factor or occupancy of selected atoms, and
>> then output the coordinates including those changes?
>> Tsutomu
> Hi Tsutomu,
>   Here are Chimera commands to set bfactor and occupancy of an atom
> (model #0, residue 13, chain B, atom CA) and write out the PDB:
> setattr a bfactor 12.3 #0:13.B at CA
> setattr a occupancy 0.123 #0:13.B at CA
> write 0 /tmp/test.pdb
> If you really mean you want change the "selected" atoms use a  
> command like:
>     setattr a bfactor 12.3 sel
> See the setattr and write documentation for more details.
>     http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html
>     http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html
>   Tom

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