[Chimera-users] occupancy field

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 2 15:39:40 PDT 2012

Hi Darjan,
If you have occupancies that are < 1.0 there may be atoms with alternate locations (more than one position included in the PDB file), and you may wish to remove all but one set of locations, for example, using the option in Dock Prep.

You can change occupancies with the "setattr" command, for example:

setattr a occupancy 1.0


Then you can save a new PDB file containing all occupancy values = 1.0.
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 Apr 2, 2012, at 4:04 AM, Darjan Andrejc wrote:

> Hey,
> Is it possible to change occupancy field to 1.0 in Chimera?
> I need a pdb file of my protein for docking and the file needs to have an occupancy field 1.0.
> Thanks for the help
> Darjan Andrejc, Mpharm
> PhD student, Department of Biotechnology
> National institute of Chemistry, Ljubljana, Slovenia

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