[Chimera-users] occupancy field

[Darjan Andrejc]

Hey Elaine,

I've managed the occupancy error. Thanks for that. I also managed to upload the two pdb files and now I'mwaiting for the job to be done.

Thank you and have a nice day!

Darjan 

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Tuesday, April 03, 2012 12:40 AM
To: Darjan Andrejc
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] occupancy field

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.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html>

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

setattr a occupancy 1.0

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

Then you can save a new PDB file containing all occupancy values = 1.0.
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 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
>