[Chimera-users] PDB Coordinates

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 1 11:41:34 PDT 2006

Hi Albion,
I believe you need to use the "Save relative to model" option in the 
Save PDB dialog.  In that option, specify the model number of the 
density map.  You can see the model numbers in the Model Panel 
(Favorites menu).  Then, even if you've rotated everything around while 
doing the docking, the PDB file will be saved relative to the 
*untransformed* density map.  Later when you open that original density 
map and the written-out PDB, the structure will be fitted to the map.  
This is described a little more in
I hope this helps,

On Sep 1, 2006, at 11:29 AM, Albion Baucom wrote:

> I have docked several models into density manually using Chimera. I
> saved the session, reopened it, and when I write out the docked PDB
> files, and read them back in, they are not oriented the same way as
> the model I wrote them from.
> Is there something I have to do to "fix" their new orientation so
> when they are written out they retain this orientation?
> I am using beta version 1 build 2199 01/24/2006 on a linux platform.
> Thanks
> Albion
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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

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