[Chimera-users] Fitting multiple atomic structures in a density map

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 12 09:51:16 PDT 2013


Hi Andy,
You might try the sequential fitting option of the "fitmap" command.  After it fits one structure, it removes the density from that part of the map before fitting the next.  Details here including link to an example video:

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

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 Jul 12, 2013, at 12:43 AM, Anindito Sen wrote:

> Dear All,
> I need to fit atomic structures of two different proteins of different sizes in a density map. The location of both the proteins in the map is well known. While using the fitting tool, I can get the atomic structure of the bigger protein docked very well, the problem arises while fitting  the smaller one. The fit option fails and docks the structure into the region of the density map where the atomic structure of the larger protein is docked , an incorrect position. 
> 
> How can I fit both the atomic structures in the density map correctly? The resolution of the density map is ~10Å  at FSC cutoff of 0.5
> Thanks
> Andy




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