[Chimera-users] em fit refinement

[Elaine Meng]

Hi Bala,
Command "fitmap" has a huge number of options, both local optimization and global search, and you could of course do more fitting starting from any current fit.  
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>

You can also always save the fit by saving the PDB files in their positions relative to the map model.  The fitted PDBs and the original map model could be input to any other program that fits coordinates into maps. There is a "Save PDB" button on the fit list from global search
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#fitlist>

...or you could just use the regular PDB-saving approaches in Chimera as mentioned here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting>

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 Aug 15, 2012, at 8:27 AM, Bala subramanian wrote:

> Friends,
> I used "fit" command to fit a structure onto a EM map and obtained a
> list of fits. Now i want to choose the best fit and refine it further.
> I would like to know if there is any way to refine a fit produced by
> fit command in Chimera. Or can i use any other software for the same,
> which can take chimera's fit as input and refine it further.
> 
> Thanks,
> Bala
> 
> --
> C. Balasubramanian
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