[Chimera-users] how to fit the em density map of crystal

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 1 09:06:43 PDT 2016


Dear Yaowang,
It is unclear whether you want to fit the map with another map or with some atomic structure.  Either way, it can be done with Chimera, but the best strategy is really a question of scientific judgment that depends on both the details of your system and the available information. 

Chimera includes tools for filtering, segmentation, and map-map or map-atoms fitting.   See:

<http://www.rbvi.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html>
<http://www.rbvi.ucsf.edu/chimera/videodoc/videodoc.html>

Several of these features are in the menu under Tools… Volume Data.  Click “Help” on any tool to see its documentation. There are also several commands that do mostly the same things, e.g. “fitmap”
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>

Maybe researchers in this area will have more specific advice.

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 1, 2016, at 8:51 AM, Yaowang Li <liyaowang2911 at gmail.com> wrote:

> Dear all,
> 
> I am thinking about how to fit the EM density map of crystal. 
> cryo-EM images of crystal were collected and reconstructed to a map, but with a poor resolution(around 7A). In this condition, which is the best way to fit the map? 
> 
> Best Regards,
> Yaowang
> LIC, Leiden University
> 




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