[Chimera-users] Docking Crystal Structure in to Cryo EM Structure

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 20 10:52:33 PDT 2016

Hi Gayan,
You will always have to use your knowledge of your system and your scientific judgment, for example in setting the appropriate isosurface level for viewing your map, preprocessing the map such as filtering, or manually placing the atomic structure in approximately the right location in the map before locally optimizing the fit.

However, there are several possibly relevant tools in Chimera depending on how you choose to attack the problem.  You might want to try more than one way.  Some ideas are

- use Segment Map and then Fit to Segments (both in menu under Tools.. Volume Data)
- and/or try Fit in Map (same menu) for local optimization of fit
- and/or use “fitmap” command, which has some options that the Fit in Map graphical interface does not, like global search and sequentially fitting multiple structures

Various metrics are provided for evaluating fits, correlation etc.  However, these tools are meant for interactive use and include various user-adjustable input parameters, so you can’t just use them as a black box and then pick the fit with the highest score.  You would need to use input settings sensible for your system, and perhaps try multiple approaches.

Details of all of these tools and commands are given in the User’s Guide, which you can access from the Help menu or see the copy on our website.

See also the “guide to volume data”

I hope this helps,
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 19, 2016, at 4:36 PM, Senavirathne, Gayan <senavirathne.1 at osu.edu> wrote:
> Hello,
>        I am trying to dock some crystal structures (PDB: 1KX5 and 3OS1) in to a cryo EM structure EMDB:2992. How can I do this task using the UCSF chimera software and how can I know the alignment is accurate? Thank you very much
> Regards,
> Gayan Senavirathne, PhD
> Postdoctoral Researcher
> The Ohio State University Wexner Medical Center
> Cancer Biology and Genetics
> 460 West 12th Avenue, Room 1040
> Columbus, OH 43210
> Phone  (313) 316-6658
> senavirathne.1 at osu.edu

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