[Chimera-users] How to analyze cryo-EM reconstruction map of virus and prepare publishable figures?

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 11 10:09:21 PDT 2019

It is beyond the scope of this mailing list to explain all steps of cryo-EM map analysis and processing (even if I had that knowledge, which I don’t).  There are probably entire textbooks on the subject.  Some ideas are to work with experienced cryoEM laboratories, and to read the experimental methods sections of papers.  Some journals even have protocols with more details about the steps of the analysis.

As for Chimera specifically, it can help with some (but perhaps not all, depending on the project) tasks related to segmentation and fitting atomic structures, and you can certainly use it to make figures for publications.

See the Guide to Volume Data Display in Chimera:

See the online tutorials, several of which include cryoEM data:

The User Guide also fully describes each of the tools in menu: Tools… Volume Data… [several tools].  You can press the Help button on each dialog to see its help page.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 11, 2019, at 4:08 AM, sunyeping <sunyeping at aliyun.com> wrote:
> Dear all,
> I am new to cryo-EM structural biology. Now I have a cryo-EM reconstruction map for a virus particle. I wish to analyze the characteristics of the virus, such as the h, k and t number, the component of an cryo-EM asymmetric unit of the capid and prepare some publishable figures. I have no idea how to do these things. Could all these be done with Chimera? Is there any tutorials or manual for these calculation, visualization and drawing? If you could recommend some ways by which I can learn to do these, I would be greatly grateful. 
> Best regards

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