[Chimera-users] creating virus capsid

Elaine Meng meng at cgl.ucsf.edu
Wed May 26 11:22:26 PDT 2010

On May 25, 2010, at 10:39 PM, 江一波 wrote:

> hello meng!
> how can i construct a virus by chimera?
> i have get a   nucleocapsid protein  about  a virus  from 
> http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=9B6E87D9&tabtoshow=Current
> such as ,i get ID :2I9F structure...one of a nucleocapsid for a virus ...this is symmetrical structure!
> i want construct a virus ...how can i do?   is there somethings  paper  about  how to construct ?
> thank you!!!

Sometimes the PDB file will include matrix information needed to build the capsid.  If it does, you can use the Chimera tool "Multiscale Models" to show the whole thing.  However, the authors of this structure (2I9F) did not include the necessary information in the PDB file.

Next I tried to see if that structure is in VIPERdb, which would also allow showing the whole thing in Chimera.  However, when I tried "File... Fetch by ID" and entered 2i9f for the VIPERdb database, it was not found.

Sorry, I don't have any ideas about how to make a whole capsid from this structure.

A different structure that does include the information is 1POV.  If you open that one, then start Multiscale Models (under Tools... Higher-Order Structure) and click the "Make models" button near the bottom, it will show the whole capsid.

Please send Chimera questions to the chimera-users at cgl.ucsf.edu address.  Thanks,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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