[Chimera-users] creating virus capsid

Tom Goddard goddard at cgl.ucsf.edu
Wed May 26 16:30:26 PDT 2010

Although PDB 2i9f is a virus nucleocapsid protein the crystal did not 
contain whole or partial capsids so the capsid organization was not 
determined from the crystallography.  How do I know that?  I displayed 
the unit cell using the "Make Copies" button in the Unit Cell dialog 
(menu Tools / Higher-Order Structure).  There are 8 copies in the unit 
cell in a clearly non-capsid arrangement.

I do not know if there is other experimental data which determines the 
capsid arrangement for this virus.  Would need to look at the associated 
journal article.


> 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 
>> <http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=9B6E87D9&tabtoshow=Current>
>> such as ,i get ID :2I9F 
>> <http://www.rcsb.org/pdb/explore/explore.do?structureId=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 
> <mailto:chimera-users at cgl.ucsf.edu> address.  Thanks,
> Elaine
> ------------------------------
> 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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