[Chimera-users] Three-dimensional structural model of the VP7 trimer

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 28 10:38:24 PDT 2016


Dear Omer Naseer,
I don’t know what you mean by “a structure like yours” but I will try to guess.  If I didn’t answer your question,  you will need to send more information, such as the PDB ID of a specific structure and an example of the type of picture you are trying to make.

First you have to find some structural data for rotavirus, for example, by searching the PDB (atomic structures) or VIPERdb (virus structures) or EMDB (electron microscopy maps).

For example, I went to the RCSB PDB  <http://www.rcsb.org/pdb/home/home.do> and searched for “rotavirus vp7” and got 7 results.   I don’t know if any of those are the specific structure you wanted to see, but any could be opened in Chimera.

In Chimera, you could use File… Fetch by ID, and in the resulting dialog choose database: PDB and enter the structure’s ID, for example, 3kz4.  That will show just the asymmetric unit, probably in ribbons.  If the image at the PDB shows the whole capsid (like a ball), you can also show the whole capsid in Chimera.  Menu:  Tools… Higher-order Structure… Multiscale Models, and in that tool click “Make Models.”  Click its Help button for more instructions on changing the appearance of the capsid or its parts using that tool.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/fetch.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>

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 28, 2016, at 9:20 AM, Dr Omer Naseer <dromersheikh at gmail.com> wrote:
> 
> Hi 
> 
> I am s student of PhD and working on the Rota virus A, I want to created "three-dimensional structural model of the VP7 trimer".  by using "UCSF Chimera", can you please tell me How to do this? because I tried a lot but unable to produce a structure like yours.
>  
> Regards
> Dr, Omer Naseer
> Ph.D Scholar
> University of Veterinary & Animal Sciences, Lahore, Pakistan.
> +92 321 640 89 56
> 




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