[Chimera-users] Visualizing an ion channel

[Elaine Meng]

Hi Francesco,
There are a few possibilities for getting or constructing multimers  
in Chimera:

- fetch predicted biological multimer from PQS (File... Fetch by ID)
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html

- Unit Cell (under Tools... Higher-Order Structure)
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/ 
unitcell.html

- Multiscale Models (under Tools... Higher-Order Structure)
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/ 
framemulti.html

The last two use matrix information in the PDB file, so it depends if  
your file has matrices.  Also, most matrices contain crystallographic  
information, not necessarily what is needed to build the biologically  
relevant multimer.  I would probably try the PQS fetching first and  
see if it gives you what you need.

Finally, apart from Chimera, there are other web-accessible databases  
(in addition to PQS) of predicted biologically relevant  multimeric  
structures that you could probably find with a little Googling.  I  
can't remember specifics right now, but they generally provide PDB  
files for download, which you could then open in Chimera.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Oct 10, 2007, at 10:23 AM, Francesco Pietra wrote:

> Hi Elaine:
> Perhaps trivial, though new for me:
>
> How to assemble reliably the essentials (to get the teepee) of the  
> four alpha
> subunits of an ion channel when the Protein Data Bank gives the pdb  
> file for
> one on the subunits? For example 2A79, a mammalian Kv1.2 ion channel.
>
> Thanks
>
> francesco pietra
>
>
>        
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