[Chimera-users] Visualizing an ion channel

[Francesco Pietra]

Hi Elaine:
I first tried (because simpler) Tools -> Higher order structure -> unit cell ->
outline unit cell make unit cell, i.e. according to the explicit procedure also
suggested by Sabuj Pattanayek. I got the impression that the resulting multimer
was not the ion channel. The K+ ions that are seen on the pdb of the Protein
Data Bank are repeated for each unit created. May be I did wrongly, however.

The PDQ route was successful, arriving at a saving a pdb file for the tetramer
with K+ at the center hole. I assume that "cleaning" to leave the essentials
around the K+ ions can be carried out with Chimera. That also new for me.

Thanks
francesco



--- Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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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> 






       
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