[Chimera-users] Visualizing an ion channel
chiendarret at yahoo.com
Thu Oct 11 00:05:30 PDT 2007
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.
--- 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)
> - Unit Cell (under Tools... Higher-Order Structure)
> - Multiscale Models (under Tools... Higher-Order Structure)
> 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.
> 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
> 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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