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@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@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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