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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