Hi John, It depends on the information in the PDB file: there may be various matrices in the header section describing operations to generate the biological multimer (BIOMT), or copies related by crystallographic symmetry (SMTRY or CRYST1), or copies related by noncrystallographic symmetry (MTRIX). Looking at the text of the file for 6RHN, I see it has BIOMT, SMTRY, and CRYST1. It sounds like you want to use BIOMT information to generate the biologically relevant form, the dimer. You could use either the command "sym" or the Multiscale Models tool. Example commands: open 6rhn sym #0 #0 To generate the other kinds of copies, you could use either Unit Cell or Multiscale Models (both are under Tools... Higher-Order Structure). Many structures do not have BIOMT information. For those, you might want to fetch the predicted biological multimer from the Predicted Quaternary Structure database. That could be done from within Chimera using "Fetch by ID" (in File menu, choose PQS option) or a command, for example: open pqsID:6rhn which in this case gives the same result as "sym" using the BIOMT information in the file. Man pages: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html#secondary
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.h...
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemul...
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html> Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 9, 2009, at 2:09 PM, Eric Pettersen wrote:
(extracted from a bug report...)
Dear Folks, How do I display a dimer, such as for 6RHN? So far I have been able to call up the monomer only, whereas the structure (and other evidence) shows it to be a dimer. Thanks, Sincerely, John Lowenstein