[Chimera-users] Displaying a dimer from a monomer

[Elaine Meng]

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.html 
 >
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html 
 >
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at 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