[Chimera-users] how to make simmetric dimer

[Elaine Meng]

Hi Francesco,
It depends on the information in the PDB file: it may include matrices describing operations to generate the  biological multimer (BIOMT), or copies related by crystallographic  symmetry (SMTRY or CRYST1), or copies related by noncrystallographic  symmetry (MTRIX).

If this information is already present in the PDB file you can just use the command "sym"  (or depending on the type of information, the Unit Cell or Multiscale Models tool) to make the corresponding multimers. 

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

If the PDB file does not contain such information, then possible approaches are:

- use File... Fetch by ID to get the PQS-predicted multimer for this structure  (however, not all structures are available from this site)

- specify the dimer axis and center yourself manually in the "sym" command (but it may be hard to figure those out)

- if there is a closely related protein with dimer of known structure, and you expect your protein to dimerize the same way, you can open the other protein, open two copies of your protein, and match them to the monomers of the other protein (for example, with MatchMaker)
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 25, 2011, at 10:59 AM, Francesco Biagi wrote:

> Hello everyone. I have a question about Chimera: I want to put two monomers (of a dimer) in simmetry. I tried to do this with mouse, with poor results.
> I would like to know if there is a method or a script that can help me. 
> Thanks to all.
> Francesco