[Chimera-users] CCL: trimer from monomer

[Elaine Meng]

Hi Kshatresh,
In Chimera there are several ways to get the trimer from the monomer.  It depends what information is included in the PDB file.  The "biological unit" is supposed to be described in BIOMT records, but many PDB files do not have useful BIOMT records, only an identity matrix.

If the PDB file does contain useful BIOMT records (example: 1hxx), you can use the command sym or the "Multiscale Models" tool.  For example, if the structure is open as model 0 you can simply use the command:

sym #0

A PDB file can also contain various other matrices that describe crystallographic symmetry and the unit cell, which may or may not bear any relationship to the biological unit.  These other matrices can also be used by the sym command (it has options), the Multiscale Models tool, and the Unit Cell tool in Chimera.

If none of the information in the PDB file makes the trimer, you might also try fetching the predicted biological unit for that PDB entry from the PQS database.  That can be done using Fetch by ID in Chimera (see the File menu).

Documentation...
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
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.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 Nov 1, 2010, at 2:07 AM, Kshatresh Dutta Dubey kshatresh#,#gmail.com wrote:

> Dear all,
> I want to model a simulate a protein which is found in trimeric form, but unfortunately i have only monomer of that protein. Can anyone suggest me how to model a trimer from a monomer. Kindly also suggest me modelling software which can do this. I have maestro, chiemera and VMD. 
> Thanks in advance
> Regards
> Kshatresh Dutta Dubey