[Chimera-users] Information

[Elaine Meng]

Hello Mabel,
Generally "multimer" refers to multiple copies of a monomer that are not bonded to each other.  If you have a monomer and you want to make the multimer, it depends on whether there is symmetry information in the original PDB file, and what kind of information. In Chimera you could try:

(A) Model Panel (in menu under Favorites) - choose your model on the left, then click "biological unit" on the right.  That requires BIOMT information in the PDB file.  If the PDB file doesn't have that kind of information nothing will happen.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
(B) Next, you could try using other types of information with Unit Cell (in menu under Tools… Higher-Order Structure)
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html>

If neither of those make the hexamer, your PDB file lacks the needed information.  In that case, it will be more difficult.  If there is a similar protein that you already have in hexamer form, you could open that structure and then 6 copies of your protein and match each copy of your protein to one of the chains in the other structure.

If your PDB file is depositied in the Protein Data Bank, another possibility is to see if other databases such as PISA have predicted the hexamer.  You may be able to download the hexamer from one of those other databases.
<http://www.ebi.ac.uk/msd-srv/prot_int/cgi-bin/piserver>

I hope this helps,
Elaine
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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 29, 2013, at 12:38 PM, Mabel Guzman Rodriguez <mabel.guzman at ipicyt.edu.mx> wrote:

> Hello!
> I few days ago I tried to use your program Chimera, the reason is because I try to make a structure of a multimer protein but I need to know how can I bond the single subunits of the protein to make an hexamer. I hope you can help me.
> Greetings
> Mabel G.