[Chimera-users] Mirror

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 6 10:16:14 PST 2013


Hi Sebastian,
Well, command "sym" will make symmetry copies, but the difficulty (for the user) may be in figuring out the center and/or axis to specify in the command.  If the receptor itself is multiple chains arranged symmetrically, it may be that the actual PDB file has only a monomer plus the requisite symmetry matrices for regenerating the multimer.  In that lucky case, you could just combine the docked molecule into the monomer structure, and then use the matrices in the PDB header to create the multimer including multiple docked molecules.  Otherwise to use sym you would have to figure out and specify the symmetry manually.

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

I had one lower-tech idea: write out the receptor and docked molecule into a single PDB file.  Reopen that PDB file so you have two copies of everything.  Use "match" (as opposed to "matchmaker," although that could possibly also work) to superimpose atoms of one copy of the receptor on corresponding symmetry atoms of the second copy of the receptor, and voila ... theoretically you would then have a copy of the docked molecule in each of the symmetrical locations.

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

Then you could delete the receptor part of the second copy, and if needed combine the additional docked molecule into the first structure.
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 Feb 6, 2013, at 3:54 AM, Sebastian Mock wrote:

> Hi,
> is there any possibility to mirror / copy a molecule.
> 
> E.g. you have two docked molecules. If I want the docking partner to be mirrored to the other side of the receptor molecule in the same exact location, but mirrored. 
> 
> Thanks in advance
> Sebastian




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