[Chimera-users] aligning molecules

[Elaine Meng]

On Nov 14, 2014, at 7:45 PM, Bhaskar Bagchi <bhaskarbagchi at gmail.com> wrote:

> Respected Sir
> I want to align ligands after docking study. Is it possible in chimera? Please help me.
> Thanking you                                                    Yours faithfully,
>                                                                        Bhaskar Bagchi
>                                                      Cheminformatics, Bioinformatics Lab                                                                   Department of Chemistry,                                                                             Raiganj College 

Dear Bhaskar Bagchi,

I may not understand your question very well,  because if you align the molecules they would no longer be in their docked positions.  However, there are several ways to align molecules in Chimera.  If non-protein, you would probably want to use the “match” command, but this also requires specifying the atoms to use, in the right order, if the two molecules don’t have all the same atom names.

See documentation for ways to align, and the “match” command specifically:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html

See also related command “rmsd” and the “ViewDock” tool for looking at docking results.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html>

It is recommended to send Chimera questions to chimera-users at cgl.ucsf.edu (CC’d here) rather than to my individual address.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco