[Chimera-users] matchmaker

[Elaine Meng]

Hi David,
Looks like I forgot to put it in the release notes, but with fairly recent daily builds of Chimera (version 1.6 rather than the production release 1.5.3), you can restrict the matchmaker alignment to specified sets of residues.

In the GUI, there are checkboxes to "Restrict matching to current selection"
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>

For the command, you can give the residue ranges in the specification of the reference and match structures:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict>

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

P.S. putting this on the chimera-users list

On Jan 19, 2012, at 3:00 PM, David Stokes wrote:

> Is there a way to align two models based on a subset of residues selected from each model (or even just a subset of residues from the reference molecule).
> I haven't found it and this would really be helpful.
> Thanks,
> David
>