[Chimera-users] Three suggestions

[Elaine Meng]

On Apr 10, 2013, at 9:54 AM, Antoine Maillard wrote:

> Concerning suggestion #1:   changing Chain ID of a portion of a chain was meant to assist matchmaker in targeting the right domain and not let it take adventice (meaningless) pieces into account. I realize now that this could be quiet a challenge for Chimera to interpret in all the procedures already available... and will stick to the cut-into-domains-of-interest approach.

Hi Antoine,
Actually you can tell MatchMaker to use only part of a chain by selecting that part and using the "Further restrict matching to current selection" option in the graphical interface, or if using the matchmaker command, specifying only the residue ranges you want to use.

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>

Maybe that will let you get the superposition you want without having to cut the domains apart or change their chain IDs.
Best,
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