[Chimera-users] Feature request: parallel MatchMaker?

Jonathan Sheehan jonathan.sheehan at gmail.com
Mon Sep 8 08:31:19 PDT 2014


I'm a huge fan of Chimera, and I frequently need to superimpose a
dozen or more comparative models onto a template protein using
MatchMaker. At present, one cannot  even rotate the view until all
matches have completed, which can take a few minutes on a single core.

Based on old messages[1], it sounds like you might be "interested in
allowing use of
multiple cores for specific compute intensive tasks," and this seems
to me like a good candidate. This use case involves many matches,
which I think are completely independent of one another. Also, these
models have identical length and sequence, so the runtimes should be
fairly close to one another (although that wouldn't necessarily be
true in the general case).

I'm sure that adding multi-threading to a tool is not trivial, but it
seems as though this feature might have a high "bang for the buck" on
today's multicore machines.

Thanks for considering it,

1. E.g.  http://www.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005901.html

Jonathan Sheehan, Ph.D.
Computational Structural Biology
Vanderbilt Univ. Ctr. for Struct. Biol.
5137 MRB3, 465 21st Avenue S.
Nashville, TN 37232-8755

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