VMD-L Mailing List

From: Robert Wohlhueter (bobwohlhueter_at_yahoo.com)
Date: Thu Jul 26 2007 - 00:27:38 CDT

Given the definition of the atomselect keyword "within <num> of <sel>", I would have expected that "<sel>" might accept any valid selection, including those from other (loaded) molecules: e.g. set s1 [atomselect 0 "within 5 of [atomselect 1 "all"]"]
or set s2 [atomselect 1 "all"]; set s1 [atomselect 0 "within 5 of $s2"]

But such specifications give me "cannot parse atom selection text" errors.

Generally speaking, how does one (can one) use the 'within' keyword to select, say, close contacts between a protein (loaded as one molecule) and a docked ligand (loaded as another molecule)? How else might one look at Hbonds between between "all" atoms of the ligand molecule and a few, close-by protein atoms?

Bob Wohlhueter
       
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