VMD-L Mailing List

From: Nuno Loureiro Ferreira (nunolf_at_ci.uc.pt)
Date: Thu Jul 26 2007 - 03:23:25 CDT

Hi Robert

How about simply concatenate the 2 molecules, and read them as a single pdb?
Cheers,
Nuno

P.S. I think some time ago, someone posted a reply to this mailing list
about how to parse a selection into another selection, not sure.

Robert Wohlhueter wrote:
> 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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