VMD-L Mailing List

From: Olaf Lenz (lenzo_at_mpip-mainz.mpg.de)
Date: Wed Apr 21 2010 - 03:19:04 CDT

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Hi everybody!

A few days, Marek Maly wrote to the list as he asked for some help
regarding his system and the pbc tools[1].

Trying to fix his problem, I found the origin of the problem. According
to the VMD User's guide[1], the "fragment" keyword selects "a set of
connected residues". I took this to mean that it simply selects all
atoms that have bonds to each other.

Only after looking up the source code of VMD I noticed that these atoms
also need to belong to the same chain and segment! This might be natural
to people from the protein community, but when you come from other
communities, this is not obvious. Is this really necessary? Where does
this definition come from?

When using VMD to visualize non-protein systems, I am used to (mis-)use
the different molecule organization levels (residue, chain, segment) in
the manner that suited me best. This works well for most cases.
Unfortunately, in the case of fragments this can easily fail, at least
when you use the "segment" or "chain" levels too freely.

I would strongly suggest to improve the documentation of the term
"fragment" in the UG. Also, for the PBCTools, it would be very useful to
have a keyword that selects a fragment of all connected atoms,
independent of any other properties.
Would it possible to introduce such a new keyword (or even change the
old one) to simply mark all sets of connected atoms, independent of the
other organizational levels?

Best regards
        Olaf

References:
[1] http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/15670.html
[2] http://www.ks.uiuc.edu/Research/vmd/current/ug/node88.html
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