VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 22 2010 - 10:26:59 CDT

Hi Olaf,
  I can look into adding a new atom selection keyword that selects
all atoms that are bonded together. Do you have any requirements
for this other than that they are the complete set of atoms that
are bonded with each other?

The existing "fragment" keyword is very closely tied to the
internal organization of VMD's data structures, and needs to remain
the way it is for the purposes of dealing with various problematic
protein and nucleic acid structures.

Cheers,
  John

On Wed, Apr 21, 2010 at 10:19:04AM +0200, Olaf Lenz wrote:
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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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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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