Thanks Bob,
I am trying with PDB but I'm not clear how to specify "residues". I
liked the SMILES string idea from SUBSTRUCTURE but it didn't seem to
work.
I have changed the atom types manually and indeed that does highlight
the atoms e.g. O becomes S (yellow) but I was hoping for a way to
select all the monomer units within a chain without changing the
underlying chemical structure so that the user could continue to make
further changes to the display if they wished. Having a C-S bond with
a C-O distance would undermine that.
All the best
Nick
--
3D Organic Animations http://www.chemtube3d.com
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On 26 May 2009, at 23:14, [email protected]
wrote:
Message: 5
Date: Tue, 26 May 2009 17:08:26 -0500
From: Robert Hanson <[email protected]>
Subject: Re: [Jmol-users] Displaying polymer chains with Jmol
To: [email protected]
Message-ID:
<[email protected]>
Content-Type: text/plain; charset="iso-8859-1"
I think you could use the PDB format and specify "residues" that
involve the
actual monomers. I would see how much you could do with that format,
since
the terms POLYMER and MONOMER are defined in relation to that. To
test, just
take any random PDB file and completely change the atom types to see
what
happens.
On Tue, May 26, 2009 at 4:49 PM, Nick Greeves <[email protected]
>wrote:
Dear All,I am trying to find way of using Jmol to display non-
biological
polymers e.g. polystyrene, nylon, bisphenol A and to highlight the
monomer
units within the chain.
I have found the commands POLYMER, MONOMER, and SUBSTRUCTURE which
look as
though they should be useful but I have been unable to make them do
anything
useful. There also seems to be some doubt whether they work
correctly.
Examining the archives I see a small amount of discussion but no
examples
of implementation. Ideally I'd like some of the features that are
available
for proteins(peptides) but these do nothing with the polymer
structures I
have generated.
Has anyone had more success with these commands?
All the best
Nick
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