Can you be more specific?

For example, a chain can be found with

select molecule=1
select molecule=2

etc., because "molecule" means "covalently bonded"

It depends if you need something totally general or you can define specifics. For example, you could generate your own "residue" labels using

@res1 atomno >= 1 and atomno < 8
@res2 atomno >=8 and atomno < 16

etc.



On Tue, May 26, 2009 at 6:10 PM, Nick Greeves <ngreeves@liverpool.ac.uk> wrote:
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

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On 26 May 2009, at 23:14, jmol-users-request@lists.sourceforge.net wrote:

Message: 5
Date: Tue, 26 May 2009 17:08:26 -0500
From: Robert Hanson <hansonr@stolaf.edu>
Subject: Re: [Jmol-users] Displaying polymer chains with Jmol
To: jmol-users@lists.sourceforge.net
Message-ID:
       <ba9c0bd60905261508w6d8a78d2j5d9ed42b9f8f0937@mail.gmail.com>
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 <ngreeves@liverpool.ac.uk>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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