Can you be more specific?
For example, a chain can be found with
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
On Tue, May 26, 2009 at 6:10 PM, Nick Greeves <firstname.lastname@example.org>
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.
Date: Tue, 26 May 2009 17:08:26 -0500
From: Robert Hanson <email@example.com>
Subject: Re: [Jmol-users] Displaying polymer chains with Jmol
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
On Tue, May 26, 2009 at 4:49 PM, Nick Greeves <firstname.lastname@example.org>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
Has anyone had more success with these commands?
All the best
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
Jmol-users mailing list
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900