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

-- 

3D Organic Animations     http://www.chemtube3d.com

Tel:             +44 (0)151-794-3506 (3500 secretary)





------------------------------------------------------------------------------
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
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users




--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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