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 > > -- > > 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 > [email protected] > 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
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