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 <[email protected]>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 > > -- > > 3D Organic Animations http://www.chemtube3d.com > > Tel: +44 (0)151-794-3506 (3500 secretary) > > > > > 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 > > > > > ------------------------------------------------------------------------------ > 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
------------------------------------------------------------------------------ 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
