From: Nick G. <ngr...@li...> - 2009-05-26 23:10:45
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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, jmo...@li... wrote: > Message: 5 > Date: Tue, 26 May 2009 17:08:26 -0500 > From: Robert Hanson <ha...@st...> > Subject: Re: [Jmol-users] Displaying polymer chains with Jmol > To: jmo...@li... > Message-ID: > <ba9...@ma...> > 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 <ngr...@li... > >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 |