Bill, The Dundee Server is really impressive. Here's the really interesting thing: When you use the JME editor on their site, it passes a 2D molfile back to the page. It's flat as a pancake, and it is what is passed on to the cgi. Yet, the final result seems to reflect the stereochemistry implied by JME wedge bonds!!!!! How do they do that? They are not doing it with the SMILES because I can delete that from the molfile, and it still works. They are also returning a separate SMILES string back to the page, but this does not get passed to the cgi. Maybe my tests were fortuitous, but I don't think so. Some how stereo information is being processed.
This would all make sense if they were using the SMILES. Daylight runs a "Depict" Web site that can translate SMILES stereo information - e.g. [h...@](F)(Cl)Br to structure. This was one of my tests on their site. I have to write to them. The limiting factor on our Jmol site, however, is UFF. Even if we can capture the stereo intent of the JME drawing, we are still limited by how the UFF minimizes. Still, your query got me to thinking. JME is primarily a query tool (unique SMILES). We're using JME on our site for small starter molecules that will be further edited in Jmol. Following your note, I modified the JME connection to serve as a query. If the SMILES of a small starter molecule is in our "load trouble maker" list, then the JME connection will really load a model from file. If the drawn structure is not on the "load trouble maker: list, then it gets processed by UFF in Jmol. Thanks for starting this chain of thought. Otis On 4/9/2010 3:48 PM, william reusch wrote: > Otis, > > By all means trust Bob's advice. I was interested in your approach > inasmuch as the Dundee Server nicely converts simple JME structures into > PDB files that yield beautiful Jmol displays, but does so in a stepwise > fashion. > http://davapc1.bioch.dundee.ac.uk/prodrg/index.html > > Bill > > > > > > > Otis Rothenberger wrote: > >> Bill, >> >> Bob's comment is right on the mark. The fastest route to a model of >> choice is selecting the best parent and then building by click/replace >> of the hydrogen atoms, which are already in reasonable stereo positions. >> In this case, the cyclohexane parent already has the appropriate chair >> with correct axial and equatorial hydrogens. Tom and I need to get a >> good list of small parent hydrocarbon models. As per my previous note, I >> also need to make the build by atom addition tool much less conspicuous. >> >> JME to Jmol does a pretty good job on alkanes and alkenes. Alkynes are a >> problem - not linear. The addition of a set of cyclic hydrocarbon >> templates would be good. >> >> Otis >> >> >> > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Otis Rothenberger chemagic.com ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
