Bill, I'm passing molfiles from JME. Actually, the SMILES is also passed in the molfile (Name Position), but its the molfile that's rendered.
The JME string might be worth a try. While the information is still 2D only, we have found that you can give UFF minimization good starts and bad starts based on the original 2D drawing. It's important to note that Jmol ignores stereo bonds from JME - only 2D info passed. Interestingly, it will pass formal charge information in the molfile, but the atom is not registered in Jmol as having the formal charge - i.e. the charges are only printed on the model. Otis On 4/9/2010 1:07 PM, william reusch wrote: > Otis, > > Are you transferring the JME structure as a Smiles string or as a JME > string. The latter has more information in it. > > Bill > > > Otis Rothenberger wrote: > >> Bill, >> >> Thanks for the comments. The 2D to 3D translation is an ongoing problem >> for us. The JME editor is light weight and it can be embedded directly >> in the application, but it passes only 2D information to Jmol. Jmol >> tries to sort this out with the UFF minimization. With really simple >> molecules this works, but there are serious limitations. We actually >> have two alternative options, and we need to discuss this in the users >> manual, a current high priority! >> >> > > ------------------------------------------------------------------------------ > 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 > [email protected] > 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 [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
