Angel- > but by far the best solution is that you use MOL format for transferring the > structure between JME and Jmol.
I don't know why I got it in my head that I had to pass the JME file. At one point, I seemed to be having CR/LF problems with molfiles going in via the Jmol DATA MODEL route. That's when I switched to the inline approach. I guess I just had this problem with molfiles via DATA MODEL in my head. I'll try JME to Jmol via molfiles. > Also, I think you are really not retaining any stereo info, the model > arrives flat, so whether you get the chair or boat is purely coincidential. Yeah, that part seemed a bit mystical to me also. Things just improved when I started using wedge bonds in JME, but I have to remember that improvement can be a random phenomenon! On the other hand, if the stereo bond data is there, is it possible that the UFF uses it? > A separate question: >> As you may already know, the >> JME hydrogens must be explicitly inserted. > Does that mean you draw them manually? Or do you have some way of doing that > in one go? > I've worked on my own 2D to 3D tool and faced that limitation. Yup! Pain in the neck, but that's the only way the H's get transferred to Jmol. This is the reason that we supply the ChemSketch option. In ChemSketch 2d, the hydrogen atoms are automatically added by the 3d optimization. The copy/paste of the molfile from ChemSketch to Jmol is relatively painless. The only downside is that the user needs a separate helper application - ChemSketch. The upside is that ChemSketch Free is a tool that organic students should have on their computers. Otis -- Otis Rothenberger http://chemagic.org ------------------------------------------------------------------------------ Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
