Angel- You are correct. I've spent an hour drawing the same structures over and over with wedge and non-wedge bonds. After the UFF, I might as well have been throwing dice, which evidently God does do in this case.
The molfiles from JME seem to work just fine, at least on my Windows computer. I have not tried it on a Mac yet. I'm working on my local server right now. I've not made the changes on the public chemagic server yet. Now that I think about it, when I had problems with molfile CR/LF issues, I was storing the JME information in a text field prior to the use of the Jmol DATA MODEL command. Now I am passing the data directly from JME to Jmol's inline load. Still, I need to check it on a Mac. The CR/LF problems pre-date the Internet. You would think that the world could agree on what constitutes a new line. That we cannot after all these years says something about the human ability to agree on any issue! It looks like my first question is resolved. Thanks for the help. Otis 2009/12/8 Angel Herráez <[email protected]>: >> 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. > > > Well, yes there may be problems in transferring the MOL data due to newlines. > I've seen > that. Good luck. > > >> On the other hand, if the >> stereo bond data is there, is it possible that the UFF uses it? > > I've digged a bit into the file readers in Jmol, and the JME parse is the > only one that still has > stereo bonds. Note that MOL format allows stereo up/down specification, but > that is not > being read by Jmol. I think that the JME code is a leftover, not tested since > nobody has > used this format, or reported to do so. > > I do not think that there is any way Jmol can retain and use those wedge > bonds info for UFF. > > > > ------------------------------------------------------------------------------ > 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 > > > -- 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
