Re: [Jmol-users] Jmol Virtual Model Kit and JME

Bob, I installed /Jmol 12.0.RC5/ on the chemagic server and set the JME transfer code in the model kit for the JME string. In playing with the new set-up, I did not see one error in stereo rendering of non-cyclic systems. Structures drawn in the JME editor are processed as follows: 1) If the

[Jmol-users] well, what do you know? Jmol and JME 2D to 3D

OK! Here we go! Super simple 2D to 3D. The JME-Jmol connection has gone unused for too long. With today's 12.0.RC5 addition of reading bond stereochemistry, Jmol now does a pretty decent job of translating 2D into 3D -- admittedly this is not going to solve all problems, but give it a try: http:/

[Jmol-users] Please clean up messages when replying to the list...

I would like to request that people please clean out the nested quotations when they reply to the list. It is reasonable to keep the pertinent information that is being commented upon, but usually multiple nested replies are just wasting bandwidth. They also make it more difficult for those wh

Re: [Jmol-users] Jmol Virtual Model Kit

Isn't that fun? I'll set up a little JME reader for that new.htm page next. It's the JME string. Previous 11.9 versions won't work because I inadvertently broke the JME reader and never thought to test it because it seemed, well, so useless before. But now I think it's pretty neat!. The JME strin

Re: [Jmol-users] Jmol Virtual Model Kit

Bob, I have it set up on my home server. I'm only working with small molecules, but I haven't had a clunker yet. Wow, I am impressed! I actually took the stereo bonds off of the JME on the chemagic site. I need to put them back. I'm still going to bypass some other misses. For example, mo

Re: [Jmol-users] Jmol Virtual Model Kit

Bob, Yes! I don't have Jmol 12.0 downloaded yet, but I'll get it now. Where are you "seeing" the stereo bonds. I don't see any stereo information in the molfile (other than the SMILES in the header) or the jme string. Are you reading this from the SMILES? Once I get this set up, Tom will be

Re: [Jmol-users] Jmol Virtual Model Kit

Hey, check this out: http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm 124. JME reader reads stereochemistry and automatically turns 2D to 3D with addition of H atoms * The JME format is a two-dimensional file format that is easy to generate

Re: [Jmol-users] Jmol Virtual Model Kit

Otis, if you think it would be valuable, we could look into reading the stereochemistry of bonds and at least shifting a whole branch up or down an angstrom in the Z coordinate based on that. wouldn't be perfect, but it might not be that hard, either. As I started to do this, I realize that the JM