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 On 4/9/2010 12:16 PM, 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! > > 1) A selection of dropdown menu starter molecules to help UFF get a > better start. Our current list is pretty weak in this regard. (suggestions?) > 2) Use ACD ChemSketch as a helper application. > > I'm interested in general feelings about the helper application > approach. This currently works with our Jmol application, but it's not > as slick as the JME connection. Still, it's pretty painless, and we need > to get it in the manual - maybe even a video: > > 1) Draw any structure in ChemSketch 2D. > 2) Staying in ChemSketch 2D, do a 3D optimization. > 3) Select the structure and copy to the clipboard - keyboard short cuts > should work. > The above puts the 3D molfile on the clipboard. > 4) Paste the "structure" into the text field in our Jmol application. > 5) Click "Run Script" (Poor wording perhaps?) > > ChemSketch 2D runs some version of CHARMM during 3D optimization and the > optimization has two qualities - it's pretty good and it respects stereo > bonds. > > Downside: It's a helper application. Upside: ACD generously makes > ChemSketch a free download for private, student, educational use. > > Otis > > On 4/9/2010 10:44 AM, william reusch wrote: > >> Otis, >> >> This is a very neat application. I hope it can be tweaked to remedy a >> few glitches. When I draw trans-dimethylcyclohexane and load the >> molecule the chair conformer of the cis-isomer is displayed. Drawing >> the cis-isomer loads the same Jmol display. If I use the X button of >> the editor to force hydrogens in the right configuration a nonsense >> structure is loaded. I am running Mac OS 10.4 >> >> Bill >> >> > -- 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
