A blog posting last night discussed the fact that we had not yet implemented a 3D optimization engine under Jmol and that the structures displayed are 2D FLAT molecules. Well I’m happy to report that less than 24 hours later (actually it was done before I woke up this morning) the optimization of 3D structures under JMol is incorporated.
Rajarshi Guha pointed us to smi23d and we have embedded this under JMol now. This is of course, beta (we stay in constant beta) and there are a couple of bugs…we’re not sure whether these are on our side or in the Optimizer and are awaiting feedback. In the previous posting on Diazonamide A I commented on the six hits. The top two do NOT optimize while the bottom 4 do. I think it’s about the fact that the structure might be TOO far away from a starting point for optimization. I’ve opened an email dialog with Rajarshi to discuss.
Please note that the 3D coordinates are calculated in real time and the JMol screen might stay empty for a while during the optimization process. Here’s what it looks like for Diazonamide A.Stumble it!