Copyright©2008 Antony Williams
I previously blogged about the fact that we had embedded a 3D optimizer under Jmol so that that 3D molecules could be displayed. There were two problems with the approach we took. 1) It was very time-consuming to wait for real-time 3D optimization for molecules 2) The 3D optimizer would sometimes fail to optimize a structure based on the starting geometry.
We have just finished publishing millions of pre-optimized structures onto the ChemSpider database. In MOST, but not all, cases the molecules are now pre-optimized. This makes display of the 3D molecule in JMol much faster. Since we were optimizing millions of molecules we did set a threshold for the time within which the molecule should reach some minimum. As a result some molecules were not optimized and the 3D coordinates are still not available so a real time optimization is attempted using smi23d as discussed previously. If you find any structures which don’t optimize please send us the ChemSpiderID and comment to feedback|at|chemspider|DOT|com.Stumble it!