On Fri, Jun 20, 2014 at 12:46 PM, Angel Herráez <[email protected]> wrote: > My concerns are about correct atom position, and also adding more > atoms that were not present and should go in the right positions too.
Understood and agreed... if I think of the nanotox field, however, they typically do not know how much, where, etc, the coating is covering the core... and I am under the impression it is actually the idea here to try to find some distribution to match experimental data... > For example, you could easily change all O atoms at a certain > distance from Si atoms and bonded in a certain way, into S atoms. But > then the bond lengths will not be correct, and how to add another > layer of atoms bonded to those S? Good questions, indeed. People have started doing QM-like things on this; for obvious reasons with methods like DFT etc. But you still have to start with some 3D model, and if this can be done with Jmol, it sounds like a win to me... Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ------------------------------------------------------------------------------ HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing & Easy Data Exploration http://p.sf.net/sfu/hpccsystems _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
