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Sent to CCL by: John Keller [jwkeller,alaska.edu]
Andrew, Jmol has a useful “compare” command. Here is a tutorial on how to use it. This deals with 2 proteins, but it could be applied to any 2 conformations. https://proteopedia.org/wiki/index.php/Jmol/superposition The online reference for all Jmol commands is at https://chemapps.stolaf.edu/jmol/docs/ John Keller Department of Chemistry and Biochemistry University of Alaska Fairbanks Sent from Mail for Windows From: Andrew DeYoung
andrewdaviddeyoung**gmail.com Hi, I'm a postdoc and quantum chemistry novice. I've run geometry optimization ("Opt") using Gaussian to find several molecular geometries corresponding to local minima on the potential energy surface for a single molecule. The geometries are similar but not exact. I'd like to overlay several geometries in order to visualize, qualitatively, how they differ. In other words I want to overlay multiple conformers. Could someone please suggest a relatively simple way to overlay geometries for visualization? I have access to GaussView, Avogadro, VMD, and any other freeware applications you can think of. The molecular geometries are in separate .log files (i.e., output from Gaussian), but of course it is easy to convert these to almost any other chemical file format, using Avogadro or the like. I realize, though, that "overlaying several conformers" is not a unique specification; one would need to specify which atom(s) to try to overlap exactly. Is there an algorithm in a computational chemistry program that does this? Thank you for any guidance you can provide! Andrew Andrew DeYoung, PhD Department of Chemistry Carnegie Mellon University |