From owner-chemistry[ AT ]ccl.net Wed Apr 27 19:13:00 2022 From: "Hans-Ullrich Siehl ullrich.siehl-*-uni-ulm.de" To: CCL Subject: CCL:G: Overlaying conformers for visualization Message-Id: <-54656-220427150825-30295-nANl1vHuUK5L3Wevg0uu4Q{:}server.ccl.net> X-Original-From: Hans-Ullrich Siehl Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 27 Apr 2022 21:08:16 +0200 MIME-Version: 1.0 Sent to CCL by: Hans-Ullrich Siehl [ullrich.siehl]![uni-ulm.de] Dear Andrew DeYoung There is an program for superposition called ´suppose´: https://structbio.vanderbilt.edu/~jsmith/suppose/suppose.man.html best regards Hans-Ullrich Siehl 27.04.2022 21:07 CET -- ********************************************************************** Prof. Dr. Hans-Ullrich Siehl Universität Ulm e-mail: Hans Ullrich Siehl ********************************************************************** On 26/04/2022 19:14, Andrew DeYoung andrewdaviddeyoung**gmail.com wrote: > 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 >