Andre= w,

Jmol has a useful =E2=80=9Ccompare=E2=80=9D comm= and. Here is a tutorial on how to use it. This deals with 2 proteins, but i= t could be applied to any 2 conformations.

https://prot= eopedia.org/wiki/index.php/Jmol/superposition

T= he online reference for all Jmol commands is at

https://chemapps.stolaf.edu= /jmol/docs/

John Keller

Department of Chemistry and Bioc= hemistry

University of Alaska Fairbanks

Sent from Mail for Windows

<= /o:p>

From: Andrew DeYoung andrewdaviddeyoung**gmail.com
Sent: Tue= sday, April 26, 2022 7:45 PM
To: Keller, John W
Subject: CCL:G: Overlaying con= formers for visualization

Hi,

I'm a postdoc and quantum chemistry = novice. I've run geometry optimization ("Opt") using Gaussi= an to find several molecular geometries corresponding to local minima on th= e potential energy surface for a single molecule. The geometries are = similar but not exact. I'd like to overlay several geometries in orde= r to visualize, qualitatively, how they differ. In other words I want= to overlay multiple conformers.

&n= bsp;

Could someone please suggest = a relatively simple way to overlay geometries for visualization? = I have access to GaussView, Avogadro, VMD, and any other freeware applicat= ions 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 the= se to almost any other chemical file format, using Avogadro or the like.

I realize, though, that "overlaying several conformers&qu= ot; 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 c= hemistry program that does this?

&n= bsp;

Thank you for any guidance yo= u can provide!

Andrew

Andrew DeYoung, PhD

Department of Chemistry

Carnegie Mellon University