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I am looking for a program to overlay the structure of small molecules as an aid for my students in comparing the results of optimization geometries using different optimization methods.

At this stage, we are thinking of atomic coodinates and a visual comparison. However, if it can be complemented with a quantitative comparison that would a welcomed extra.

We work with the Windows versions of Gaussian 09 and GaussView 5.

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    $\begingroup$ Could you please elaborate a bit more? Is it solely atomic 3D coordinates that are compared, or there is more parameters such as electron density or Hirshfeld surfaces? Do you want to compare quantitatively (e.g. visually) or qualitatively (e.g. calculating deviations)? $\endgroup$ – andselisk Mar 11 at 15:35
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    $\begingroup$ At this stage, we are thinking of atomic coodinates and a visual comparison. However, if it can be complemented with a quantitative comparison that would a welcomed extra. $\endgroup$ – PAEP Mar 11 at 18:30
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You can use the "compare" command in the Jmol program, either online or as free-standing program. A tutorial on how to use the program for this purpose is here, http://proteopedia.org/wiki/index.php/Superposition_with_jmol. It outputs the root mean square of the pairwise differences (RMSD) as well as the superposed coordinates.

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You can do a structural comparison with VMD, using the RMSD trajectory tool. The RMSDTT is a default plugin for VMD (it comes with it, no need to do any fancy installation, so should help students access it).

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There's a "pair-fitting" function in pymol that will align molecules given some user-defined reference atoms, and output an RMSD across those points of comparison. You can get pymol educational version for free, so students would be able to install it themselves.

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I would say Chimera, no question. It has a good GUI with a lot of tools, including ensemble comparison. I find it both much easier and much prettier than VMD which has been recommended here.

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    $\begingroup$ Having used both VMD and Chimera, I'd beg to differ :P. By and large, it's down to user preference. $\endgroup$ – jezzo Mar 12 at 14:22
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    $\begingroup$ Oh, it was bliss when I found Chimera compared to VMD :P but yes, obviously it is preference. Hopefully the OP will find one program to their liking. $\endgroup$ – Antimon Mar 12 at 21:06

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