Software recommendations for overlaying molecular structures

I am looking for a program to overlay the structures 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 coordinates and a visual comparison. However, if it can be complemented with a quantitative comparison that would a welcomed extra.


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




The [`compare`](https://chemapps.stolaf.edu/jmol/docs/#compare) command in free and open source programs [Jmol](https://jmol.sourceforge.net) (offline) or [JSmol](https://chemapps.stolaf.edu/jmol/jsmol/simple.htm) (online) outputs the root mean square of the pairwise differences (RMSD) as well as the superposed coordinates. For an extended tutorial see [Proteiopedia — Jmol/Superposition](https://proteopedia.org/wiki/index.php/Jmol/Superposition).


 9

You can do a structural comparison with [VMD](https://www.ks.uiuc.edu/Research/vmd/), using the [RMSD trajectory tool](https://www.ks.uiuc.edu/Research/vmd/plugins/rmsdtt/). 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).


 7

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](https://pymol.org/edu/?q=educational/), so students would be able to install it themselves.


 5

I would say [Chimera](https://www.cgl.ucsf.edu/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.


 4