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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.

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The compare command in free and open source programs Jmol (offline) or JSmol (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.

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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
    Commented Mar 12, 2020 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
    Commented Mar 12, 2020 at 21:06

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