Hello Tyler! The match will always be pairwise. So you would need to pick one structure as the "reference" and then match each other one to that. For example, if molecule A is the reference and B,C,D are additional molecules you want to overlay, then you'd need to do the following matches: B-A, C-A, D-A. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Feb 15, 2022, at 10:38 AM, Tyler St Denis via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hello,

I have had success overlaying two small molecules in chimera by using the following process and using the "match sel" command in the command line. Each molecule I want to compare has 3 similar nitrogens

http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-August/010205.html

Though this process works for overlaying two small molecules, it does not work for a third. The first error I received indicates "an odd number of atoms has been selected." Clearly the 'match sel' command works by comparing pairs of homologous atoms -- is there a way to expand this 'pair' to a larger set (e.g. triplets) to multiple small molecules?

Thanks!

Tyler