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 _______________________ Tyler G. Saint-Denis, Ph.D. Postdoctoral Fellow T. Don Tilley, Ph.D. Laboratory College of Chemistry University of California, Berkeley tstdenis@berkeley.edu 914-462-1954 [05537c13-eec7-4b35-bc2c-f774f520f544]