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On 03/09/10 12:44, Rex Palmer wrote: > This is not really protein crystallography but we are trying to model > build a ligand into a protein binding site. A similar ligand is > already in place and we want to replace this by initially > superimposing a phenyl ring which is common to both ligands. We > understand that such superpositioning can be done with eg Quanta but > do not have access to this program. Does anyone know of a downloadable > program that we could use instead? > Something like this is in Coot, but not exactly what you say that you want (because this method uses LSQ fit on all the atoms that match by sub-graph analysis [1]): http://www.biop.ox.ac.uk/coot/doc/coot.html#Ligand-Overlaying Paul. [1] Krissinel & Henrick "Common subgraph isomorphism detection by backtracking search" (2004) /Software - Practics and Experience/, *34*, 591-607.