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.
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