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.
