[Chimera-users] ligand comformation clustering
bokcmho at ust.hk
Wed May 5 18:39:54 PDT 2010
How to cluster the different conformations of a ligand after a docking
experiment according to their relative orientations in the binding
pocket? Any software can help to do so? I've tried the Ensemble Cluster
function in Chimera but it seems clustering the different conformations
according to the relative positions of the atoms of the ligand itself.
I know that the command rmsd #0.1:UNK #0.2:UNK (UNK is the ligand) could
be a way to illustrate how distant in average between different
conformations. How could I make use of this command in script so that I
could have all the possible comparisons and cluster them in a sensible way?
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