[Chimera-users] ligand comformation clustering

Maurice Ho bokcmho at ust.hk
Wed May 5 18:39:54 PDT 2010

Hi there,

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?

Best regards,
Maurice Ho

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