Hi Maurice, if you use DOCK for the docking, you can cluster the conformations within DOCK (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm). The default value is 2A, I think, but you can change that. I am not too familiar with scripting in Chimera, but I think that if you simply write all the commands you want to perform, save them as cmd file, you should be able to run it within Chimera (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile). You could also write a python code to run more systematically in Chimera (I am not familiar with that, see the Chimera Programmer's Guide). Otherwise, you can relatively easily write a simple code that systematically reads ligand files, calculates rmsd, and clusters based on given threshold (e.g. in Matlab, python of even excel). Hope this helps, Ben On 5/5/2010 9:39 PM, Maurice Ho wrote:

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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users