[Chimera-users] ligand comformation clustering

Ben Keshet keshet1 at umbc.edu
Thu May 6 07:11:26 PDT 2010

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 
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,

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
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> Chimera-users at cgl.ucsf.edu
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