[Chimera-users] automating ensemble clustering in chimera

Conrad Huang conrad at cgl.ucsf.edu
Wed Oct 15 12:00:34 PDT 2008

Unfortunately, the nmr clustering code is closely tied to its graphical 
user interface, so there is no simple calls into Chimera for scripting. 
  However, the function that does all the work is relatively simple, so 
I've abstracted it into its own function which takes a list of models 
(all with exactly the same set of atoms) and returns a list of pairs. 
The first element of the pair is a cluster representative model; the 
second element is a list of all models in the cluster, including the 
representative.  I've included the code as an attachment.  There is a 
small example at the end of the code on how to use the "cluster" 
function.  Please let me know if this is what you were looking for.  Thanks.


Katryna Cisek wrote:
> Dear Chimera Users,
> How can I automate/import the Ensemble Cluster (Structure Comparison,
> MD/Ensemble Analysis; cluster members of a conformational ensemble,
> determine cluster representatives) module into a python script?
> Thanks,
> Katryna
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> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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