[Chimera-users] Ensemble Cluster via command line

Conrad Huang conrad at cgl.ucsf.edu
Mon May 10 12:06:04 PDT 2010

Unfortunately, the EnsembleCluster interface is designed around the GUI 
and it's non-trivial to separate the clustering code out cleanly into a 
non-GUI interface.  On the plus side, if you're willing to play with 
Python a bit, I already have some code (attachment cluster.py) that 
calls the underlying NMRCluster code.  If you run the command:

	chimera --nogui your.pdb cluster.py

you should get some output that looks like:

Cluster 39: size:4, rep:#0.409, members:#0.494 #0.353 #0.409 #0.475
Cluster 40: size:4, rep:#0.277, members:#0.277 #0.311 #0.309 #0.346
Cluster 41: size:4, rep:#0.451, members:#0.451 #0.495 #0.490 #0.493
Cluster 42: size:4, rep:#0.215, members:#0.215 #0.243 #0.400 #0.444
Cluster 43: size:4, rep:#0.229, members:#0.355 #0.428 #0.189 #0.229
Cluster 44: size:4, rep:#0.231, members:#0.200 #0.231 #0.337 #0.389

as well as a PDB file named "reps.pdb" that includes the representative 
model for each cluster.  Is that close to what you need to do?


On 5/7/10 3:08 AM, Jan H. Löhr wrote:
> Dear Chimera users,
> I have been using the Ensemble Cluster tool to cluster a set of PDB-files.
> Now I would like to do this via command line or python script without GUI in
> order to run it multiple times.
> However, it seems the Ensemble Cluster tool cannot be used via command line.
> The only thing I have been able to is to load it up with 'start Ensemble
> Cluster'.
> Is there a way to access the tool via command line?
> Or is there a way to record my mouse actions and translate them to
> commandline-style?
> Here are the steps I am trying to do:
> Load PDB-file (multiple models in it)
> Start Ensemble Cluster
> Parts to Match: :xxx-yyy	(optional)
> OK
> Write List of modelnames/cluster
> End
> This can be done by mouse, but apparently not by commandline, can it?
> Thank You
> Jan
> Univ. Hamburg, Germany
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