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? Conrad 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

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