[Chimera-users] nmrclust additional request

Elaine Meng meng at cgl.ucsf.edu
Fri May 22 10:00:40 PDT 2009

Hi Austin,
You can do that now by having Ensemble Cluster choose the members of  
each cluster in the Model Panel and then using that panel's "write  
PDB" function.

The Ensemble Cluster dialog has a "Treatment of Chosen Clusters"  
section at the top.  If it is hidden, reveal that section by clicking  
the black triangle.  Then check the option to "Choose [all members]  
in Model Panel."  (or, if you just wanted "representatives," you  
could set it to that instead of "all members")

Then, when you click on a line for a given cluster in the Ensemble  
Cluster dialog, it will automatically pop up the Model Panel with all  
the members of that cluster already chosen on the panel's left side.   
You would just need to scroll the function buttons on the right  
(which are alphabetical) down and click on the button marked "write  
PDB."  The same models will already automatically be chosen in the  
write PDB dialog -- there are some other options including whether  
you want all the chosen models in one PDB file, or each as a separate  
PDB file -- and you can specify output name(s) and location.


If you did that for each cluster, you could close the original data  
and then open just the structures for the cluster of interest.

Alternatively, instead of saving and reopening files, you could just  
delete all the structures NOT in the cluster of interest.  You could  
do that by turning on the "Select atoms of [all members]" option in  
the "Treatment of Chosen Clusters" section in Ensemble Cluster, then  
clicking on the line for the cluster of interest, then in the main  
Chimera menu, choosing "Select... Invert (all models)" and then  
"Actions... Atoms/Bonds... delete."  Then to work with the next  
cluster you would need to close this cluster, open the original data  
of all clusters again, and repeat.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 22, 2009, at 7:03 AM, Austin B. Yongye wrote:
> Hi chimera-users/developers,
> Is there a way to save all the structures (not only the  
> representative structures) of all the clusters identified from an  
> ensemble cluster analysis into their respective clusters? The  
> g_cluster tool of gromacs does these, but I don't think it uses  
> Kelley values to determine the optimal number of clusters. Any help  
> will be greatly appreciated. I would like to perform further  
> analyses on each cluster.
> Thanks,
> Austin-

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