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. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ ensemblecluster/ensemblecluster.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> 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 ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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-