Hi all, I need to calculate an average structure (or select the most representative member of), from an NMR emsemble structures in Chimera. Is it possible? Thanks for any helps. Lucio
Hi Lucio, Sorry, Chimera doesn't calculate an average structure from an ensemble. However, "Ensemble Cluster" (in the menu under Tools... MD/Ensemble Analysis) will give clusters, and for each cluster, the best representative. That's not exactly what you asked for (the one best representative), but may be worth a look: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ensemblecluster/ens...> This tool is also used in the "Model Panel and Ensembles" tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 9, 2011, at 9:00 AM, Lucio Ferella wrote:
Hi all, I need to calculate an average structure (or select the most representative member of), from an NMR emsemble structures in Chimera. Is it possible? Thanks for any helps. Lucio
May be this can be useful http://structbio.vanderbilt.edu/~jsmith/suppose/ Marco Def. Quota "Elaine Meng" <meng@cgl.ucsf.edu>:
Hi Lucio, Sorry, Chimera doesn't calculate an average structure from an ensemble. However, "Ensemble Cluster" (in the menu under Tools... MD/Ensemble Analysis) will give clusters, and for each cluster, the best representative. That's not exactly what you asked for (the one best representative), but may be worth a look:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ensemblecluster/ens...>
This tool is also used in the "Model Panel and Ensembles" tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 9, 2011, at 9:00 AM, Lucio Ferella wrote:
Hi all, I need to calculate an average structure (or select the most representative member of), from an NMR emsemble structures in Chimera. Is it possible? Thanks for any helps. Lucio
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