Hello, I want to use Chimera to generate clusters of a molecular dynamics trajectory. I have been looking for info about the clustering algorithm it uses, but I was not able to find anything. I guess it employs a default technique, does anybody know which one? Regards. David-.
Hi David, The clustering description in the MD Movie (trajectory viewer) page says to see Ensemble Cluster for details: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#clustering> Here is the Ensemble Cluster documentation, including literature reference for the method: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ensemblecluster/ensemblecluster.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 10, 2018, at 1:29 PM, David Adrian Saez San Martin <davidsaez@udec.cl> wrote:
Hello, I want to use Chimera to generate clusters of a molecular dynamics trajectory. I have been looking for info about the clustering algorithm it uses, but I was not able to find anything. I guess it employs a default technique, does anybody know which one? Regards. David-.
Dear Elaine, Thanks for your helpful answer. Great software, very useful. Regards. David. On Tue, Jul 10, 2018 at 5:12 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi David, The clustering description in the MD Movie (trajectory viewer) page says to see Ensemble Cluster for details: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/ movie.html#clustering>
Here is the Ensemble Cluster documentation, including literature reference for the method: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ ensemblecluster/ensemblecluster.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 10, 2018, at 1:29 PM, David Adrian Saez San Martin < davidsaez@udec.cl> wrote:
Hello, I want to use Chimera to generate clusters of a molecular dynamics trajectory. I have been looking for info about the clustering algorithm it uses, but I was not able to find anything. I guess it employs a default technique, does anybody know which one? Regards. David-.
participants (3)
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David Adrian Saez San Martin -
David Sáez
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Elaine Meng