[Chimera-users] How to know the cut-off used in ensemble cluster?

Conrad Huang conrad at cgl.ucsf.edu
Mon Jun 1 14:40:17 PDT 2020

As you mentioned, the cutoff is specific to each data set.  As described 
in the NMRCLUST paper, the cutoff is based on a "penalty value" as a 
function of the number of clusters.  The penalty value is the sum of the 
average "spread" (distance between two samples within a cluster) and the 
number of clusters.  We simply choose the number of clusters as the one 
with the lowest penalty value.  I did not bother reporting the actual 
penalty value because it does not really correspond to a physical 
quantity, and the chosen penalty value is not useful without the context 
of all other penalty values.

If I were doing it over, I would probably include a penalty-vs-#cluster 
plot and allow users to change the cutoff, but we have moved on to 
ChimeraX development and, sadly, there is not enough time to do 
everything we want.


On 6/1/2020 10:16 AM, Ibrahim Mohamed wrote:
> i am using MD movie to cluster my Molecular Dynamics results. how can i 
> know the cut-off used by chimera to do this? i know that it depends on 
> the data itself, but how can i know this cut-off for specific data?
> Thanks
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