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

[Conrad Huang]

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.

Conrad

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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