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markovmodel / pyemma_tutorials

How to analyze molecular dynamics data with PyEMMA
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notebook 5 / hmm memberships #69

Closed franknoe closed 6 years ago

franknoe commented 6 years ago

In this plot the visualization makes a discretization error in the assignment of the transition state region. In this region an clear assignment is not possible. It would be better to somehow show the fuzzy assignment (membership). Maybe that's best done in four plots, but perhaps there is a pallette that also works in one plot.

image

franknoe commented 6 years ago

Same here, and maybe elsewhere

image

cwehmeyer commented 6 years ago

I'll have a look whether that is plotting-related or caused by the metastable assignment.

cwehmeyer commented 6 years ago

This is not a bug but the result of a very sparse clustering.

thempel commented 6 years ago

Issue resolved by #83 and pyemma.plots update (thanks @cwehmeyer and @marscher).