Created
June 24, 2016 12:59
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Example PCA implementation and analysis
@kain88-de, do you want to link to this gist from https://github.com/MDAnalysis/mdanalysis/wiki/Tutorials ?
Btw, you could also color the residue B-factors by the magnitude of the variance in the 1st PC and display: This should show very clearly which domains are involved in the motion.
@orbeckst We can make this a tutorial once @jdetle has implemented a PCA :-). I don't know much about the coloring in nglview.
@jdetle. replace %matplotlib inline
with %matplotlib nbagg
to get interactive plots. I personally like the static pictures here because they are rendered in github, the js isn't.
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This would make a nice tutorial!
For information: The trajectories can be obtained from Data download for the 2015 CECAM Workshop.