Plotting transition pathway using MSM and projected on tICs

[sbhakat]

Hi,

I am trying to plot a 2D FES plot using MSM and tICA data. I have n_timescales =5. If I understand correctly this plot will give top 5 (or more precisely I want top 5 transition pathways) transition paths along the tIC space. However in the section 'FES from MSM and tICA' in the notebook the plot looks absolutely crazy in terms of scaling and everything.

Am I doing something crazy here. Any help? bpti_msm_loop(1).pdf