TODO

[msmbuilder]

TODO

[cxhernandez]

bump @brookehus (once you've submitted your paper 😄)

[jeiros]

Have you considered UCSF Chimera for visualization? I know it has a Python API although I'm not too familiar with it.

Interesting repo btw! 👍

[cxhernandez]

• feature projections
  • hexbin 2d landscape
  • kde 1d landscape
  • kde 2d landscape
  • cornerplot (esp good for PCA/tICA)
  • time-series trace
• clustering
  • voronoi plot
• msm plots
  • force-directed graph
  • raw versus msm counts
  • timescale plots
• tpt plots
  • force-directed paths
• information theory plots
  • dendrogram
  • chord diagrams
• structures
  • nglview color-by-metric
  • nglview interactive 2d landscape
  • vmd scripts (for hi-res structures)
  • pymol scripts (for hi-res structures)
  • pymol interface (e.g. ipymol)
• movies
  • PC/tIC movies

cc @mpharrigan @msultan for more plot ideas

[msultan]

errorbars,
movie makers

[cxhernandez]

errorbars

I imagine this might be done with a kwarg for relevant plots? Let me know if you had something in mind

movie makers

Could you elaborate? Am I going to be making a movie making API?

This refers to animating plots.

[cxhernandez]

cc-ing @dr-nate, @brookehus, @evanfeinberg, @nlatorra, @Eigenstate, @jchodera, @steven-albanese and @maxentile, in case you have plot ideas or VMD/PyMOL scripts to contribute 😄

[cxhernandez]

bump @msultan

[cxhernandez]

Have you considered UCSF Chimera for visualization? I know it has a Python API although I'm not too familiar with it.

I have, but I haven't used the Python API. Generally, I'd like to contain all dependencies within conda, and with pychimera it seems like you still need a local installation of Chimera which makes it kind of a deal-breaker 😕

I think nglview is going to be the default for the MSMExplorer, but we'll offer automated scripting tools for VMD, PyMOL, and Chimera, as people contribute them (and as soon as we think of a good API for this).