Hi and congratulations on making a powerful tool for separating conformational states. I have some very interesting results that I hope to share soon.
I would like to include a one-dimensional particle histogram as a panel in one of my figures. The graphical output from the “intermediates” mode is essentially what I need, except without the triangular overlay of each particle subset. Are the relevant data exposed somewhere?
Something like this:
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
cs = np.load("xxx/component_000_particles.cs")
Thanks for the kind words and great to hear about your interesting results!
@DanielAsarnow’s suggestion is right on. The latent coordinates for every particle are recorded in the output .cs files in the 3DVA job directory. We have a longer tutorial about working with .cs files here: