ValueError: largest specified index (9562.0 * stride=9562.0 * 1=9562) is larger than trajectory length

[Qianchen-Liu]

I have two trajectories:
trajj=['strip_prod.dcd','strip_prod2.dcd']; each trajectory file includes 4797 frames.
data = pyemma.coordinates.load(trajj, features=feat)
Then I did TICA and k-means clustering, and I would like to visualize the structure of each cluster using molPX.
tica = pyemma.coordinates.tica(data,lag=8)
tica_concatenated = np.concatenate(tica.get_output())
data_sample, geoms = molpx.generate.sample(trajj, pdb, cluster,
n_geom_samples=100,
#keep_all_samples=True # read the doc for this argument
)
I got the error:
ValueError: largest specified index (9493.0 * stride=9493.0 * 1=9493) is larger than trajectory length 'strip_prod.dcd' = 4797

I was wondering where the specified index comes from and how to solve it. Thank you in advance!!

[Qianchen-Liu]

As the length of cluster and trajectories are different, I change the molpx.generate.sample as data_sample, geoms = molpx.generate.sample(trajj, pdb, Y_tica,
n_geom_samples=100,
#keep_all_samples=True # read the doc for this argument
)
And it works, but when I want to plot:
linked_ngl_wdg = molpx.visualize.sample(data_sample,
geoms.superpose(geoms[0]),
plt.gca(),
clear_lines=False,
#plot_path=True
)
linked_ngl_wdg
I got "ValueError: unitcell angle < 0". Could you help me with this? Thank you!!

[jackdmarquez]

@Qianchen-Liu did you get this working?