ValueError: Mixing trajectories with and without unit cell

[averysader]

ValueError: Mixing trajectories with and without unit cell

[mattwthompson]

I noticed the version of MDTraj you're reading the example from is pretty out of date (sometime in 2016). In this case it shouldn't matter since the file hasn't been updated since around then, but you should try to use a more recent version (1.9.x). That being said, the actual source code you're running up against is even older, so I'm not sure why this is failing for you. My guess is you're using your own trajectory, not the ala2.h5 file provided?

It's probably be best to just set leaders.unitcell_vectors to whatever unitcell vectors you have in your production trajectory.

[averysader]

Hi Matt, thanks for replying quickly.
I'm using version 1.9.7 for analysis, but the docs are not loading for me. Anyway, I am in fact using my own trajectory.
If I understand the documentation correctly, the unitcell_vectors method takes a 3x3 array of XYZ coordinates generated by the MD program and the number of frames in the trajectory as input? At which point in the code would I have to append the unit cell vectors? Right after 'leaders' is defined as a set of XYZ coords?

leaders = md.Trajectory(xyz=np.empty((0, subsampled.n_atoms, 3)),
topology=subsampled.topology)
leaders.unitcell_vectors(array, shape = (n_frames, 3, 3)) <--- Here?
leader_labels = []

Please forgive my ignorance as I'm trying to work through this as best I can. In my case, I suppose my number of frames that will go into 'leaders' is dictated by other parameters in the code, right? I hope this is clearly stated.

Thanks again,

• Avery