[BUG]? - Animate does not appear to work

[coltonbh]

Describe the bug
Running viewer.animate does not appear to work. Am I doing something wrong?

To Reproduce

import py3Dmol as p3d

# Convert all structures to XYZ strings
xyz_strings = [structure.to_xyz() for structure in xtb_opt.results.structures]

# Create the viewer
viewer = p3d.view(width=800, height=600)

# Add all models to the viewer and set the frames for animation
for xyz in xyz_strings:
    viewer.addModel(xyz, "xyz")

viewer.setStyle({"stick": {}, "sphere": {"scale": 0.25}})
viewer.zoomTo()

# Set animation parameters
viewer.animate({'interval': 100, 'loop': 'forward', 'reps': 0})

# Display the viewer
viewer.show()

Expected behavior
I would expect the image to be animated. Instead all the images are superimposed without any animation.

Screenshots

Desktop (please complete the following information):

• OS: Linux
• Browser Same result in VSCode, Chrome, Firefox, etc.
• Version 2.2.0

Additional context

Thanks so much!

[dkoes]

You are adding each structure as an individual model. You need to add them as frames. Concat all the xyz files together and pass the string to addModelsAsFrames.
https://3dmol.csb.pitt.edu/doc/GLViewer.html#addModelsAsFrames

[coltonbh]

Lemme give this a try!

[coltonbh]

Amazing! This works like a charm:

import py3Dmol as p3d

# Convert all structures to XYZ strings
xyz_strings = [structure.to_xyz() for structure in xtb_opt.results.structures]
xyz_total = "".join(xyz_strings)

# Create the viewer
viewer = p3d.view(width=800, height=600)

# Add all models to the viewer and set the frames for animation
viewer.addModelsAsFrames(xyz_total, "xyz")
viewer.setStyle({"stick": {}, "sphere": {"scale": 0.25}})
viewer.zoomTo()

# Set animation parameters
viewer.animate({'interval': 100, 'loop': 'forward', 'reps': 0})

# Display the viewer
viewer.show()

Thanks for the quick help. Love py3Dmol and having good support makes it so much more usable :)

A final question--is there a way to add a slider for the animation so I can investigate a trajectory one frame at a time instead of an automatic loop animation?

Thanks!

[dkoes]

That's issue #790. It isn't something that belongs in the main library, but in the UI wrapper, and it hasn't been implemented yet.

[coltonbh]

Excellent. Thanks so much for the guidance and feedback. I've build a few cool things on top of py3Dmol and will ping you when they're ready. Thanks for such a great library!