Change between different models in a multimodel PDB file without having to reload the widget

[mverissi]

Dear developers,

I have a multimodel pdb file generated from a geometry optimization of a molecule and I would like to visualize it using nglview much in the same way as one can do in PyMol. In PyMol, once a multimodel PDB file is loaded, you can switch between the different models through buttons that appear in the lower left of the PyMol window. Is there any way of doing this with nglview without generating a trajectory file such as Gromacs' xtc?

With the multimodel file name already set in the variable multi_pdb_file, I tried

import nglview as nv

view = nv.show_structure_file(multi_pdb_file, gui=True, default=True)
view.center()
view._remote_call('setSize', target='Widget', args=['','600px'])

view

but there is no way to switch, for example, from model 1 to model 2 apart from adding code that explicitly loads that model, in which case the widget has to be reloaded. I would like to avoid this because this distracts me from seeing the (small) changes in geometry from one model to the next (or previous).

Best,

Marcos

[hainm]

@mverissi Please try this and let me know if that helps

#765 (comment)

[mverissi]

Thanks, @hainm . I'll try it and let you know.

[mverissi]

Hey @hainm, thanks for the reply. What you suggested works, but it's not what I would like. Your suggestion either displays only one or all structures in the pdb file at a time. However, if I want to switch to another of the structures in the multimodel pdb file, I have to reload the widget. I'm attaching a screenshot of PyMol - in the lower right corner I have circled the animation controls in yellow. It allows me to smoothly switch between adjacent models and have an animation of the geometry optimization.

As far as I can see, the only way I can view an animated trajectory in nglview is to create a Gromacs xtc or trr, or the equivalent files for other MD software, and then use the corresponding method (nglview.show_mdtraj for a Gromacs trajectory, nglview.show_parmed for a pytraj trajectory, and so on). Is that correct? The problem is that my multimodel pdb is not generated by a molecular dynamics program, so I just have the pdb.

Best,

Marcos

[hainm]

@mverissi Please see below (I paste the code too)

from ipywidgets import IntSlider
from ipywidgets import link

slider = IntSlider(min=1, max=10)

def on_change(change):
    frame = change['new']
    print(frame)
    view._remote_call('setSelection', target='compList', args=[f'/{frame}'], 
               kwargs=dict(component_index=0))
    
slider.observe(on_change, names='value')
slider