Show multi-model of NMR structures

[platinhom]

I want to show a NMR structure (such as 1d3z.pdb) with many models. However, when I display the structure, it only show the first model.

If I use the display again , it can show normally.

The question is: how can I show all the models normally at the first time?

I have tried to use add_representation(selection='/0'), add_representation(selection='/1') ... to add many representations, but it also fail.

import nglview as nv
view=nv.show_pdbid('1d3z', color='modelindex')
view.update_cartoon(color='modelindex')

# It will only show one model
view

# It will show all models normally
view

Thanks in advance!

• Version report

NGLview version 1.1.7

[hainm]

The question is: how can I show all the models normally at the first time?

hi @platinhom, nglview displays 1st model as default. Please use default_representation=False).

If I use the display again , it can show normally.

This seems like a bug in nglview.

[platinhom]

@hainm Thanks to your reply! I have tried :

view1 = nv.show_pdbid('1l2y',default_representation=False)
view1

But nothing shown at all. Python version 3.6.5, ipywidgets==7.2.1, ipykernel==4.8.2, notebook==5.5.0

I also tried it in Py2.7.15. It still only show the first model:

[hainm]

Hi You need to add a new representation. That’s why you saw ‘view.add_cartoon’ in my example.

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[platinhom]

@hainm It works well now. Thanks! I spell wrong on "representation" in my previous case 😂.
It work well on 1ly2 case. But in the case 1d3z it still fail. Maybe something wrong on that structure.

[hainm]

Hi can you upload that file?

[platinhom]

just try:

view = nv.show_pdbid('1d3z',default_representation=False)
view.add_cartoon(color='chainindex')
view

or download from PDB: 1d3z

Thanks~

[hainm]

thanks. Seems like an issue with nglview (works fine with NGL: http://nglviewer.org/ngl/)

[hainm]

@platinhom ah ah, I know why now. You need to use 'view.center` to center the molecule too. (default representation does that).

[hainm]

Just FYI, once you can show multi model, you can select to display one of them.

model 1

view._remote_call('setSelection', target='compList', args=["/1"], 
               kwargs=dict(component_index=0))

all models

view._remote_call('setSelection', target='compList', args=["*"], 
               kwargs=dict(component_index=0))

[platinhom]

@hainm Thanks. It's great idea to control the display by given selection.