nglview about biosimspace HOT 14 CLOSED

Hi Toni, this is what I get doing $HOME/sire.app/bin/pip show package:

nglview: 1.0
numpy: 1.14.0
ipywidgets: 7.1.1
ipykernel: 4.8.0
jupyter: 1.0.0

(NGLview only requires ipywidgets and numpy, but I've see reports regarding issues with certain versions of ipywidgets.)

It looks like you are using a more recent version of nglview which was pushed to pip a few weeks ago. I'll see if that version works for me too. (That said, I'm sure you were using the same version as me when we failed getting it to work in Nottingham.)

Just to make sure: you are running the nglview_patch.sh script in the demos directory? This fixed the empty display problem for me since there was an issue with handling binary data streams.

from biosimspace.

Hello again,

I've just upgraded all of my pip packages and the molecule viewer still works. One thing I spotted is that someone has fixed the binary data stream issue, so the viewer now works for me without needing the patch script. (They have added a conditional check for binary data.)

It could be possible that the patch has actually broken a working nglview installation, so perhaps try reinstalling it.

Cheers.

from biosimspace.

The patch changes a line from 'rb' to 'b' right?

I just tried to fix that manually.

from biosimspace.

No, it changes 'rb' to 'r', but it shouldn't be needed with the version of nglview that you have since they have fixed the issue.

from biosimspace.

I am just doing a clean install to see if it works.

from biosimspace.

I did a clean install of Sire and BioSimSpace into sire with the latest version on github. the 'rb' and 'r' bit seems to look fine code wise, but still the problem of no display persists following your instructions.

from biosimspace.

Hmmm, I'm at a loss. Have you tried with a different browser?

When you say "no display". Do you mean that the GUI appears but there is no molecule, or nothing at all?

Also, is this a problem running the amber.py demo, or are you trying to visualise a different molecule. I think NGLview can have issues with very large systems, e.g. solvated systems, and a fix to deal with this is running jupyter as follows:

$HOME/sire.app/bin/jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000

If the file is bigger than 5MB it may not be possible because of the Jupyter transfer limit.

(You may have already tried this.)

from biosimspace.

I have tried with Chrome. Same problem. I have been searching online. I may post something on the NGL git page.

I tried to just go back to nglviews examples. See this:

i should be able to see the protein structure if I do something like that I assume. Doesn't seem to work for me.

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What happens if you type w.display(gui=True)?

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Then I get the gui, whithout the molecule shown. As in what I get when just running the bits in the amber notebook.

from biosimspace.

Okay, that's what I expected.

This issue has been mostly tracked here. Might be worth adding to the discussion there, or seeing if there's anything in the comments that we've not tried.

from biosimspace.

Can you try one thing? Print these for me?

import traitlets, ipywidgets, notebook, numpy, nglview, ipykernel print(traitlets.__version__, ipywidgets.__version__, notebook.__version__, numpy.__version__, ipykernel.__version__)

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@ppxasjsm what does the web console say?

(In Chrome: right click -> Inspect -> Console)

You might want to try: nglviewer/nglview#718 (comment)

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I'll close this for now since it seems to be a problem with NGLView rather than BioSimSpace. Feel free to add another comment if you discover a solution. This will help us when deciding the best way of bundling the various python dependencies, e.g. if the conda version of a package works, but the pip one doesn't.

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