Add this command to install instructions to ensure nglview works out of the box.

[nhstanley]

Hey guys, I just did a fresh install of htmd, and I had trouble getting nglview to work. The magic fix was this command:

jupyter-nbextension enable nglview --py --sys-prefix

Which was found on the nglview installation instructions. It might be a good idea to include that in the install page or in the tutorials so that others don't waste time hunting it down, or worse, thinking htmd itself is broken.

Cheers, Nate

[stefdoerr]

Yes I had the same issue some weeks ago but thought it might just be my installation. Preferably we should bring it up with the ngl folk though as it's not related to us

On August 9, 2017 10:58:10 PM GMT+02:00, Nate Stanley notifications@github.com wrote:

Hey guys, I just did a fresh install of htmd, and I had trouble getting nglview to work. The magic fix was this command:

jupyter-nbextension enable nglview --py --sys-prefix

Which was found on the nglview installation instructions. It might be a good idea to include that in the install page or in the tutorials so that others don't waste time hunting it down, or worse, thinking htmd itself is broken.

Cheers, Nate

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[hainm]

I've tried with a completely new env with nglview 0.6.5 from bioconda and things are fine with only 2 commands

conda create -n nglview-release python=3.6 numpy -y && source activate nglview-release
conda install nglview -c bioconda -y

[j3mdamas]

Hi Nate, Thanks for the heads up. Yes, we've had some problems with it, specially when updating older installations.

But I can definitely take this issue and look at it in more detail when I have some time.

Thanks!

[j3mdamas]

We'll try to have some help in the documentation related, but that's as much as we can have, from our point of view. These are user defined settings that get stored, in general, in ~/.jupyter/nbconfig/nglview.json.

[giadefa]

I still don't understand if it works out of the box or one needs the command that Nate says.

On 5 September 2017 at 17:39, João M. Damas notifications@github.com wrote:

We'll try to have some help in the documentation related, but that's as much as we can have, from our point of view. These are user defined settings that get stored, in general, in ~/.jupyter/nbconfig/nglview.json.

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[stefdoerr]

That's funny. It works out of the box if out-of-the-box means a new computer. Not a new conda installation. Because once conda (or whoever does it) messes up your ~/.jupyter configuration of nglview a new conda installation won't save you. Only deleting the folder, modifying the file or -better- running Nate's command does.

On Tue, Sep 5, 2017 at 6:27 PM, Gianni De Fabritiis < notifications@github.com> wrote:

I still don't understand if it works out of the box or one needs the command that Nate says.

On 5 September 2017 at 17:39, João M. Damas notifications@github.com wrote:

We'll try to have some help in the documentation related, but that's as much as we can have, from our point of view. These are user defined settings that get stored, in general, in ~/.jupyter/nbconfig/nglview. json.

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[j3mdamas]

Moving to 1.12.0. I think it also requires to check out how the webgl is working in general

[j3mdamas]

I'll close this ticket and move it to a general nglview update and testing in https://github.com/Acellera/htmd/issues/512