Re: [AMBER] jupyter notebook

From: Hai Nguyen <>
Date: Mon, 23 Nov 2020 20:59:56 -0500

On Thu, Nov 19, 2020 at 2:18 AM aishen <> wrote:

> Hi,
> First thanks for sharing this amber20 tutorial with jupyter notebook. As
> I am new to amber I use them a lot to learn how I could use them with
> pymol because I don't like vmd (though it's an excellent soft) but the
> interface in linux is not very agreable (I know pro don't care much
> about this), so I prefer use nglview, threejs or ammolite/biotite to
> get a pymol sight.
> My question is : Does anybody know more attempt amber in jupyter
> notebook than on the web site ?
Hi Henri,
nglview is simply a visualization software, so you can just let your
imagination run wild.
I don't have a direct answer for you, but I suggest to:
- play with NGL webapp (which is used by nglview):
- read the docs:
- see how nglview is used by other softwares:
or cando:

- for direct questions about nglview, it would be better to open a new
issue here:

Disclaim: I am the lead developer of nglview and was the person who wrote
the nglview-related tutorials in amber.

> Best regards
> Henri
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Received on Mon Nov 23 2020 - 18:30:03 PST
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