TOC
===

- [Notes](#notes)
- [Examples](#examples)
- [Animations](#animations)
- [Unstable Features](#unstable-features)
- [Tips](#tips)

Notes
-----

- [View static notebook on nbviewer server](http://nbviewer.jupyter.org/github/arose/nglview/tree/master/examples/)
- [View live demo](http://mybinder.org/repo/hainm/nglview-notebooks)

Examples
--------

- [representations and selection language](notebooks/representations_and_selection_language.ipynb)
- [using two screens](notebooks/using_two_screens.ipynb)
- [view trajectory](notebooks/view_trajectory.ipynb)
- [make movie](http://ambermd.org/tutorials/analysis/tutorial_notebooks/nglview_movie/)
- [render and export image for publication](notebooks/export_image.ipynb)
- [membrane](images/membrane.gif)
- [display ccp4 file](images/display_ccp4_file.md)
- [protein mutation and minimization with AmberTools](notebooks/protein_mutation_pdb4amber.ipynb)

Animations
----------
- [mdanalysis](mdanalysis.md)
- [pytraj](pytraj.md)
- [mdtraj](mdtraj.md)
- [parmed](parmed.md)
- [Structure minimization](parmed_minimization.md)

Unstable Features
-----------------
- [customize color](customize_color.md)
- [change theme](images/dark_theme.md)
- [display GUI](images/display_gui.md)
- [pop up viewer](images/viewer_pop_up.md)
- [real time MD visualization](https://github.com/arose/nglview/tree/master/examples/sandbox)

Tips
----

- [Using notebook remotely](http://ambermd.org/tutorials/analysis/tutorial_notebooks/remote_notebook/)
