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Examples
========
This page provides a series of examples, tutorials and recipes to help you
get started with ``mdtraj``.
Each subsection is a notebook. To open these notebooks in a "live"
Jupyter/IPython session and execute the documentation interactively, you
need to download the repository and start the Jupyter notebook.
If you installed `MDTraj` from source, you will need to navigate to
:code:`path-to-mdtraj/examples`. The notebook files for these examples and
the notebooks are available in the top level `examples folder
<https://github.com/mdtraj/mdtraj/tree/master/examples>`_ on github too. In
the directory with the notebook files, start an IPython notebook server:
.. code:: bash
$ jupyter notebook
.. warning:: The pre-filled out notebooks are far less fun than running them
yourself!
.. toctree::
:maxdepth: 1
introduction
atom-selection
centroids
clustering
hbonds
pi_stacking
iterload
native-contact
openmm
pca
ramachandran-plot
rmsd-benchmark
rmsd-drift
solvent-accessible-surface-area
two-pass-clustering
Let us know if you would like to contribute other example notebooks, or
have any suggestions for how these can be improved.
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