APBS-PDB2PQR examples and tutorials
===================================

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PDB2PQR operations
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In order to perform electrostatics calculations on your biomolecular structure of interest, you need to provide atomic charge and radius information to APBS.
Charges are used to form the biomolecular charge distribution for the Poisson-Boltzmann (PB) equation while the radii are used to construct the dielectric and ionic accessibility functions.

The PDB2PQR web service and software will convert most PDB files into PQR format with some caveats.
Although PDB2PQR can fix some missing heavy atoms in sidechains, it does not currently have the (nontrivial) capability to model in large regions of missing backbone and sidechain coordinates.
Be patient and make certain that the job you submitted to the PDB2PQR website has finished and you have downloaded the resulting PQR file correctly.
It usually takes less than 10 minutes for the job to finish.

This tutorial assumes that you have `registered <http://eepurl.com/by4eQr>`_ and have access to `the PDB2PQR web server <http://apbs.poissonboltzmann.org>`_.

.. toctree::
   :caption: PDB2PQR examples
   :maxdepth: 1

   adding-hydrogens
   parameterizing-ligands

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APBS examples
===================

APBS examples start with a PQR file (e.g., generated by PDB2PQR).
Some of these examples can be performed through the PDB2PQR web interface but most require a command-line APBS program.

.. toctree::
   :caption: APBS examples
   :maxdepth: 1

   solvation-energies
   binding-energies
   salt-linkage
   parallel-apbs

.. todo::
   
   Migrate geoflow, pbsam, pbam examples over from :file:`examples` directory.

.. _visualizing:

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Visualizing results
===================

There are several programs available for visualizing APBS results.
The easiest is the PDB2PQR web server which provides `3Dmol.js <http://3dmol.csb.pitt.edu/>` and `Jmol <http://jmol.sourceforge.net/>` browser-based visualization capabilities.

Other programs include:

* `PyMOL <http://www.pymol.org>`_
* `VMD <http://www.ks.uiuc.edu/Research/vmd/>`_
* `PMV <http://mgltools.scripps.edu/>`_
* `Chimera <https://www.cgl.ucsf.edu/chimera/>`_

.. toctree::
   :caption: Visualization examples

   using-pymol
   unitymol

.. todo::

   Add VMD tutorial.