.. -*- coding: utf-8 -*-

.. |->| replace:: →


Ligands
-------

- Download 1AKE_ from the PDB (or use `1ake.pdb` from the `course
  directory`_)

- show protein chain A

- show the co-crystallized ligand Ap5 (``resname AP5``)

  - resname AP5, licorice, color: name

- show charged residues within 5 Å of the ligand 

  - ``same residue as (charged and within 5 of resname AP5)``
  - use representation *licorice*, color: name for the residues, make ligand
    VDW.
  - Which side chains make contact with the ligand?
  - What have they got in common? (Tip: try out color: restype)

- water

  - show crystal water oxygens as VDW or licorice (small spheres)
  
.. _`course directory`:
   https://becksteinlab.physics.asu.edu/pages/courses/2016/PHY542/practicals/vmd/files/
.. _1AKE: http://www.rcsb.org/pdb/explore/explore.do?pdbId=1AKE
.. _1AKE pdb: http://doi.org/10.2210/pdb1ake/pdb