Visualizing structural biology: an interactive introduction
- About this tutorial. Installation. Technical issues and
visualization: the PDB
- Overview of the PDB: what is in it? How to use it?
Starting with PyMOL.
a globular protein: Myoglobin
- Learn about general structures of proteins by exploring
Myoglobin. Explore the basic biochemical properties of the molecule and
find the connections with the actual structure. Get into the
basics of using PyMOL for molecular visualization: mouse controls,
objects and selections.
catalysis: Citrate Synthase
- Understand binding events and enzymatic catalysis at
a structural level. More on mouse controls, objects, and advanced
in PyMOL. Structural superimposition to explore protein dynamics.
- What is particular about membrane proteins, in
non-membrane ones? Study the
Bacteriorhodopsin. Learn the command line input mode of PyMOL. It
has benefits in reproducibility of scenes and automation of
- Protein complexes and DNA - protein complexes are
the first step towards the rational design of new molecules to modulate
cell-function. More complex tasks with the command line. Learn how to
make publication-quality pictures with PyMOL.
- NMR structures vs X-Ray
- Learn differences between X-ray structures
and NMR structures in the PDB. Advanced PyMOL concepts: scripts for
automation of tasks. Movies.
- Self-assessment exercises
This tutorial has been developed at the Molecular
Bioinformatics Laboratory - Heinrich-Heine-Universität Düsseldorf