Molecular Graphics of Macromolecules

Type of instruction




Part of degree program


Recommended in

Semesters 1-4

Typically offered in

Autumn/Spring semester

Course description

1. Methods for generating high-resolution structure of macromolecules I: X-ray diffraction techniques.

2. Methods for generating high-resolution structure of macromolecules II: NMR spectroscopy. Neutron diffraction. Fibre diffraction. Electron microscopy techniques.

3. PDB: the protein structure data bank. Experimentally and in silico derived structures and databases. Structural genomics. The protein structure universe.

4. History of molecular visualization and molecular graphics. 3D literacy. Arts of macromolecules.

5. Hands-on instructions to use RasMol and RasTop molecular visualization programs. Creation of molecular scripts.

6. Introduction and use of Chime and Jmol internet browser plugins. Online macromolecular visualization.

7. Introduction to the Protein Explorer program package. Easier-to-use program for educational and scientific purposes.

8. Other free molecular visualization software I: KineMage and DeepView (Swiss-Pdb Viewer)

9. Other free molecular visualization software II: PyMol and Yasara. Advantages and disadvantages.

10. Other free molecular visualization software III: VMD, MolMol, MolPov, Dino, BallView, Chimera, Astex Viewer, etc (>75).

11. Publication quality molecular graphics: PovRay, 3DRaster. Unix-based graphics programs: MolScript, Midas, O.

12. Animations in molecular graphics. Protein Morpher and ProteinComparator program.

13. Intrinsically disordered proteins. Prediction programs and visualization.

14. Molecular graphics vs. molecular modeling. Ab initio and homology modelling. Swiss-Model, ESyPred3D, SDSC1 and other modelling programs. Molecular dynamics simulations, molecular docking.

  • John K. Gilbert: Visualization in Science Education, Springer Science & Business Media, 2006