4-Day Macromolecular Visualization Course
University of Barcelona

April, 2001 - Eric Martz (emartz@microbio.umass.edu) and Gabriel Pons (gpons@bellvitge.bvg.ub.es)

Rationale: In this day of exploding bioinformatics information from genomics and proteomics, it is ever more important to be conversant with macromolecular three-dimensional structure, and how it relates to protein and nucleic acid function and rational drug design. This workshop will enable participants to find published molecular structure data, and visualize and interpret 3D molecular structure. Participants will be enabled to incorporate computer visualization of protein, DNA, and RNA into their teaching and research.

Software: The central tool for this workshop is Protein Explorer (www.proteinexplorer.org). Protein Explorer is free, operates on Windows or Macintosh (also linux), and is much easier to use, yet much more powerful than RasMol. Protein Explorer has been adopted for visualization of macromolecular 3D structure by the Protein Data Bank (www.pdb.org).

Level & Pace: This workshop is designed for educators and biological scientists familiar with basic biochemistry, but with no previous molecular visualization software experience. It progresses rapidly to powerful tools that will be of interest to researchers, including specialists in protein structure and bioinformatics. Experienced participants are encouraged to work at their own speed, ahead of the group -- there is plenty of power in Protein Explorer to discover!

Hyperlinks: To click the hyperlinks below, go to this document on the web,


Tuesday April 24. Basics. How to use Protein Explorer to visualize structural features of proteins and nucleic acids.
Observations may be recorded on a form provided.

  1. Use of the mouse to rotate the molecule; clicking to identify atoms.
  2. Identifying and becoming familiar with the computer representations for chains, backbones, disulfide bonds, solvent, and ligands.


  3. Selecting, emphasizing, and hiding portions of the molecule.
  4. Zooming, centering.
  5. Backbone, trace, cartoon, stick, ball and stick, spacefill to van der Waals radii.
  6. Coloring by element (Corey, Pauling, Koltun color scheme).
  7. Coloring cartoons by secondary structure.
  8. Identifying the amino and carboxy termini (5', 3' ends): N->C Rainbow (Group) color scheme.
  9. Interpreting the distribution of hydrophobic, polar, and charged residues (Polarity color schemes).
  10. Coloring to distinguish A, T, G, C, U. How to distinguish DNA from RNA.
  11. Coloring by disorder: temperature factor coloring.


  12. Protein Explorer's Sequence display.
  13. Protein Explorer's clickable Seq3D

  14. Free time to review and explore.

Wednesday April 25: Finding molecules of interest. Exploring and interpreting their structures. Animations.
Observations may be recorded on a form provided.

  1. Overview of origin, nature, and limitations of molecular structure data (X-ray crystallography, nuclear magnetic resonance).
  2. The Protein Data Bank
  3. Finding molecules of interest.
  4. Getting information about your molecule.
  5. Animations.

  6. Free time to explore participant's molecules.

Thursday April 26: Contact surfaces reveal noncovalent bonds. Cation-pi interactions and salt bridges. Coloring a 3D protein by conservation/mutation from a multiple protein sequence alignment (MSA3D).

  1. Contact surfaces. Example: Gal4 contacting DNA (1d66), showing:
  2. Visualizing cation-pi interactions and salt bridges.
  3. Preferences in Protein Explorer.

  4. Demonstration of Protein Explorer's MSA3D.
  5. Building a multiple protein sequence alignment.
  6. Locating regions of conservation or mutation with Protein Explorer's MSA3D.

  7. Free time to review and apply new methods to your molecule.

Friday April 27: Optional day (attendence not required) for individual work, or topics chosen by those attending.
Use what you've learned. Possible new topics:

  1. Hydrogen bonds.
  2. The Noncovalent Bond Finder.
  3. Introduction to using the RasMol/Chime Command Language.

  4. Building a web page with hyperlinks to Protein Explorer that prespecify molecules for your teaching or research.
  5. Ready-to-use tutorials in Chime for teaching
  6. Rolling probe surfaces and molecular electrostatic potential coloring.

  7. Searching by structure without reference to sequence:
  8. Aligning two or more chains or molecules, and how to view the alignment.
  9. Modeling: mutation, homology modeling, crystallographic contacts.
  10. Building Chime presentation websites.

  11. Keep in touch!

  12. Free time for individual work.

Example Molecules: PDB ID Codes
For ready-made tutorials, see the World Index by subject/molecule name.
*Antibody (Fab-lysozyme) 1fdl
*Antibody (intact IgG) 1igt
-Bacteriorhodopsin 1c8r
-Capsid, rhinovirus, intact rhino-ca
-EF hand, morph reco_ef2***
*Hemoglobin, oxy 1hho, 1hho.mmol*
*Hemoglobin, deoxy 2hhd
*Hemoglobin, sickle 1hbs
-Hemolysin ("mushroom") 7ahl
-HIV protease-inhibitor 1ohr
*Major Histocompatibility I (with virus peptide) 2vab
*Major Histocompatibility II (with virus peptide) 1dlh
-Nucleosome-DNA 1aoi
-Potassium Channel 1bl8
-RNA Polymerase, T7 1qlv
* SV40 capsid assembly
-T cell receptor 1sbb
* See ready-to-use tutorial(s) on this molecule at the World Index.
** Get mmol files from Probable Quaternary Structures, msd.ebi.ac.uk/Services/Quaternary/quaternary.html
*** Also available on PE's Animations page.

Collaborations are invited that use Protein Explorer to display information about macromolecular structure, particularly information which may be the result of your research.