3-Day Macromolecular Visualization Course
University of Massachusetts, Amherst

June 11, 13, 15, 2001 - Eric Martz (emartz@microbio.umass.edu)
with Wayne Decatur and Kelcy Newell.
Chemical Engineering Computer Lab, Lederle GRC Rm. 201/203.
9:00 AM to 5:00 PM each day (break for lunch, informal coffee breaks).

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!

Monday June 11. 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. (Cf. 104d)
  11. Coloring by disorder: temperature factor coloring.


  12. Protein Explorer's clickable Seq3D

    Crystallography, NMR, Finding Molecules of Interest

  13. Overview of origin, nature, and limitations of molecular structure data (X-ray crystallography, nuclear magnetic resonance).
  14. The Protein Data Bank
  15. Finding molecules of interest.

    Oligomers, Single Chains, & Other Information about Your Molecule

  16. Getting information about your molecule.

Wednesday June 13: Introduction to homology modeling and submission of sequences. 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).

    9:00-10:00 Homology Modeling
  1. Introduction to homology modeling.
  2. Submission of sequences to SWISS MODEL.

    10:00-17:00 Protein Explorer, continued.

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

  6. Demonstration of Protein Explorer's MSA3D.
  7. Building a multiple protein sequence alignment.
  8. Locating and coloring regions of conservation or mutation with Protein Explorer's MSA3D.

Friday June 15: Animations, structure searching and alignments. DeepView: Constructing models with mutations, and homology modeling. Participants' requests.

  1. Animations.

  2. Searching by structure without reference to sequence: (Try the bacterial cell division protein 1FSZ§.)

  3. Aligning two or more chains or molecules, and how to view the alignment.

  4. Modeling: mutation and homology modeling in DeepView.

    The following topics could be discussed on request, time permitting.

  5. Hydrogen bonds.
  6. The Noncovalent Bond Finder.
  7. Introduction to using the RasMol/Chime Command Language.
  8. Rolling probe surfaces and molecular electrostatic potential coloring.

  9. Building a web page with hyperlinks to Protein Explorer that prespecify molecules for your teaching or research.
  10. Ready-to-use tutorials in Chime for teaching
  11. Building Chime presentation websites.

    Keep in touch!

Example Molecules: PDB ID Codes (Enter codes into Bare Explorer)
For ready-made tutorials, see the World Index (molvisindex.org) by subject/molecule name.
-Acetylcholinesterase w/ inhibitor 1vot
-Alpha hemolysin transmembrane heptamer 7ahl
*Antibody (Fab-lysozyme) 1fdl
*Antibody (intact IgG) 1igt
- ATP (with double bonds)
-Bacteriorhodopsin 1c8r
-Calcineurin (ser/thr phosphatase)
  w/ FKBP, FK506 1tco
-Calcium transporting ATPase, transmembrane
  & 3 soluble domains 1eul
- Crystal of NaCl
  (from Young/Mehl Crystals)
-EF hand, morph rv_mgef2***
*Hemoglobin, oxy 1hho, 1hho.mmol*
*Hemoglobin, deoxy 2hhd
*Hemoglobin, sickle 1hbs
-Hemolysin ("mushroom") 7ahl
-HIV protease-inhibitor 1ohr
* Lipid bilayer with gramicidin channel (theoretical
  model, Crouzy et al, Biophys J 67:1370, 1994)
*Major Histocompatibility I (with virus peptide) 2vab
*Major Histocompatibility II (with virus peptide) 1dlh
-Nucleosome-DNA 1aoi
-Potassium Channel 1bl8
*Ribosome w/ 3 tRNA's, mRNA 1gix,1giy
  (or complete ribosome backbone).
-RNA Polymerase, T7 1qln
-T cell receptor 1sbb
-Transfer RNA, Phe 1tra
-Virus, rhino, intact capsid rhino-ca
  (from Bock/UWisc Virus Visualization)
- Virus, SV40, capsid model
  (1 atom/chain, in bare Chime)
* Virus, SV40 capsid assembly (Tutorial)
* See ready-to-use tutorial(s) on this molecule at the World Index (molvisindex.org).
** Get mmol files from Probable Quaternary Structures, msd.ebi.ac.uk/Services/Quaternary/quaternary.html
*** Also available on PE's Animations page.
§ Example 1FSZ thanks to Gabe McCool. See also his presentation on 1FSZ in PE.