2-Day Macromolecular Visualization Course
Wyeth Pharmaceuticals, Cambridge MA USA

July 9/10 & 11, 2003 - Eric Martz (emartz@microbio.umass.edu)
with Rajiv Chopra, Cuihua Liu and Diana Ditmore
Room 6002, 150 Cambridge Park Drive
10:30-5:00 Wednesday, 9:00 to 5:00 Thursday & Friday (break for lunch, coffee breaks).
This document is on-line: http://www.umass.edu/molvis/workshop/wyeth03.htm

Rationale & Goals: 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 drug design. This workshop will enable participants to find published macromolecular structure data, and visualize and interpret 3D macromolecular structure. Participants will be enabled to incorporate computer visualization and qualitative analysis of 3D structure of protein, DNA, RNA, and protein-ligand interactions into their 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) and several other bioinformatics resources.

Level & Pace: This workshop is designed for researchers familiar with basic biochemistry, but with no previous molecular visualization software experience. It progresses rapidly to powerful tools that will be of interest to 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 to discover within Protein Explorer and its links to other resources!

First Day, July 9 or 10. Basics. How to use Protein Explorer to visualize structural features of proteins and protein-ligand interactions.

    Netscape 4.8 is best, but Internet Explorer is OK.
    Go to www.proteinexplorer.org


  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.

    Features (PE Alpha version only)

  3. Understanding and using information provided in the PDB file header by the authors of the structure.
  4. The Help/Index/Glossary (green for "go"), a major component of PE's knowledge base.


  5. Selecting, emphasizing, and hiding portions of the molecule.
  6. Selecting arbitrary atoms/chains/residues by clicking on them.
  7. Saving/recalling selected sets.
  8. Zooming, centering.
  9. Backbone, trace, cartoon, stick, ball and stick, spacefill to van der Waals radii.
  10. Coloring by element (Corey, Pauling, Koltun color scheme).
  11. Coloring cartoons by secondary structure.
  12. Identifying the amino and carboxy termini (5', 3' ends): N->C Rainbow (Group) color scheme.
  13. Interpreting the distribution of hydrophobic, polar, and charged residues (Polarity color schemes).
    1. Potassium channel: 1bl8. Trp prefers lipid-water interface.
    2. Gramicidin in a lipid bilayer: bilagram.pdb
  14. Coloring to distinguish A, T, G, C, U. How to distinguish DNA from RNA. (Cf. 104d)
  15. Coloring by disorder: temperature factor coloring.

    Global Protein Structure Issues

  16. How are 3D macromolecular structures obtained? Crystallography, NMR, and homology modeling.
  17. What fraction of the human proteome has known structure? A few percent.
  18. Is Structural Genomics the answer? Not in the next few years.
  19. Intrinsicially unstructured proteins:

  20. Finding published molecules of interest:
    1. Atlas of MacroMolecules: molvis.sdsc.edu/atlas/atlas.htm
    2. PDB at a Glance: cmm.info.nih.gov/modeling/pdb_at_a_glance.html


    3. PDB Lite: www.pdblite.org
    4. SearchFields at the Protein Data Bank www.pdb.org
    5. Prilusky's OCA http://bioportal.weizmann.ac.il/oca-bin/ocamain


  21. PE Site Map (PE Alpha version only)
    Residue ranges for the CDR's in the Fab of 1FDL are:
      Heavy chain (H)
    • CDR1: 31-35
    • CDR2: 50-66
    • CDR3: 98-105

      Light chain (L)

    • CDR1: 24-34
    • CDR2: 50-56
    • CDR3: 90-97
    For shortcuts and tricks in using PE to visualize epitope-paratope contacts, see step #35 in this Antibody Structure Tutorial.
  22. OPTIONAL: Protein Explorer's Sequence display - finding gaps
    1. Insertions and non-physical gaps: 1igt.
    2. Physical gaps: 2ace, 1fod.
    3. Microheterogeneity: 1cbn.
  23. Protein Explorer's clickable Seq3D
    1. Sequence to 3D structure mapping.
    2. Finding all instances of one amino acid (e.g. cysteine).
    3. Selecting and coloring an arbitrary range of residues (see example in box at right).

  24. Noncovalent Bonds: Contact surfaces. Example: Gal4 contacting DNA (1d66), showing:
    1. Sequence specific recognition DNA bases by zinc finger domain of protein
    2. Hydrophobic protein-protein interaction
    3. Nonspecific charge interactions at DNA backbone phosphates

Second Day - Friday July 11: Specific Oligomers, Evolution/Conservation, Animations of conformational changes, Advanced features, Participants' requests.

    External Resources (via PE Site Map in Alpha version; via Mol Info in PE Beta)

    1. Probable Quaternary Structures (Specific Oligomers)
    2. Conserved Regions (Evolution: ConSurf)
    1. Crystal Contacts
    2. Fewer or Single Chains
    3. Model Quality (& examples of errors in published PDB files)
    4. RCSB's Structure Explorer
    5. NCBI's Entrez Structure

  3. Animations.
    1. Multiple-model NMR PDB files: simulation of thermal motion.
    2. Morphs of conformational changes.

  4. Protein Comparator.
  5. Preferences in Protein Explorer.
  6. Aliases for RasMol/Chime commands.

Additional topics by request, time permitting (or to explore on your own):
  1. Visualizing cation-pi interactions and salt bridges (QuickViews, DISPLAY)
  2. QuickViews Plus (scroll down in the QuickViews frame).
    1. Example: Display contacts to lysozyme by Fab in 1FDL, then overlay a cartoon display of all protein. Color the cartoon by chain, then by structure.

    Advanced Explorer

  3. The Noncovalent Bond Finder
  4. Rolling probe surfaces and molecular electrostatic potential coloring
  5. Including ligands in displays of cation-pi interactions and salt bridges

  6. Searching by structure without reference to sequence: (Try the bacterial cell division protein 1FSZ§.)
    Structure is more conserved than sequence! (Chothia et al., 2003; Precis)
    1. Shindyalov & Bourne's Combinatorial Extension cl.sdsc.edu/ce.html
    2. NCBI's Vector Alignment Search Tool (VAST) www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml

  7. World Index of Molecular Visualization Resources molvisindex.org
    1. Tutorials on hundreds of specific macromolecules
    2. Tools for creating tutorials
    3. Deutsch? ¿Español? Français? Italiano? Português?
    4. SwissPDB-Viewer Resources
    5. Sources of atomic coordinate (PDB) files (metabolites, inorganic crystals, lipid micelles, etc.)
    6. EMail Lists
    7. Galleries
    8. Software

  8. Martz Chime Resources www.umass.edu/microbio/chime
    1. Amino Acid Quizzer
    2. DNA, Hemoglobin, Antibody, MHC
    3. Lipid Bilayers and Gramicidin Channel
    4. IR Spectra with animated vibrations
    5. Protein Morpher
    6. Toobers in Science Education
    7. History of Visualization of Biological Macromolecules
        Where did Chime come from? What about Fred's Folly and Byron's Bender? See early computer images, physical models including the latest by computer-driven laser-powered rapid-prototype engineering, and the latest molecular sculpture.
    8. Knots in Proteins

  9. Morphing conformational changes to view as animations in PE: see Protein Morpher.

  10. Homology (comparative) modeling: Introduction.

  11. Aligning two or more chains or molecules, and how to view the alignment.
    1. The CE site cl.sdsc.edu/ce.html will align any two protein chains quickly and easily (but hetero atoms are discarded).
    2. DeepView www.expasy.ch/spdbv/mainpage.html can align anything (one or more than one chains), selecting any subset of atoms for the alignment (other atoms following), and retaining hetero atoms. The results can be saved as a PDB file, but will need manual editing to separate models with MODEL [N] and ENDMDL records so that Protein Explorer can distinguish the models. Gale Rhodes provides a DeepView tutorial: click on the section Comparing Proteins.

  12. Mutating your model:
    1. Changing residue sidechains and rotamer minimization with DeepView
    2. DeepView beginners should start with the superb Molecular Modeling for Beginners by Gale Rhodes, Univ. Southern Maine.
    3. DeepView resources are indexed at molvisindex.org.

  13. Building a web page with hyperlinks to Protein Explorer that prespecify molecules for your teaching or research. Methods.

  14. Presenting molecular structures in Chime websites:
    1. A well tested and debugged template (but will soon be obsolete) www.umass.edu/microbio/chime/prsswc/template.htm
    2. Script recorder (under development) so you can play back views acheived in PE.
    3. Examples of Presentations in Protein Explorer (PIPE) www.umass.edu/microbio/chime/pipe. Support for PIPE is not yet released.

Keep in touch!

* 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.