Macromolecular 3D Structure Visualization & Structural Bioinformatics
Osaka University, Japan
Nanobiology 3F
9:00 AM - 12:30 PM, 1:30 PM - 5:00 PM, Wednesday June 6, 2007.

Thanks to Professor Keiichi Namba for hosting this course.
Thanks to Katsumi Imada, Shigehiro Nagashima, and Kana Moriya, and to
teaching assistants Nao Moriya, Takashi Fujii, and Masafumi Shimada.

Lead Instructor: Eric Martz, Ph.D.
Main author of FirstGlance in Jmol and Protein Explorer - Prof. Emeritus, Univ. Mass. Amherst;
This document is on-line:

Please see the Course Announcement
for level, language, objectives, software, computers, what is not covered.

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 introduce participants to finding published macromolecular structure data, and visualizing and interpreting 3D macromolecular structure using state of the art, free software. Structural bioinformatics servers will be introduced that yield a wide range of types of key information, yet are easy to use. Authoring tools that facilitate preparation of interactive macromolecular structure presentations, such as those at MolSlides.Org, will be demonstrated.

Software: The central tools for this workshop (all free) are:
FirstGlance in Jmol (
and Jmol java applet
  • Operates in all popular browsers and platforms, including Windows, OSX, and linux.
  • Operates on-line only.
  • Open source.
  • Assumes that you are already familiar with basic principles of protein structure.

    Exceptional ease of use. Limited set of "canned" views.

    Adopted by Nature Structural and Molecular Biology and other bioinformatics resources.
    Built upon the free, open source Jmol java applet.
    Protein Explorer in Chime (
    and Chime plugin
    Not used in this workshop because it doesn't work easily on Apple Macs.
  • Operation limited to Windows (including on Intel Mac OS X).
  • Operates on-line or off-line (downloaded).
  • Open source.
  • Much more powerful than FirstGlance: customizable views with surfaces. Extensive explanations and guides help students and researchers understand and interpret. Won the 2003 MERLOT Classic Award in Biology for exemplary online learning resources: "The Protein Explorer has revolutionized the teaching of biology at a molecular level". Able to build MolSlides in Jmol. Adopted by numerous bioinformatics resources. Built upon the free MDL Chime plugin (source code not open).

    Level & Pace: This workshop is designed for faculty, postdocs, research staff and graduate students 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 these tools!

      Take a Look at FirstGlance in Jmol

    1. Go to
    2. Click on the Gallery, and look at any molecule.
    3. Try different views.

      Overview of Popular Molecular Visualization Software

      Web Browser Software:
    4. Jmol java applet.
      1. Nothing to install except java, works in all popular browsers, Windows & Mac OS X.
      2. Free, open source (user community "owns" it), actively developed.
      3. FirstGlance in Jmol ( is a user interface, or "wrapper".
      4. Compare with Jmol by itself, for example under Display Options at the Protein Data Bank.
      5. FirstGlance in Jmol is free, open source.
      6. Best thing for proteins since 2004.     Jmol.Org     Sites Using Jmol (growing rapidly!)     How to Use Jmol By Itself.
    5. Chime browser plugin.
      1. Windows only!     Requires installation.     Best thing available from 1996-2004.
      2. Free, proprietary source (user community has no control), little development since 1998.
      3. How to Use Chime.     About Chime.
      4. Protein Explorer (requires Chime, is a user interface, or "wrapper".
      5. Protein Explorer is free, open source.
    6. Others..

      Stand-Alone Software:
    7. PyMol ( Popular with crystallographers because of its power and gorgeous publication-quality images. User friendliness: poor. Documentation: not up to date. Not free (except for teaching); open source.
    8. RasMol: Best available from 1993-1997 and still widely used. User friendliness: poor (but see user interface RasTop). Documentation: good. Free and open source.
    9. DeepView also known as Swiss PDB-Viewer: Powerful modeling capabilities (see Molecular Modeling below). User friendliness: poor. Documentation: good. Free but proprietary source.
    10. Many others: home pages. Comparison of Protein Explorer, Cn3D, DeepView: Martz, 2003.

      Review of Protein Chemistry and Structure.

    11. Central Dogma: DNA mRNA Protein.     DNA structure in Jmol
    12. 20 Amino acids
    13. Polypeptide chain geometry and steric restrictions
    14. Covalent and non-covalent chemical bonds
    15. Secondary Structure
    16. Folding: hydrophobic collapse
    17. Protein folds cannot be reliably predicted from sequence alone (using ab initio theory).

      FirstGlance in Jmol for Simple Visualization

    18. At, enter 1PGB (a Protein Data Bank identification code). Try these controls:
      1. Introduction
      2. and
      3. Top 2 rows of views
      4. Vines
      5. Buttons
      6. Center Atom
      7. Reset
      8. More Views
        • Cation-pi interactions and salt bridges (1AXI, 1M4U PQS for inter-chain)
        • Distances
        • Color by uncertainty
    19. Explore 1HHO in, especially:
      1. Ligands button
      2. for full names of ligands
      3. Hide
      4. Find (explain the distributions of gly, pro, ala, glu, phe, viewed one at a time)
      5. Contacts to HEM
    20. 1BKX: More Views, Non-standard amino acids
    21. 2ACE:

      Introduction to Structural Bioinformatics

    22. Slides Covering:     (from
      Finding published molecules of interest:

    23. Browsing Molecules
    24. Searching for Molecules
      Structural Bioinformatics Servers with High Value and Ease of Use:

      Major histocompat- ibility protein (MHC I 2VAA): evolutionary conservation and variability from ConSurf. More.. Potassium channel (1R3J) showing membrane surface planes (from OPM). PowerPoint-Ready Animation
      from Polyview-3D. Click on
      the above image for a
      larger view and explanation.
    25. Identifying Functional Sites & Seeing Protein Evolution:
    26. Orientations of Proteins in Membranes.
    27. Make Animated PowerPoint Slides and Publication-Quality Images easily with Polyview-3D.

    28. Save any molecule you see!
    29. All-Atom Contact Analysis (clash scores with hydrogens, model quality): MolProbity. (1CBX)

      Jmol in Scientific Journals:

    30. FirstGlance in Jmol: Nature Structural and Molecular Biology

    31. "Jmolized" Figures: ACS Chemical Biology
      Protein Explorer (more help for beginners than FirstGlance) & MolSlides:

      Use Firefox (or Netscape 7.2 or Mozilla).
      • Internet Explorer cannot save MolSlides, and usually cannot display the Features of the Molecule control panel in Protein Explorer.
      • Netscape 4.8 cannot save MolSlides, but does everything else in Protein Explorer, and it works with older Chime-based websites.
      • Netscape 8 does not work with Protein Explorer.
      Go to ProteinExplorer.Org

    32. Protein Explorer     (8 years of Eric's work!)
      1. FrontDoor (About Protein)
      2. FirstView (explanation of backbone traces, ...)
      3. Features of the Molecule (1E3Q): Resolution, R, Rfree
      4. QuickViews for Custom Views (Seq3D)
      5. Help/Index/Glossary:

    33. What Are MolSlides?
      1. View MolSlide Examples:
      2. Demonstration: Making MolSlides in Jmol     (Procedure)
      3. Importing and Adapting MolSlides

      Educational Resources

    34. BioMolecular Explorer 3D: Molecules for High School

    35. MolviZ.Org: Martz Central: Resources for High School, College, and Researchers.

    36. Bird Flu: N1 vs. Tamiflu Lesson Plan:
    37. MolVisIndex.Org: World Index of Molecular Visualization Resources
    38. Animations / Morphs: Conformational Changes

      Molecular Modeling (Time Permitting, or Later Private Sessions)

    39. 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

    40. Aligning two or more chains or molecules, and how to view the alignment.
      1. The CE site will align any two protein chains quickly and easily (but hetero atoms are discarded, and its database has not been updated since 2001).
      2. DeepView 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.

    41. Homology (comparative) modeling: Introduction.

    Keep in touch! n