Practical Macromolecular 3D Structure Visualization & Structural Bioinformatics
A One-Day Workshop -- Osaka University, Japan

Friday, May 9, 2014, 9:00 - 17:00, Nanobiology Building, Room 308.
Bringing A Laptop Computer Is Encouraged (details, registration)

Host and Co-Instructor: Keiichi Namba.
Thanks to Tohru Minamino and Kana Moriya Nishimura.
Teaching assistants Shoko Toma, Takuma Fukumura, and Yurika Yamada.

Eric Martz, Ph.D.: Lead Instructor.
Principal author of FirstGlance in Jmol; co-developer of Proteopedia and the ConSurf Server.
Professor Emeritus, University of Massachusetts, Amherst --

This document is on-line:

Please see the Course Announcement

Objectives: Participants will use highly user-friendly software for visual investigation of 3D molecular structures of proteins, nucleic acids, and their interactions with each other and with ligands, substrates, and drugs; and of protein evolutionary conservation. Hands-on experience will be largely with molecules of each participant's choosing. Participants will learn how to create publication-quality molecular images, rotating molecules in Powerpoint slides, and custom on-line rotating molecular scenes in Jmol.

Software: All software in this course is free, and works on Windows, Mac OS X, or linux.

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!

        Startup: Installing and Enabling Java

  1. Installing and Enabling Java

    You can see molecules without Java, using JSmol. in the two main tools of this course: Proteopedia.Org and FirstGlance.Jmol.Org. For most other sites that display molecules in Jmol, you will need to install and enable Java.

    Java will also make Proteopedia and FirstGlance run faster and smoother.

    In this course, we will use all 3 forms of Jmol that work in web browsers: See four forms of Jmol.

    1. Follow these instructions for installing/updating and enabling Java.
    2. TA's and Instructors will help you!
    3. Can you see this Gal4:DNA complex with Java (Jmol_S)?

    4. If you got Java to work, use the Preferences tab in FirstGlance to make Java the default. Then this link to Gal4:DNA should use Java (Jmol_S).

    5. Some sites use an older, unsigned Jmol Java applet. An example is this explanation of Protein Secondary Structure. Can you see the molecule? Make sure to Enable Unsigned Java Applets for this website. Later in the course, you may want to enable other websites.

    Get Started Individually At Proteopedia

    Before we start the next section together, while the group is getting organized ...

  2. Go to Proteopedia.Org and take a look around.
  3. Try searching for some of your favorite molecules.

  4. Workshop Overview

  5. Workshop Overview (Powerpoint Slides)

  6. Proteopedia.Org Part I
    Protein Data Bank & PDB Codes
    Crystallographic Resolution

  7. The Protein Data Bank (PDB) -- World Wide: -- USA:RCSB -- Japan:PDBj -- Europe:PDBe
  8. PDB identification code examples:

  9. Proteopedia.Org:
    1. Main page: green links connect text to molecular scenes.
    2. Molecules explained by users. Example:
    3. Random articles or molecules.
    4. Identify by touching (shows a "hovering" report).
    5. Pop up any molecular scene.
    6. Save any page for off-line projection.
    7. Explanations of structural biology terms and concepts, e.g. asymmetric unit, Protein Data Bank, hydrogen bonds, temperature value, etc. all at About Macromolecular Structure.
    8. Pages in Japanese, Chinese, Arabic, Turkish, Russian, etc.
    9. Has a page for each of the >90,000 PDB entries, showing it in Jmol.
    10. Title and Abstract.
    11. Shows resolution (see below).
    12. Link to FirstGlance in Jmol on every PDB code page.

  10. X-Ray Crystallography and Resolution
    Finding published molecules of interest
    Each participant should find a molecule of personal interest.

  11. Searching for Molecules
    Get the amino acid sequence of your protein. You could find it in UniProt.Org.
    Use the sequence of your protein to search for 3D structures.
    Write down the PDB code(s)!
    Not for sequence searching, but sometimes useful.
  12. Can't find an empirical 3D model for your sequence?
  13. Browsing Molecules: Good places for students to choose molecules for class assignments.

    Review of Protein Chemistry and Structure.
    We'll do this quickly. The links are for participants who are educators.

  14. Central Dogma: DNA mRNA Protein.     DNA structure in Jmol / Estructura del ADN
  15. 20 Amino acids
  16. Polypeptide chain geometry and steric restrictions
  17. Covalent and non-covalent chemical bonds
  18. Typical hydrogen bond within a protein: hydrogen donor atom is covalently bonded to hydrogen; acceptor atom is not. In proteins, donor-acceptor distance can be 2.5 to 3.5 Å.
  19. Secondary Structure
  20. Folding: hydrophobic collapse
  21. Protein folds cannot be reliably predicted from sequence alone (using ab initio theory).

  22. Evolutionary Conservation: ConSurfDB & ConSurf
      Major histocompatibility protein (MHC I 2VAA): evolutionary conservation and variability from ConSurf. More..

  23. Identifying Functional Sites & Seeing Protein Evolution:
    1. At 2vaa in Proteopedia, show Evolutionary Conservation.
    2. Also check 4enl (enolase), and 1qdq (cathepsin B, noting the conserved surface Gly, Pro -- Why?).
    3. ConSurf's Mechanism: Simplified;   Details;   Technical.
    4. Note the Caveats in Proteopedia's Evolutionary Conservation.
    5. There are two ConSurf Servers:
      1. ConSurfDB (DataBase)
        • Pre-calculated for every chain in the PDB.
        • Results are shown in Proteopedia.
        • Multiple Sequence Alignments typically include proteins of more than one function, so some conservation may be hidden.
      2. ConSurf
        • Set up each job by hand.
        • Easily select sequences for a single protein function, revealing conservation (within a family of proteins performing a single function) that may be hidden in ConSurfDB.

    6. If you have a serious interest in the conservation in your protein,

FirstGlance in Jmol: Easy Visualization of Any Macromolecule

Terminology: "visualization" vs. "modeling". (Light modeling tools)

  1. There are two ways to get FirstGlance:
    1. Go to Proteopedia.Org, enter the PDB code in the search slot. Below the molecule, under Resources, click on the link to FirstGlance.
    2. Go to FirstGlance.Jmol.Org and enter the PDB code. (Or go directly to
    3. Preferences are independent. If you want to use Java, you need to set that preference at BOTH sites.

  2. Explore 1izh in FirstGlance.
    1. Introduction
    2. Molecule tab
      1. Year, Method.
      2. Resolution.
      3. Free R
      4. Chain details.
      5. Sequences: Crystallized vs. Full Length. Alignment at UniProt (1d66).
      6. Abstract.
      7. Citations.
      8. Text contents of the PDB file.
    3. Views tab
      1. Top 3 rows of views:
        Secondary Structure / Cartoon / N->C Rainbow
        Composition / Hydrophobic/Polar / Charge..
        Local Uncertainty (2vaa) / Vines / Thin Backbone
      2. Buttons.
        Ligands+ / Water / Slab
      3. 1pgb: Hydrophobic core: Hydrophobic/Polar, then Slab.
      4. 1pgb: Amphipathic helices and strands. (In FirstGlance, Hide a range (the helix or strand) then invert.)
      5. Compare with 1bl8 or 7ahl.
    4. Resources tab
      1. See lipid bilayer boundaries.
    5. 1pgb: Tools tab with Views.
      1. Salt bridges.
      2. Distances.
      3. Salt bridges in Charge View.
      4. Charges with Slab on.
      5. Sidechain distributions in Vines View.
      6. Find (review Chart of AA): PHE, (VAL,LEU,ILE), ASN, THR

    Contacts: Anti-Alzheimer's drug analog (*) interaction with acetylcholinesterase (Dvir et al./Sussman, 2002).

  3. Explore 2mcg in FirstGlance.
    1. Tools tab
      1. Disulfides/S/Se

  4. Explore 3onz in FirstGlance. (Letter O not numeral zero!)
    1. Molecule tab
      1. Two chains, not sequence identical.
      2. Missing residues.
      3. Ligands+ and non-standard residues
    2. Views tab
      1. Ligands button; smaller ligands.
      2. Hide (chain, toluene, isolated His).
      3. Contacts
      4. Non-covalent interactions for HEM in chain A (blue chain).
    3. Resources tab
      1. Biological unit.

    Introduction to Structural Bioinformatics and Genomics
    Educators: You are welcome to use the slides linked below, or to adapt content from them into your own slides.

  5. Slides Covering:     (from

    Proteopedia.Org (Part II): Authoring

  1. Add Molecular Scenes and Content to Proteopedia.Org
  2. Its a wiki: you or your students can add pages or customized molecular scenes in Jmol.
  3. Great for journal supplementary materials or research group websites as well as molecular structure tutorials and student reports.
  4. Protect your pages from being changed by anyone else, e.g. Nucleosomes (protected).
  5. An easy Scene Authoring Tool attaches your customized views to Green links.
  6. This is, by far, the easiest place to create molecular tutorials, e.g. Nucleosomes (publically editable).
  7. Sandboxes (enough for your entire class!) allow students to try authoring temporary molecular scenes -- without individual accounts. Screenshots can document student work. See Teaching Strategies Using Proteopedia.

    Animated Powerpoint Slides and Publication-Quality Images: Polyview-3D
      PowerPoint-Ready Animation from Polyview-3D. Click on the image for a larger view and explanation.

  1. Make Animated PowerPoint Slides and Publication-Quality Images easily with Polyview-3D.

We won't have time to go through the following resources in detail, so the links and information below are provided mostly for you to use, if you wish, after the workshop.
      Potassium channel (1R3J) showing membrane surface planes (from OPM).

  1. FirstGlance -> Resources Tab: Orientations of Proteins in Membranes.

    Jmol in Scientific Journals:

  2. Interactive 3D Complements in Proteopedia: "Supplementary Materials"

  3. FirstGlance in Jmol: Look for the 3D View links in Nature Structural and Molecular Biology

  4. "Jmolized" Interactive 3D Journal Figures:
    Educational Resources

  5. Tutorials disponible en español at MolviZ.Org (Estructura del ADN; Modelo de bicapa lipídica y canal de gramicidina; Estructura del agua: enlaces de hidrógeno) and BioModel (Estructura de proteínas; Glúcidos, Lípidos, Vitaminas, Aminoácidos, Hélice alfa, Hebra beta, Lisozima, Nucleósidos, ADN, ARN, et al.)

  6. HighSchool.MolviZ.Org: Resources for High School Teachers.
  7. BioMolecular Explorer 3D: Molecules for High School.
  8. Molecular Workbench (from Concord Consortium): Activities for High School Students with built-in assessment and reporting.

    If this image is not moving, reload the page!
    Morph of the lactose repressor bending DNA as it recognizes the operon. More..
  9. Teaching Scenes, Tutorials, and Educators' Pages in Proteopedia, including Molecule of the Month.
  10. Teaching Strategies Using Proteopedia.
  11. MolviZ.Org: Martz Central: Resources for High School, College, and Researchers.

  12. Bird Flu: N1 vs. Tamiflu Lesson Plan:
  13. Animations / Morphs: Conformational Changes (see MOVIE at right).

    Molecular Modeling (Time Permitting, or Later Private Sessions)

  14. 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

  15. Structural Alignment of two or more chains or molecules, and how to view the alignment.
  16. Homology (comparative) modeling:

Keep in touch!