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

Monday June 1, 2009, 9:00 AM - 12:30 PM, 1:30 PM - 5:00 PM, Nanobiology 3F
Please Bring a Laptop Computer (details, registration)
Thanks to Professor Keiichi Namba for hosting this course.
Thanks to Katsumi Imada, Shigehiro Nagashima, and Kana Moriya, and to
teaching assistants Tatsuya Ibuki, Akihiro Kawamoto, and Fumiaki Makino.
Lead Instructor: Eric Martz, Ph.D.
Principal author of FirstGlance in Jmol and Protein Explorer; Proteopedia development team member.
Professor Emeritus, University of Massachusetts, Amherst -- emartz@microbio.umass.edu

This document is on-line:
Workshops.MolviZ.Org

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!

    Get Started Individually At Proteopedia

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

  1. Go to Proteopedia.Org.
  2. Take a look around.
  3. Try searching for one of your favorite molecules.

  4. Proteopedia.Org (Part I)

  5. Proteopedia.Org: The best place to start exploring any macromolecule!

  6. Finding published molecules of interest
    Each participant should find a molecule of personal interest.

  7. Browsing Molecules
  8. Searching for Molecules
    • Proteopedia.Org. One-slot search (no advanced search). See Help:Searching.
    • PDBLite.org   Simple, one-slot search. Clear help.
    • OCA (developed by Jaime Prilusky at Weizmann)   Powerful and straightforward.
    • Research Collaboratory for Structural Bioinformatics (RCSB, USA), part of the World Wide Protein Data Bank (wwpdb.org):
      • One-slot search at main page, pdb.org.
      • Or click Advanced Search at pdb.org   Powerful but sometimes difficult to use; help is often inadequate.

    Overview of Popular Molecular Visualization Software
    Quick comparisons with other programs you've heard about.
    We'll skip this section. It is here for reference.

  9. Terminology: "visualization" vs. "modeling".

    Web Browser Software:
  10. Jmol java applet.
    1. Nothing to install except java, works in all popular browsers, Windows, Mac OS X, or linux.
    2. Free, open source (user community "owns" it), actively developed.
    3. FirstGlance in Jmol (firstglance.jmol.org) is a user interface, or "wrapper".
    4. FirstGlance in Jmol designed for journals (used by Nature and others), very easy to use, has limited set of "canned" views.
    5. Compare with Jmol by itself, for example under Display Options at the Protein Data Bank.
    6. Jmol's built-in Menu and Console.
    7. Best thing for proteins since 2004.     Jmol.Org     Sites Using Jmol (growing rapidly!)     How to Use Jmol By Itself.
  11. Chime browser plugin.
    1. Windows only!     Requires installation.     Best thing available from 1996-2004.
    2. Free but proprietary closed source (user community has no control), little development since 1998.
    3. How to Use Chime.     About Chime.
    4. Protein Explorer (requires Chime, proteinexplorer.org) is a user interface, or "wrapper".
    5. Protein Explorer (unlike FirstGlance in Jmol) has extensive help for students, makes customized molecular views, maps sequence to structure.
    6. Protein Explorer is free, open source (but Chime is not), and is technically fussy to get to work.
  12. Others..     Comparison of FirstGlance in Jmol vs. Protein Explorer.

    Stand-Alone Software:
  13. PyMol (pymol.sourceforge.net): 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. Polyview-3D offers a user-friendly form for making images with PyMol.
  14. RasMol: Best available from 1993-1997 and still widely used. User friendliness: poor (but see user interface RasTop). Documentation: good. Free and open source.
  15. DeepView also known as Swiss PDB-Viewer: Powerful modeling capabilities (see Molecular Modeling below). User friendliness: poor. Documentation: good. Free but proprietary source.
  16. COOT (Crystallographic Object-Oriented Toolkit) recently very popular with crystallographers for model-building from electron density maps. Open source (GNU GPL).
  17. Many others: home pages. Comparison of Protein Explorer, Cn3D, DeepView: Martz, 2003.

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

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

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

  27. Identifying Functional Sites & Seeing Protein Evolution:
    1. At 2vaa in Proteopedia, show Evolutionary Conservation.
    2. ConSurf Mechanism.
    3. If the sequences in the ConSurfDB result include too many molecules of different functions (here is how to find out), refine the result with the ConSurf Server: consurf.tau.ac.il. Here are instructions in Proteopedia.

    FirstGlance in Jmol: A Simple Viewer for Any Macromolecule

  1. At firstglance.jmol.org, 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

      Contacts: Anti-Alzheimer's drug analog (*) interaction with acetylcholinesterase (Dvir et al./Sussman, 2002).
    7. Reset
    8. More Views
      • Cation-pi interactions and salt bridges (1AXI, 1M4U PQS for inter-chain)
      • Distances
      • Color by uncertainty:   Thermal vs. static disorder (" temperature").
  2. Explore 1HHO in firstglance.jmol.org, especially:
    1. Ligands button
    2. for full names of ligands. (Easier in Proteopedia.)
    3. Hide
    4. Find (explain the distributions of gly, pro, ala, glu, phe, viewed one at a time)
    5. Contacts to HEM (see snapshot at right)
    6. Probable Quaternary Structure Server: Specific Oligomers.
  3. 1BKX: More Views, Non-standard amino acids
  4. 2ACE:

    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 bioinformatics.proteinexplorer.org)
    • Why do we care about 3D macromolecular structure?
    • What are 3D structure data?
    • Where do 3D structure data come from?
    • How much 3D structure knowledge do we have?
    • What are the primary and derived 3D structure databases?

    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.
  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.

    • Just fill out an easy form, submit it, and (shortly) voila!
    • Center and orient the molecule as you wish.
    • Coloring can be customized. Highlight residues that you specify.
    • Accepts PDB files obtained from ConSurf to color your figures or slides by evolutionary conservation.


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.
    Membranes, Model Quality, etc.
      Potassium channel (1R3J) showing membrane surface planes (from OPM).

  1. Orientations of Proteins in Membranes.
  2. Model Quality/Reliability? Check out MolProbity. (Try 1CBX)
    • Adds hydrogen atoms and does "all atom contact analysis".
    • Flips asparagine, glutamine, and histidine side chains where it reduces atomic clashes.
    • Provides a clash score to compare with other models of similar resolution.
    • Generates an interactive Ramachandran plot.
    • You can download the PDB file with hydrogens and flips.

  3. Save any molecule you see!
    • In Proteopedia, use the pdb link in the blue Coordinates section below the molecule.
    • Jmol: click on the word "Jmol" (below the molecule, lower right corner), then top item on menu, then bottom item on submenu.
      • If the data display in the browser as text: File, Save As, and save as plain text (filename should end ".pdb").
    • Upload saved molecule (PDB file), possibly after deleting unwanted portions with a text editor, to firstglance.jmol.org

    Jmol in Scientific Journals:

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

  5. "Jmolized" Figures: ACS Chemical Biology
    Educational Resources

  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.

  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. MolVisIndex.Org: World Index of Molecular Visualization Resources
    • Includes Tutorials, K-12 Resources, Spanish Resources, and many more.

  14. Jmol Tutorial-Authoring Template
    • Much more complicated to use than Proteopedia.Org, with these advantages:
      • Supports multiple chapters.
      • Text "details" remain hidden during lecture projections.
      • Sliders zoom and slab the molecular view.
      • Compares 2, 3, or 4 synchronized views or molecules at once,
      • See all these in the Demonstration Tutorial.

  15. Animations / Morphs: Conformational Changes

    Molecular Modeling (Time Permitting, or Later Private Sessions)

  16. 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.

  17. 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, and its database has not been updated since 2001).
    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.

  18. Homology (comparative) modeling: Introduction.


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