Practical Macromolecular 3D Structure Visualization & Structural Bioinformatics
A Two-Day Workshop -- University of Massachusetts, Amherst

Wed & Thurs, May 26-27 and (duplicate workshop) June 2-3, 2010, 9:00 AM - 1:00 PM, Integrated Sciences Building 321
Bringing A Laptop Computer Is Encouraged (details, registration)
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. Workshop Overview

  5. Workshop Overview (Powerpoint Slides)

  6. Proteopedia.Org (Part I)

  7. The Protein Data Bank (PDB) -- World Wide: -- USA:RCSB -- Japan:PDBj -- Europe:PDBe
  8. PDB identification code examples:
    • 1hho oxy-hemoglobin.
    • 1d66 Gal4 transcriptional regulator bound to DNA.
    • 104d DNA/RNA hybrid.
    • 1bl8 potassium channel.

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

  10. X-Ray Crystallography and Resolution
    • 85% of models in the PDB come from X-ray crystallography experiments.
    • X-ray crystallography produces an electron density map (EDM).
    • The average uncertainty in an EDM is measured by its Resolution in Ångstroms:
      • 1.2 Å Excellent -- backbone and most sidechains very clear. Some hydrogens resolved.
      • 2.5 Å Good -- backbone and many sidechains clear.
      • 3.5 Å OK -- backbone and bulky sidechains mostly clear.
      • 5.0 Å Poor -- backbone mostly clear; sidechains not clear.
      • See the MOVIE.

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

  11. Searching for Molecules
    Best Method: Use the sequence of your protein to search for 3D structures. Write down the PDB code(s)!
    • 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. (Quick for text searching; Not for sequence searching).
      • Or click Advanced Search at pdb.org   Powerful but sometimes difficult to use; help is sometimes inadequate.
        (Good for sequence searching. Offers the most detailed information about hits.)

    • PDBsum   Good for sequence searching. Useful short summaries of hits.
    • OCA   Powerful and straightforward. Good for sequence searching. Useful results table.
    • Proteopedia.Org. One-slot search (no advanced search). (Not for sequence searching). See Help:Searching.
    • PDBLite.org   Simple, one-slot search. Clear help. Good for students searching by name. (Not for sequence searching).

  12. Can't find a structure for your sequence?
  13. Browsing Molecules: Good places for students to choose molecules for class assignments.

    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.

  14. Terminology: "visualization" vs. "modeling".

    Web Browser Software:
  15. 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.
  16. Chime browser plugin.
    1. Windows only! Does NOT work in Mac OS X.     Requires installation.     Was best available 1996-2004, now obsolete.
    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"; has become obsolete due to dependence on Chime.
  17. Others..     Comparison of FirstGlance in Jmol vs. Protein Explorer.

    Stand-Alone Software:
  18. 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.
  19. RasMol: Best available from 1993-1997 and still widely used. User friendliness: poor (but see user interface RasTop). Documentation: good. Free and open source.
  20. DeepView also known as Swiss PDB-Viewer: Powerful modeling capabilities (see Molecular Modeling below). User friendliness: poor. Documentation: good. Free but proprietary source.
  21. COOT (Crystallographic Object-Oriented Toolkit) recently very popular with crystallographers for model-building from electron density maps. Open source (GNU GPL).
  22. 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.

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

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

  32. 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: A Simple Viewer for Any Macromolecule

  1. At 1pgb in Proteopedia.Org, go to Resources: FirstGlance, then in FirstGlance in Jmol, try these controls:
        (Want to explore a downloaded PDB file? Upload it to the main page of FirstGlance: firstglance.jmol.org.)
    1. Introduction
    2. "Missing" Information?
      • Notice that FirstGlance does not show the name of the molecule or its resolution, nor does it give full names of ligands etc.
      • This is because it was designed to supplement a journal article, or a Proteopedia page that already provided such information.
      • However, more information about the molecule is readily available within FirstGlance: Key Resources: and and
    3. Top 2 rows of views (tooltips, automatic help)
    4. Vines (controls in bottom left panel)
    5. Buttons (Ligands+, etc.)
    6. Center Atom

      Contacts: Anti-Alzheimer's drug analog (*) interaction with acetylcholinesterase (Dvir et al./Sussman, 2002).
    7. Reset
    8. More Views
  2. Display 1hho in FirstGlance and explore these views:
    1. Ligands button (full names of ligands are in Proteopedia)
    2. Hide
    3. Find (explain the distributions of gly, pro, ala, glu, phe, viewed one at a time)
    4. Contacts to HEM (see snapshot at right)
    5. Key Resources: Probable Quaternary Structure Server: Specific Oligomers/Biological Units (Example: 1a4f).
  3. 1BKX: Non-standard residues in Proteopedia vs. FirstGlance (under More Views).
  4. 2ACE in FirstGlance: Key Resources:

    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 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.

    • 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. Supplementary Materials in Proteopedia

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

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

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

  10. Teaching Scenes, Tutorials, and Educators' Pages in Proteopedia, including Molecule of the Month.
  11. Teaching Strategies Using Proteopedia.
  12. MolviZ.Org: Martz Central: Resources for High School, College, and Researchers.

  13. Bird Flu: N1 vs. Tamiflu Lesson Plan:
    If this image is not moving, reload the page!
    Morph of the lactose repressor bending DNA as it recognizes the operon. More..

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

  15. Animations / Morphs: Conformational Changes (see MOVIE at right).

  16. 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.


    Molecular Modeling (Time Permitting, or Later Private Sessions)

  17. 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.

  18. Structural Alignment of two or more chains or molecules, and how to view the alignment.
    • 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.

  19. Homology (comparative) modeling:


Keep in touch! n