Practical Macromolecular 3D Structure Visualization & Structural Bioinformatics
A One-Day Course

Israel Structural Proteomics Center and Bioinformatics & Biological Computing
Weizmann Institute of Science, Rehovot, Israel
Room changed due to large number of participants: Classroom #5, Ruthie and Samy Cohn Building
Laptop computer now required: no computers can be provided in this room.

9:00 AM - 12:30 PM, 1:30 PM - 5:00 PM, Wednesday April 2, 2008.

Thanks to Joel L. Sussman, Jaime Prilusky, and Hershel Safer for hosting this course.
Thanks to Irit Orr, Rotem Sertchook, and Eran Hodis for assistance.

Lead Instructor: Eric Martz, Ph.D.
Principal author of FirstGlance in Jmol and Protein Explorer - Prof. Emeritus, Univ. Mass. 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!

    Try Out Molecular Exploration in 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
    Quick comparisons with other programs you've heard about.

  4. Terminology: "visualization" vs. "modeling".

    Web Browser Software:
  5. 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 ( 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.
  6. 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, 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.
  7. Others..     Comparison of FirstGlance in Jmol vs. Protein Explorer.

    Stand-Alone Software:
  8. 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. Polyview-3D offers a user-friendly form for making images with PyMol.
  9. RasMol: Best available from 1993-1997 and still widely used. User friendliness: poor (but see user interface RasTop). Documentation: good. Free and open source.
  10. DeepView also known as Swiss PDB-Viewer: Powerful modeling capabilities (see Molecular Modeling below). User friendliness: poor. Documentation: good. Free but proprietary source.
  11. 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.

  12. Central Dogma: DNA mRNA Protein.     DNA structure in Jmol
  13. 20 Amino acids
  14. Polypeptide chain geometry and steric restrictions
  15. Covalent and non-covalent chemical bonds
    Typical hydrogen bond within a protein: hydrogen donor atom is covalently bonded to hydrogen; acceptor atom is not.
  16. Secondary Structure
  17. Folding: hydrophobic collapse
  18. Protein folds cannot be reliably predicted from sequence alone (using ab initio theory).

    FirstGlance in Jmol: A Simple Viewer for Any Macromolecule

  19. 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

      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
  20. 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 (see snapshot at right)
  21. 1BKX: More Views, Non-standard amino acids
  22. 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.

  23. Slides Covering:     (from
    Finding published molecules of interest
    Each participant should find a molecule of personal interest.

  24. Browsing Molecules
  25. Searching for Molecules
    Evolutionary Conservation: ConSurf
      Major histocompatibility protein (MHC I 2VAA): evolutionary conservation and variability from ConSurf. More..

  26. Identifying Functional Sites & Seeing Protein Evolution:

    Author Molecular Tutorials Easily: Proteopedia.Org

  1. Proteopedia.Org

    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 use 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)
  3. Save any molecule you see!

    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. BioMolecular Explorer 3D: Molecules for High School

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

  8. Bird Flu: N1 vs. Tamiflu Lesson Plan:
  9. MolVisIndex.Org: World Index of Molecular Visualization Resources
  10. Jmol Tutorial-Authoring Template
  11. Animations / Morphs: Conformational Changes

    Molecular Modeling (Time Permitting, or Later Private Sessions)

  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

  13. 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.

  14. Homology (comparative) modeling: Introduction.

Keep in touch! n