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

Wednesday June 17 & Friday June 19, 2015.
9:00 AM - 1:00 PM each day, Integrated Sciences Building 321.

Bring Your Laptop Computer, Please!

Taught by Eric Martz, Ph.D.
principal author of FirstGlance in Jmol ( buttons in the journal Nature), MolviZ.Org,
team member of Proteopedia.Org, and coauthor of the ConSurf Server.

This document is on-line:

Please see the Workshop Announcement


Software: All software in this course is free, and works on Windows, Mac OS X, or linux. The major tool is FirstGlance.Jmol.Org, adopted by Nature ( buttons) and other journals and resources.


        Get Started:
            Use the Chrome browser
            Installing and Enabling Java

    Each person please get started:

  1. If you brought your own laptop, you are welcome use it. (iPads will be too slow.)
  2. Use the Chrome browser. If you do not have it, take a few minutes to install it ( (Chrome will be faster/smoother than Safari, and Firefox is even slower for this software. Internet Explorer and Opera are unusably slow with this software.)
  3. In the Chrome browser, go to our syllabus: Workshops.MolviZ.Org. Now you can see this document in your browser.
  4. Go to Atlas.MolviZ.Org.
  5. In the Atlas, choose any molecule deemed Straightforward and click on the link to FirstGlance. After a minute or so to load, you should see a rotating molecule. Have a look around at the information, views and tools in FirstGlance.
  6. If you have any difficulty or the molecule does not appear, or does not rotate, ask for help!

  7. OPTIONAL: Installing and Enabling Java

    You can see molecules without Java, using JSmol, in the primary tool of this course: FirstGlance.Jmol.Org. For some older sites that display molecules in Jmol, or for especially large molecules, you may need to install and enable Java.

    Java will also make FirstGlance run faster and smoother.

    In this course, there are resources that use all of the 3 forms of Jmol that work in web browsers:
    • JSmol (no Java)
    • Jmol_S (signed Java applet)
    • Jmol (unsigned Java applet, deprecated)
    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.

  8. Workshop Overview

  9. Workshop Overview (Powerpoint Slides)

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

  12. PDB identification code examples:

  13. Proteopedia.Org:
    1. Main page: green links connect text to molecular scenes.
    2. Molecules explained by users. Example:
    4. Pages in Chinese, Japanese, Arabic, Turkish, Russian, etc.

  14. X-Ray Crystallography and Resolution
    Finding molecular models of interest
    Each participant should find a molecule of personal interest.

  15. Finding molecular models of interest:
    Each person: please find a 3D model of a molecule related to your research or interests.
    You will use the model that you select for the rest of the workshop.
    How To Find Models:

    Review of Protein Chemistry and Structure.

  16. Central Dogma: DNA mRNA Protein.     DNA structure in Jmol / Estructura del ADN
  17. 20 Amino acids
  18. Polypeptide chain geometry and steric restrictions
  19. Covalent and non-covalent chemical bonds
  21. Secondary Structure
  22. Folding: hydrophobic collapse
  24. Fold does not always equal function: About 10% of proteins are thought to be fully disordered to support their functions, and 40% of eukaryotic proteins have at least one long disordered region. This is termed intrinsic disorder. Examples: 1jsu, 2rrl.

  25. Evolutionary Conservation: ConSurfDB & ConSurf
      Enolase (4enl; a glycolytic enzyme) evolutionary conservation from ConSurf. Catalytic cleft is at the left. More..

  26. Background: see Introduction to Evolutionary Conservation.
    1. Enzyme example: ConSurf-colored sequence -- enolase 4enl in Proteopedia -- 4enl ConSurf Result -- enolase in Wikipedia.
    3. Detail of MSA with color. ConSurf does a much more sophisticated job of calculating evolutionary conservation scores than this simple example!

  27. Identifying Functional Sites & Seeing Protein Evolution:

    1. Go to Proteopedia.Org and enter 4enl in the search slot at left.
    2. Click the load full button to load all atoms. (To improve performance, initially Proteopedia loads only the alpha carbon atoms.)
    3. Look for Evolutionary Conservation and check the checkbox to color each amino acid by evolutionary conservation.
    4. On the less conserved side of the molecule, touch the isolated highly conserved residues to display the amino acid and sequence number. Gly236 and Pro290 are highly conserved. Why?.
    5. Important: Many molecules do not have evolutionary conservation available in Proteopedia. For these, and for homology models, you must calculate the conservation using the ConSurf server.
      1. Go to the ConSurf Server.
      2. Select Amino Acids.
      3. Check YES there is a known protein structure.
      4. Enter the PDB code, or upload your homology model.
      5. Select a chain for analysis. ConSurf can analyze only one chain at a time.
      6. Check NO, you will not be uploading a multiple sequence alignment. (ConSurf will create one for you.)
      7. Leave all parameters at their pre-set defaults. (OPTIONAL: If you want a research grade result, check "Let me select the sequences for the analysis manually out of BLAST results", and see Limiting ConSurf Analysis to Proteins of a Single Function.)
      8. Enter your email address at the bottom of the form (this is important so you don't lose your results). Optionally enter a job title.
      9. Click the button Submit. It may take an hour or more to complete this calculation.
      10. When it is finished, under Final Results, click the link View ConSurf Results with FirstGlance in Jmol.
      11. Example: 4enl result in ConSurf.

    6. ConSurf's Mechanism: Simplified;   Details;   Technical.
    7. Note the Caveats in Proteopedia's Evolutionary Conservation.
    8. There are two ConSurf Servers:
      1. ConSurfDB (DataBase) NOT WORKING IN MAY, 2015
        • Pre-calculated for every chain in the PDB.
        • Results are shown in Proteopedia.
      2. ConSurf
        • Set up each job by hand.

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

FirstGlance in Jmol: Easy Visualization of Any Macromolecule


  1. To start FirstGlance, go to FirstGlance.Jmol.Org and enter the PDB code, or upload your homology model.

    Unusually large models may take a long time to display and be sluggish to manipulate in FirstGlance. For such cases, using Java will enable much better performance in FirstGlance. Java is not needed for most models. Ask the instructor for advice. Here are instructions for Installing and Enabling Java.

  2. Explore 1izh in FirstGlance.
    1. Introduction
    2. Molecule Information 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 / Vines / Thin Backbone
      2. Buttons.
        Ligands+ / Water / Slab
      3. 1pgb: Hydrophobic core: Hydrophobic/Polar, then Slab.
      4. 1pgb: Amphipathic helices and strands. (In FirstGlance, use Isolate.. on each end of a helix or strand.)
          Potassium channel (1R3J) showing membrane surface planes (from OPM). See the Resources tab in FirstGlance.
      5. Compare with the Hydrophobic/Polar View of 1bl8 or 7ahl.
    4. Resources tab
      1. See lipid bilayer boundaries (1bl8 or 7ahl).
    5. 1pgb: Tools tab with Views.
      1. Salt bridges.
      2. Cation-pi interactions.
      3. Distances.
      4. Salt bridges in Charge View (Red sidechain touching blue sidechain).
      5. Charges with Slab on.
      6. Sidechain distributions in Vines View (rings buried; charges on surface).
      7. Find (review Chart of AA): PHE, (VAL,LEU,ILE), ASN, THR

  3. Explore 9ins in FirstGlance.
    1. Tools tab
      1. Disulfides/S/Se

  4. Explore 3onz in FirstGlance. (Letter O not numeral zero!)
    1. Molecule Information 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. Tools tab
      1. Contacts
      2. Non-covalent interactions for HEM in chain A (blue chain).
    4. Resources tab
      1. Biological unit.

  5. Solution Nuclear Magnetic Resonance (NMR)

    Introduction to Structural Bioinformatics and Genomics

  6. Slides Covering:     (from
    Animated Powerpoint Slides and Publication-Quality Images: Polyview-3D

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

    Proteopedia.Org (Part II): Authoring

  1. Add Molecular Scenes and Content to Proteopedia.Org

  8. Jmol in Scientific Journals:

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

  10. FirstGlance in Jmol: Look for the buttons in Nature and Nature Structural and Molecular Biology.

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


  13. HighSchool.MolviZ.Org: Resources for High School Teachers.
  14. Toobers in Science Education!

    If this image is not moving, reload the page!
  17. Teaching Strategies Using Proteopedia.
  18. MolviZ.Org: Martz Central: Resources for High School, College, and Researchers.

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

    Molecular Modeling (Time Permitting, or Later Private Sessions)

  21. Mutating your model:
    1. Changing residue sidechains and rotamer minimization with DeepView.


Keep in touch!