Practical Macromolecular 3D Structure Visualization & Structural Bioinformatics
A One-Day Workshop --
Osaka University, Japan
Monday, May 14, 2012, 9:00 - 17:00, Nanobiology 3F.
Bringing A Laptop Computer Is Encouraged
Host and Co-Instructor:
Thanks to Tohru Minamino and Kana Moriya Nishimura.
, 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:
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.
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
Get Started Individually At Proteopedia
Before we start the next section together, while the group is getting organized ...
- Go to
- Take a look around.
- Try searching for one of your favorite molecules.
Workshop Overview (Powerpoint Slides)
Proteopedia.Org Part I: The best place to begin understanding any macromolecule's structure.
Protein Data Bank & PDB Codes
The Protein Data Bank (PDB) --
World Wide: -- USA:RCSB -- Japan:PDBj -- Europe:PDBe
PDB identification code examples:
- 1hho oxy-hemoglobin.
- 1d66 Gal4 transcriptional regulator bound to DNA.
- 104d DNA/RNA hybrid.
- 1bl8 potassium channel.
The best place to start exploring any macromolecule!
- Main Page: green links change the molecular scene.
- Shows, in Jmol, all published macromolecular structures.
Yep, the entire Protein Data Bank! >81,000 models.
- Highlights ligands and
giving their full names.
2oa5, 2dxb, 1m5r)
- Title, Abstract and Journal Citation for each structure.
- Identifies functional groups of amino acids by evolutionarily conservation.
- Links to FirstGlance in Jmol (and other salient
resources) for further
- Save any page for off-line projection.
- Explanations of structural biology terms and concepts, e.g.
asymmetric unit, Protein Data Bank, hydrogen bonds, temperature value,
etc. all at
About Macromolecular Structure.
X-Ray Crystallography and Resolution
- 88% 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
- 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
is the most useful single parameter for assessing overall reliability of a
- Local uncertainty (per atom) can be displayed as
(under More Views.. in FirstGlance in Jmol).
- See also
Quality Assessment for Molecular Models.
Finding published molecules of interest
Each participant should find a molecule of personal interest.
Searching for Molecules
Use the sequence
of your protein to search for 3D structures.
Write down the
- At pdb.org,
click Advanced Search. Choose the Query type
"Sequence Features: Sequence". Paste your sequence in the large box and
click Submit Query.
Powerful but sometimes difficult to use; help is sometimes inadequate.
Offers the most detailed information about hits.
Useful short summaries of hits.
Powerful and straightforward.
Useful results table.
Not for sequence searching, but sometimes useful.
Can't find an empirical 3D model for your sequence?
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.
Web Browser Software:
Jmol java applet.
Nothing to install except
java, works in all popular browsers, Windows, Mac OS X, or linux.
Free, open source (user community "owns" it), actively developed.
FirstGlance in Jmol
is a user interface, or "wrapper".
FirstGlance in Jmol designed for journals (used by Nature
and others), very easy to use, has limited
set of "canned" views.
FirstGlance is much easier to use than is Jmol by itself.
FirstGlance makes the power in Jmol accessible.
Best thing for proteins since 2004.
Sites Using Jmol (growing rapidly!)
How to Use Jmol By Itself.
Chime browser plugin.
Obsolete! Windows only; none for Mac OS X. No longer
Was widely used when it was the best available: 1996-2004.
Free but proprietary closed source (user community has no control), little development since 1998.
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.
RasMol: Best available from 1993-1997.
User friendliness: poor.
Free and open source.
DeepView also known as Swiss PDB-Viewer:
Powerful modeling capabilities
(see Molecular Modeling below).
User friendliness: poor.
Free but proprietary source.
(Crystallographic Object-Oriented Toolkit) recently
very popular with crystallographers for model-building from
electron density maps. Open source
Effective use requires learning a complex command language. Useful for experts.
The rest of us should use
(contains Jmol) and
FirstGlance in Jmol.
Works in Windows, Mac OS X, or linux.
Free, open source (user community "owns" it), actively developed.
Review of Protein Chemistry and Structure.
We'll do this quickly. The links are for participants who are educators.
DNA mRNA Protein.
DNA structure in Jmol
Estructura del ADN
20 Amino acids
Polypeptide chain geometry and steric restrictions
Covalent and non-covalent chemical bonds
- Codon = 3 nucleotides; 4 nucleotides3 =
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.
Folding: hydrophobic collapse
cannot be reliably predicted
from sequence alone (using ab initio theory).
- Covalent bonds: lengths and angles nearly constant
- Non-covalent bonds: variable lengths and angles
- Salt bridges (up to 4.0 Å in proteins)
Hydrogen bonds (2.5-3.5 Å donor-to-acceptor in proteins)
Cation-pi interactions (up to 6.0 Å in proteins)
- van der Waals interactions (up to 4.0 Å in proteins)
Evolutionary Conservation: ConSurfDB & ConSurf
Major histocompatibility protein (MHC I 2VAA):
Identifying Functional Sites & Seeing Protein Evolution:
- At 2vaa in
show Evolutionary Conservation.
- Also check
(cathepsin B, noting the conserved surface Gly, Pro --
- ConSurf's Mechanism:
- Note the Caveats in
Proteopedia's Evolutionary Conservation.
- There are two ConSurf Servers:
- 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.
- 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.
- If you have a serious interest in the conservation in your protein,
and explore these views:
FirstGlance in Jmol: Easy Visualization of Any Macromolecule
Terminology: "visualization" vs. "modeling".
(Light modeling tools)
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:
- "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
Key Resources: and
- Top 2 rows of views (tooltips, automatic help)
- Vines (controls in bottom left panel)
- Buttons (Ligands+, etc.)
- Center Atom
- More Views
1BKX: Non-standard residues in Proteopedia vs. FirstGlance
(under More Views).
2ACE in FirstGlance: Key Resources:
- Ligands button (full names of ligands are in Proteopedia)
- Find (explain the distributions of gly, pro, ala, glu, phe,
viewed one at a time)
- Contacts to HEM (see snapshot at right)
- Key Resources:
Probable Quaternary Structure Server: Specific Oligomers/Biological Units
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.
- 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
- Add Molecular Scenes and Content to
- Its a wiki: you or your students can add pages or customized
molecular scenes in Jmol.
- Great for
journal supplementary materials
research group websites
as well as
molecular structure tutorials
your pages from
being changed by anyone else, e.g.
- An easy Scene Authoring Tool attaches your customized
views to Green links.
- This is, by far, the easiest place to create molecular tutorials,
Nucleosomes (publically editable).
(enough for your entire class!) allow students to try
authoring temporary molecular scenes -- without individual accounts.
Screenshots can document student work.
Teaching Strategies Using Proteopedia.
Animated Powerpoint Slides and Publication-Quality Images:
from Polyview-3D. Click on
the image for a
larger view and explanation.
Make Animated PowerPoint Slides and Publication-Quality
Images easily with
- 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.
Once you have an animation from Polyview-3D:
- Windows Powerpoint: Simply drag the animation directly from the
Polyview-3D web page and drop it into a powerpoint slide.
- Mac OS X Powerpoint: (This works in Powerpoint:Mac 2008.)
Control-Click (Right-Click) on the animation in the Polyview-3D web page, and
select Save Image As ...
Save the image to the Desktop.
- Drag the image file (filename ending in .gif) from the Desktop and
drop it into a Powerpoint slide.
The animation will run only when the slide is projected.
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
Orientations of Proteins in Membranes.
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.
- Upload any saved molecule (PDB file), possibly after deleting unwanted
portions with a text editor, to
Jmol in Scientific Journals:
Interactive 3D Complements in Proteopedia:
- FirstGlance in Jmol: Look for the 3D View links
Nature Structural and Molecular Biology
- "Jmolized" Interactive 3D Journal Figures:
- Tutorials disponible en español at
MolviZ.Org (Estructura del ADN; Modelo de bicapa
lipídica y canal de gramicidina; Estructura del agua:
enlaces de hidrógeno)
BioModel (Estructura de proteínas; Glúcidos,
Lípidos, Vitaminas, Aminoácidos, Hélice alfa,
Hebra beta, Lisozima, Nucleósidos, ADN, ARN, et al.)
HighSchool.MolviZ.Org: Resources for High School Teachers.
- BioMolecular Explorer 3D: Molecules for High School.
- Molecular Workbench (from Concord Consortium):
Activities for High School Students with built-in assessment and reporting.
Teaching Scenes, Tutorials, and Educators' Pages in Proteopedia, including Molecule of the Month.
- Teaching Strategies Using Proteopedia.
MolviZ.Org: Martz Central: Resources for High School, College, and Researchers.
- 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
MolVisIndex.Org: World Index of Molecular Visualization Resources
- Includes Tutorials, K-12 Resources, Spanish Resources, and many more.
Animations / Morphs: Conformational Changes
(see MOVIE at right).
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
- Mutating your model:
Changing residue sidechains and rotamer minimization with
- DeepView beginners should start with the superb
Molecular Modeling for Beginners
by Gale Rhodes, Univ. Southern Maine.
- DeepView resources are indexed at
- Structural Alignment of two or more chains or molecules, and how to view the alignment.
can align macromolecules
(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 Jmol can distinguish the models.
Gale Rhodes provides a
DeepView tutorial: click on the section Comparing Proteins.
Structural Alignment Tools.
- Homology (comparative) modeling:
Keep in touch!