Students
- Tutorials show you
how the 3D structures of DNA, hemoglobin, and many other
macromolecules support their functions.
- Find and explore
the 3D structure of any
macromolecule easily.
- Identify
the parts of any 3D protein molecule whose mutations
are lost from the gene pool,
because they must be conserved in order to perform
crucial functions.
- Easily make 3D macromolecules
rotate in your Powerpoint® slides.
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Educators
- Project the following resources in lectures,
offer them to your students,
or assign them.
- Some resources are targeted specifically to
high school level;
(see
HighSchool.MolviZ.Org);
most are suitable for college and graduate levels.
- Ready-made Tutorials on 3D structures of
DNA, hemoglobin, lipid bilayers, water, and many other
macromolecules.
-
Some tutorials include challenge questions (answers on request).
-
Customize interactive molecular views easily
to show in class,
and for your students to rotate, zoom, and admire.
- Find and explore
the 3D structure of any
macromolecule easily.
- Identify
the parts of any 3D protein molecule whose mutations
are lost from the gene pool (because they must be conserved
[see Gallery]
in order to perform
its functions) or most rapidly (to support function, e.g. escape
of influenza hemagglutinin from immunity.
- Easily make 3D macromolecules
rotate in your Powerpoint® slides,
and your students can do the same.
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Researchers
- Find and explore
the key structural features of any
macromolecule, easily.
- Locate
the positions of crucial residues or sequences.
- See noncovalent bonds
between any moiety and the remainder of the structure.
-
Annotate interactive macromolecular structures,
without learning scripting languages,
for journal supplementary materials or your
lab group's website at
Proteopedia.Org,
a free structural biology wiki with scene-authoring tools.
- Identify functional regions
by coloring amino acids
with their levels of evolutionary conservation --
in minutes, totally automatically if you wish.
Locate conserved residues, e.g. for functional mutagenesis studies.
- Make
publication-quality molecular figures
with ease,
highlighting specific residues or regions, and customizing rendering
and colors.
- Easily make 3D macromolecules
rotate/animate in your Powerpoint® slides.
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Everyone
- Use state-of-the-art interactive 3D molecular visualization tools
that you can expect to have available for years to come.
- These are the easiest to use tools available.
- All technologies on this page are free!
- No installation is needed. Nothing to download.
They just work immediately in your web browser!
- Work on all popular computers: MS Windows,
Mac OS X, linux.
- Work in the
most popular web browsers:
Chrome, Safari, Firefox.
JSmol (NO Java needed) is employed by
most of the sites that best meet the above
goals.
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I. Tutorials with interactive, mouse-rotatable molecular
views:
-
MolviZ.Org has Jmol-based tutorials on DNA* double helix,
hemoglobin, antibody, collagen, lac repressor*,
major histocompatibility proteins*,
lipid bilayers and channels, water*, and more.
* These tutorials have challenge questions, some with lesson plans.
-
Other websites with extensive ready-made tutorials
on specific molecules.
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II. Jmol Tutorial-Authoring Systems
Create your own tutorials easily at
Proteopedia.Org,
a wiki with Scene Authoring Tools.
You don't need to learn any script, HTML, or other
languages. Your descriptions and molecular scenes will be online immediately!
See
Getting Started Authoring in Proteopedia.
Jmol Tutorial-Authoring Template (JTAT)
Caution:
Not yet upgraded to use JSmol (no Java). Upgrade expected sometime in 2018.
Download a template for building tutorials that will display in a
web browser.
Supports multiple chapters and views comparing 2, 3, or 4
molecules side by side (with synchronization of mouse-directed
rotations or zooms). Your tutorial will include a slider for
zooming (or slabbing), spin toggle and centering buttons, details
that display only when requested, and "How To" put views in
Powerpoint slides, etc.
Considerably more challenging to use than Proteopedia,
but you have more control and the product tutorial is more user
friendly. The tutorial must be uploaded to a server to provide
online access, or the tutorial can be shown offline.
See the
JTAT Demonstration Tutorial and
tutorials on several molecules.
See
Comparisons of these and other Jmol tutorial-authoring
systems.
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III. Explore Any Molecule
FirstGlance in Jmol
(firstglance.jmol.org)
- Easy enough for students, but powerful enough for researchers.
- One-click each to see secondary structure, ligands, water, hydrophobic
vs. hydrophilic, charge, disulfide bonds, salt bridges, cation-pi interactions.
- Color keys, help, tool tips appear automatically.
- Highlights missing residues and interprets model reliability.
Explains crystallographic disorder and Rfree.
- Shows the biological unit (functional assembly).
- Locate amino acids or nucleotides by name, sequence, or sequence numbers.
- Isolate any chain, ligand, range of residues, etc. by clicking on them.
- Hide any chain, residue, or atom by clicking on it.
- See the noncovalent interactions with any moiety you designate (by clicking
on it), divided into seven categories (hydrogen bonds, van der Waals, etc.).
-
Adopted by the journal
Nature
(see their
 buttons),
among
others.
-
More..
Paste animated molecular scenes into Powerpoint®
Find Molecules To Explore:
- Browse the
Atlas of Macromolecules, which
lists over 150 macromolecules, many shown in snapshots. Links are provided
within the Atlas
to explore each in FirstGlance in Jmol.
- Search
- Easiest:
from the amino acid sequence in
UniProt.Org -
Instructions.
-
Search in
OCA, which has
direct links to
FirstGlance in Jmol.
- Advanced Search at the US Protein Data Bank
Harder to use, though more powerful.
Instructions.
Lacks a direct link to
FirstGlance in Jmol, so write down the
4 character PDB
identification codes
for molecules of interest to give to FirstGlance.
-
No empirical structure? Create a Homology Model using this
Practical Guide.
Proteopedia.Org
- Has a resource-rich page for every published macromolecule (>100,000).
New pages added weekly.
- Create customized molecular views easily with the built-in
Scene Authoring Tools. See
Getting Started Authoring in Proteopedia.
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IV. See Protein Evolution with the
easy-to-use
ConSurf Server.
Comparing amino acid sequences in a family of proteins reveals
highly conserved residues (or highly variable, think
influenza).
Evolutionary conservation of a patch of residues identifies it
as supporting or performing a crucial function.
Introduction to Evolutionary Conservation.
Just specify a
PDB
identification code
and the name of one chain, and the rest is completely automatic!
Functional patches of highly conserved (or highly variable) residues
can be visualized easily using FirstGlance in Jmol, which is
integrated into ConSurf.
ConSurf finds protein sequences related to your 3D structure,
performs multiple sequence alignments, constructs a phylogenetic
tree, and assigns a conservation level (and confidence interval)
to each amino acid, all automatically!
Optionally, you can select the sequences and upload your own
multiple sequence alignment, which will be used by ConSurf's
state-of-the-art algorithms, all of which are published in peer-reviewed journals.
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V. Animate Molecules in Powerpoint.
Print Publication-Quality Molecular Views.
Easy Enough for Students Assignments!
FirstGlance in Jmol is the easiest way to make high quality images
and presentation-ready animations.
See Examples.
However, FirstGlance does not support customization
of colors and rendering in the molecular view.
Also the images generated by Jmol in FirstGlance are not quite as high quality as those generated
by PyMOL.
Polyview-3D generates its images and animations at truly publication quality using PyMOL.
Furthermore, it supports full customization of the molecular view.
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