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 online Quizzes with immediate feedback.
-
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
(see
examples)
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, iPads/tablets, smart phones.
- Work in all
popular web browsers:
Chrome, Safari, Edge, Firefox, Opera.
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,
coronavirus spike protein,
hemoglobin‡, antibody‡, collagen, lac repressor*,
influenza and tamiflu,
major histocompatibility proteins‡,
lipid bilayers and channels, the Ramachandran principle‡, water*, and more.
‡ These tutorials have online quizzes with immediate feedback.
* 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.
HIGHLY RECOMMENDED!
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III. Explore Any Macromolecule
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At right: Half of an SV40 Virus Capsid, colored from
closest
to
farthest
from center.
Various color schemes are available,
such as assigning one color to each group of sequence-identical chains.
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FirstGlance in Jmol
(firstglance.jmol.org or google firstglance as one word,
no space)
- 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.
-
Many unique capabilities and conveniences, extensive help and background
information
not found in PyMOL, ChimeraX, MolStar, iCn3D. See
list of unique features with snapshots.
- Highlights missing residues and interprets model reliability.
Explains crystallographic disorder, interprets and explains Rfree.
- Shows the biological unit (functional assembly) by default. Very large
assemblies, such as virus capsids, are simplified automatically to backbone atoms,
or subsets of backbone atoms, which are sufficient for visualizing the overall structure
and architecture.
- Locate amino acids or nucleotides by name, sequence, or sequence numbers.
- Isolate any chain, ligand, range of residues, etc. by clicking on it.
- 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.).
-
More..
Make animated molecular scenes you can drop into Powerpoint®
Find Molecules To Explore:
- QUICK-START FirstGlance:
Protein-DNA
Polio Virus Capsid*
Membrane Pore
(+ Membrane Boundaries)
Holliday Junction §
Evolutionary Conservation
AlphaFold Prediction
* In the Views tab, click Slab, then check both checkboxes in the Slab options.
§ Hide protein (in the
Focus Box).
- Browse
- Search
Proteopedia.Org
- Has a resource-rich page for every published macromolecule (>200,000).
New pages added weekly.
-
Browse by clicking Random (at the upper left in Proteopedia.Org).
- 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.
ConSurf Quick Start
Visualizing Conservation
Interpreting ConSurf Results
Introduction to Evolutionary Conservation.
Just specify a
PDB
identification code or upload an
AlphaFold Prediction
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 A Variety Of Animated Examples.
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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