2018, September 22:
Provided open-ended questions (colored green) at the bottom of each chapter.
Answers are provided
for immediate feedback.
Also provided an on-line quiz with multiple choice questions. When answers are submitted,
you get immediate scoring.
Enlarged element color keys, centered all of them, and tidied up nearby color keys.
Chapter 3, view 9: pointed out that hydrogen bonds are non-covalent,
with a link to more info.
Histidine is a new View 3 in Chapter 5, related to charges, with new details about pKa.
Chapter 6, regulation, has two new views showing the formation of pH-dependent
salt bridges that foster oxygen release, involving
the C-terminal histidine of the beta chain, in the deoxy conformation.
The importance of binding of water to protein surface newly exposed during the
transition from deoxy to oxy is now mentioned in Details under View 3 in Chapter 6.
Chapter 6 now cites reference 4, and
new reference 5.
The list of molecules (PDB files) employed was updated to include 2dn1 and 2dn2.
Links to an interactive Ramachandran Principle tutorial were added to Chapter 3 on
2018, August 28: Release of the JSmol implementation of JTAT including
the hemoglobin tutorial, but not yet any of the other tutorials. Java no longer required.
Enhancements to this version of the hemoglobin tutorial:
The many enhancements to JTAT since the 2007 implementation of the hemoglobin tutorial
are now included: Details that can be hidden; a centering tool; zoom and optional slab sliders;
a listing of PDB codes used.
The sections "Glycine Representations" and "Peptides and Backbones" were replaced with a link
to a new "Introduction to Molecular Visualization" in Proteopedia.Org.
Mention of the mystery of how oxygen enters and exits, with references to current thinking.
Some visually smoother transitions.
When describing one alpha helix, superimposition of the backbone trace on the main-chain atoms,
addition of hydrogen atoms,
Additional views to clarify "Amphipathic Alpha Helices".
Use of the new slab ("cut") slider for viewing the hydrophobic core. New views on charge
distribution and salt bridges in "Hydrophobicity, Polarity, & Charge".
A new chapter "Regulation of Oxygen Binding" that animates the T <-> R transition at the
level of heme, and for the entire tetramer. Also shows
where 2,3-diphosphoglycerate binds to foster oxygen release.
In "Sickle Hemoglobin", new graphics (from Wikimedia Commons) to relate the molecular views
to red blood cells and their flow through capillaries. A simpler color scheme. Link to an
external video covering the cause, symptoms, and treatments for sickle disease.
A new view that shows a polymerized pair of 8-molecule strands.
Journal references are provided, in addition to some additional
2015 and 2018, Eric Martz made several attempts to get JSmol to work in JTAT, but was unsuccessful.
In January 2018,
Eric and Bob Hanson both attended the 10th anniversary celebration for Proteopedia.Org.
The morning following that meeting, Bob and Angel Herráez spent 3 hours working with Eric
on getting JSmol to work in JTAT, and Bob eventually succeeded. This opened the door for
Eric to proceed to upgrade JTAT to JSmol and make a number of improvements, and to port the
hemoglobin tutorial (and others in JTAT) to the new JSmol version.
2010-2015: The demise of Java applets in web browsers made the Java-requiring 2007
version of the hemoglobin tutorial more and more difficult to use.
Jmol is written in Java, and runs as a
standalone application, as well as a Java applet in web browsers. Web browsers began to remove
support for Java applets, perhaps mostly due to persistent security issues. Bob Hanson,
the primary developer of Jmol, pulled off an amazing transformation of the web-browser form
2008, 2010: 2008 September: The first release of the
"Jmol Tutorial-Authoring Template" (JTAT), which included the (unchanged 2007) Hemoglobin tutorial.
2010, September: JTAT was upgraded, but the hemoglobin tutorial remained as it had been in
the 2007 early pre-release version of JTAT. Now released were JTAT-based
tutorials on Antibody, Major
Histocompatibility Complex, Collagen (by Karl Oberholser, later superceded by his Collagen
tutorial in Proteopedia.Org), and Andrew Carter's "Exploring DNA".
The JTAT project was initiated concurrently with the creation of Proteopedia.Org by Jaime Prilusky,
Joel Sussman, and Eran Hodis at the Weizmann Institute of Science in Rehovot, Israel. By the
time JTAT was well along, it became apparent that it was enormously easier to create
molecular visualization tutorials in Proteopedia. But, having already invested considerable
time, and because of some modest advantages of JTAT, Eric decided to finish JTAT. However,
the JTAT documentation strongly recommended that people planning to author tutorials start
in Proteopedia. Only a tiny few tutorial authors (if any other than Eric) would prefer to
2007, April: The hemoglobin tutorial was released using Java-dependent Jmol.
The porting was done by
Frieda Reichsman and Eric Martz. They had begun work on a "Jmol Tutorial-Authoring Template" (JTAT)
that was later used for tutorials on Antibody, Major Histocompatibility Complex, and (with his
blessing) a port of Andrew Carter's Chime tutorial "Exploring DNA". The Jmol hemoglobin
tutorial was linked to MolviZ.Org (which was the home of all the Chime-based tutorials and
resources) in July, 2007.
2006: Demise of
MDL Chime. Chime was
the brilliant creation of primarily Tim Maffet (an employee of MDL),
was the best free molecular visualization engine from its release in 1997
until about 2006. It incorporated much of the source code of RasMol, which Roger Sayle
had generously placed in the public domain.
Chime was very widely used, both by the academic community and
by drug companies in commercial settings.
Chime remained free, but MDL, the company that created it, ceased to maintain it. Also
they declined to open the source code to the user community. A version for
Mac OS X was never created.
The lack of development of Chime caused frustration in its user
community. Michael "Miguel" Howard solved this problem by volunteering, in 2002-2006, to
develop open-source Jmol (a project which began before 2000) to become a replacement for Chime.
Subsequently, Robert M. Hanson took over develpment of Jmol.
1998, January & February: Compatibility with Windows 95 and the Netscape Navigator 4.04
web browser. Added font size control and optional color schemes in the Utility menu. Made a
correction regarding the distal histidine residue, thanks to feedback from Judith Voet
1997, September: Chime website. Adapted from the RasMol version by student
Rashie Athukorala with Eric Martz. Content was the same as the RasMol version, but each
molecular view was attached to a button with some description in the website.
This mode was much easier for students to use, and could also be used to illustrate a lecture.
In addition to the self-paced tutorial mode, there were continuous play modes where the transitions
between molecuar views proceeded automatically. Continuous play modes were useful at meetings.
A projector could be left showing the tutorial in an endless loop.
1996, March: Rasmol Movie Script.
This played like a silent movie. There were no controls.
Included an introduction to molecular visualization simulating polymerization of several
amino acids. Tetramer (αβ)2,
hemes, oxy and deoxy, isolation of a single amphipathic alpha helix with
hydrogen bonds. Slab to show the hydrophobic core. Sickle hemoglobin and polymerization.
Minor bug fixed February 1997.