Dear John,
Your plans brought to mind an earlier experience I had with educators.
This concerns macromolecules, not organic chemistry. I have no
experience with educational visualization in teaching organic chemistry.
When I first discovered *RasMol* (1995) I was thrilled at how easily I
could explore proteins and nucleic acid structures. I got a grant from
the US NSF to teach college educators how to use it in their teaching.
The plan was 2 all-day sessions to teach them how to use it (command
language), followed by a 3rd day, a year later, for them to report back
on their experiences. Dozens of college profs came from all over the
NorthEastern USA, and they were thrilled too. But when they came back a
year later, few had great success. What I observed on that 3rd day was
that, despite their enthusiasm, few could remember how to answer
fundamental questions using command language: How many chains are
present? Is there protein and/or DNA? Are there ligands? They were stuck
at the default ball-and-stick rendering colored by element.
I was forced to realize that for the majority of students, educators and
researchers, who use molecular visualization perhaps only a few times a
year, command language is too complicated.
That, and encouragement by Joel Sussman (head of the Protein Data Bank
at that time), inspired me to develop "*Protein Explorer*" (named by
Joel), using the *Chime* browser plugin. The goal was that anybody could
get an informative first view of any protein, and see other key
structural features (secondary structure, N and C termini, charge
distribution, hydrophobic surface or core, salt bridges, disulfide
bonds, hydrogen bonds, cation-pi interactions, etc. etc.) just by
clicking buttons. Explanatory help and color keys always appeared
automatically. Protein Explorer was very popular. Users could
concentrate on the science instead of on the software.
Protein Explorer won the 2003 Merlot Classic Award in Biology: "Protein
Explorer has revolutionized the teaching of biology at a molecular level".
Protein Explorer faded away when Chime did, ca. 2005. Luckily, Michael
"Miguel" Howard had begun making *Jmol* able to handle proteins, and
implemented the RasMol/Chime commands and color schemes for
macromolecules, and then Bob Hanson gave Jmol power beyond our wildest
dreams.
Protein Explorer had two overarching goals: show the structure, and
enable customized renderings and color schemes -- all without knowing
any command language. It made for a fairly complex user interface
although still far easier to use than command language.
Meanwhile, Evelyn Jabri did a stint on the Editorial Board of /Nature/.
She had prior experience using Protein Explorer in chemistry classes at
Indiana University. She encouraged me to make something to enable
readers of Nature to interact with newly published macromolecular
structures in the easiest way possible. The result was FirstGlance in
Jmol. The name was inherited from an extremely minimal viewer,
FirstGlance in Chime, that Jaime Prilusky, Joel Sussman and I developed
for the Protein Data Bank (then at Brookhaven National Lab) in the late
1990's. At this point, FirstGlance in Jmol has grown well beyond a
"first glance".
FirstGlance *does not* allow customization of colors or renderings. It
uses canned views designed to show key structural features effectively.
That greatly simplified its user interface. It went into service at
/Nature/ in 2007, where buttons labeled "3D" employ it to this day. It
is widely used by students and educators as well as researchers and
several structural bioinformatics servers, currently about 400 times a
day during the spring and fall semesters. It has been used over
1,000,000 times since its inception, by half a million people.
Luckily, an easy way to customize colors and renderings was created by
Jaime Prilusky, Eran Hodis, and Joel Sussman in 2007: *Proteopedia.Org*.
Its /Scene Authoring Tools/ enable rich customization with buttons,
menus and form slots (no command language needed). Customized molecular
scenes are immediately online to share with anyone.
Proteopedia is easy enough that college students can develop content
<http://proteopedia.org/wiki/index.php/Teaching_Scenes%2C_Tutorials%2C_and_Educators%27_Pages>
with little or no training. Quite a few educators assign student teams
to develop customized scenes. A few have also involved high school
students
<http://proteopedia.org/wiki/index.php/High_school_teachers%27_resources>.
FirstGlance facilitates understanding macromolecular structure,
whereupon Proteopedia enables sharing customized scenes that highlight
key structure-function relationships.
My conclusion is that to empower students and educators to visualize
molecular structures, one's success will be much broader to the extent
that one can utilize resources that do not require learning and
remembering command language. Then users can concentrate on the
molecules, rather than the software.
Granted, developing such resources takes a great deal of time. Hopefully
you can find some gems for organic chemistry in the wiki list Websites
Using Jmol <http://wiki.jmol.org/index.php/Websites_Using_Jmol>.
-Eric
On 6/1/16 8:38 PM, John Keller wrote:
Hi Eric,
Thanks for the links. I have a lot of experience with elementary
level Jmol (Windows versions) for teaching applications in organic and
general chemistry. Jmol can be intimidating, especially since it seems
to be under continual development with changing features and commands
that work in some versions and not in others (such as “bondorder”).
However, the average computer-savvy, Mac-using chemistry teacher
should be able to use a subset of commands to illustrate small
molecules in various ways for themselves, and for their students.
I am giving a workshop on Web Based Molecular Modeling at the
American Chemical Society Northwest Regional meeting (NORM2016) in
about a month. The main emphasis will be on how to use WebMO, Jmol and
other free or low cost resources in teaching HS and college general
chemistry. I will mention your excellent sites in the context of
bio-molecule visualization.
After I sent my email to the list, I did find a page where someone
described how to create a OS X package that will install just like a
something from the App Store. I just bought an older Mac so I will be
able to speak the Apple lingo with teachers at this workshop!
John Keller
University of Alaska Fairbanks
Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
Windows 10
*From: *Eric Martz <mailto:ema...@microbio.umass.edu>
*Sent: *Wednesday, June 1, 2016 1:25 PM
*To: *jmol-users@lists.sourceforge.net
<mailto:jmol-users@lists.sourceforge.net>
*Subject: *Re: [Jmol-users] Jmol for mac installation
Dear John,
Jmol, by itself, is challenging to use for most purposes. It has an
extensive command language with thousands of commands and
permutations. Therefore many people, myself included, have created
explanations or tutorials that show molecules using Jmol, but are much
easier to use, with built-in help that is lacking in Jmol per se.
Examples are
* http://biomodel.uah.es/en/model3 (Carbohydrates, Lipids, Vitamins,
Proteins, Nucleic Acids)
* http://MolviZ.Org (DNA, hemoglobin, antibody, water, lactose
repressor, collagen, etc.)
* http://Proteopedia.Org has many articles with interactive molecule
in Jmol. Use the search slot, or browse lists at:
* http://proteopedia.org/w/High_school_teachers%27_resources
*
http://proteopedia.org/w/Teaching_Scenes%2C_Tutorials%2C_and_Educators'_Pages
<http://proteopedia.org/w/Teaching_Scenes%2C_Tutorials%2C_and_Educators%27_Pages>
For general exploration of any macromolecule, I believe
http://FirstGlance.Jmol.Org is easiest (disclosure of possible bias: I
wrote the user interface) but it is designed for research or
specialized study. If you want to give students access to specific
molecules not available in existing tutorials, you can make your own
web page with links that show the molecule in FirstGlance, or your own
page in Proteopedia.Org.
To answer your question:
Jmol is not, as far as I know, available in the Apple Store. You
download it free from http://Jmol.org.
Jmol is available as a stand-alone application (Jmol.jar). It has
almost no built-in help. To do more than see the initial view of a
molecule, you need to use the menu (complicated, no help) or learn the
commands. Yes, you can drop it onto the Mac Dock (on the right end).
The resources I listed above, designed for students and educators, all
work in a web browser, using the plug-in form of Jmol (JSmol or the
Java applet). For those, all you need is a bookmark or link. Nothing
needs to be installed, except Java which is not necessary for most
purposes.
Please don't hesitate to ask if we can help.
-Eric
On 6/1/16 3:41 PM, John Keller wrote:
Hi All,
I don't see Jmol in the Apple App Store. Is there an easy way for
a Mac user, such as a high school teacher, to install Jmol on
their OS X machine? Hopefully this would place the Jmol icon on
the toolbar too.
John Keller
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- Martz.MolviZ.Org <http://Martz.MolviZ.Org>
* Top Five 3D MolVis Tools: Top5.MolviZ.Org <http://top5.MolviZ.Org>
* FirstGlance: 3D Molecules in /Nature/: FirstGlance.Jmol.Org
<http://firstglance.jmol.Org>
* Protein 3D Structure Wiki: Proteopedia.Org <http://proteopedia.Org>
* Education: Biochem in 3D at MolviZ.Org <http://MolviZ.Org>
* Find Functional Patches in Proteins: ConSurf <http://consurf.tau.ac.il>
* Atlas of Macromolecules: Atlas.MolviZ.Org <http://atlas.MolviZ.Org>
* Interactive Molecules in Architectural Spaces:
MolecularPlayground.Org <http://molecularplayground.Org>
* Workshops: Workshops.MolviZ.Org <http://workshops.MolviZ.Org>
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