Video.
A
video with Eric Martz introducing FirstGlance and explaining the design goals
was posted on YouTube in March, 2021.
Name.
FirstGlance in Jmol was inspired by FirstGlance in Chime,
which was written by Eric Martz in 1998 in collaboration with
Jaime Prilusky,
and with the support of
Joel Sussman
and the Protein Data Bank.
FirstGlance in Chime was deployed in 1998 at the Brookhaven Protein
Data Bank, and beginning the following year, at the RCSB Protein Data Bank.
It remained available at the latter through 2005.
The name FirstGlance refers to the initial view offered, which is designed
to be maximally informative "at first glance".
MDL Chime (now long defunct)
was a browser plugin derived from
RasMol. Chime
had a large impact on education, communication, and research in the
biochemical community, as evidenced by the hundreds of tools and tutorials
that utilized it.
MDL Chime was free, but
its proprietary source code was closely guarded by
the corporation that owned it, MDL Information Systems .
Chime first became available in late
1996. MDL stopped serious development of Chime by late 1998.
Protein Explorer (1998-2006) was an extensive user-interface ("wrapper")
for Chime,
providing access to much of the power of Chime without the need to learn Chime's large command
language.
Eric Martz was the principal architect and code developer.
Protein Explorer provided canned views to reveal important structural features
(such as secondary structure, distribution of charges and hydrophobic vs. polar residues, etc.).
It also offered capabilities for customizing color schemes and renderings. And in its
final stages, it attempted to offer an easy method to capture selected views in a
presentation format. In 2003, Protein Explorer won the international
Merlot Classic Award in Biology, which stated that
"Protein Explorer has revolutionized the teaching of biology at a molecular level".
Use of Protein Explorer, at its height in the early 2000's
over 10,000 visits/month, faded away with the demise
of Chime.
Demise of Chime.
Despite its considerable power, the limitations of Chime (including
its unavailability for Mac OSX or linux) and the freeze in its development
in late 1998 were frustrating to its user community. An open-source replacement
was needed, and this need was met by
Jmol beginning
in 2004.
Jmol replaces Chime.
Jmol was available for small molecules from the late 1990's thanks to the
work of Dan Gezelter and others. In 2002, Michael Howard, having become aware of the
frustration in the community of Chime users, began adapting Jmol to work with
macromolecules. By 2006, Howard, in an amazing tour de force,
had forged Jmol into a replacement for Chime, including
the complete Chime command language (a superset of Roger Sayle's original RasMol
command language).
Robert M. Hanson
then took over development of Jmol, expanding
its capabilities with remarkable brilliance and creativity.
Nature inspires FirstGlance.
In 2005, Evelyn Jabri was an editor at Nature. Previously, Jabri had been on the faculty of
Indiana University, where she used Protein Explorer in her teaching. Jabri contacted Eric
Martz, expressing the interest of Nature in providing a way for online readers to see
and explore newly published macromolecular structures.
Nature had a track record of supporting open-source projects.
This inspired Martz to initiate development of FirstGlance in Jmol as open-source
freeware. The first working version of FirstGlance was released in October, 2005. In 2006,
Nature Structural and Molecular Biology provided links, in articles reporting new
structures, to view those structures in FirstGlance. Following the open-source spirit of
FirstGlance, newly-published structures could be viewed in FirstGlance
from the Contents page,
without a subscription
to the journal. FirstGlance remained the principal visualization option offered by
Nature Structural and Molecular Biology for the next 12 years.
In 2006, Nature followed the lead of Nature Structural and Molecular Biology.
FirstGlance was the principal visualization option offered by Nature for the ensuing
decade. A number of other journals also offered FirstGlance (see
Adoptions).
Usage.
From 2006-2019, FirstGlance has been used to visualize molecules over a million times. In the
year July 2019 - June 2019, molecules were displayed on average 218 times/day.
Scope of FirstGlance.
FirstGlance in Jmol offers canned views designed to reveal important structural features.
Each such view has its own fixed rendering and color scheme. FirstGlance offers no customization
of colors or rendering, which simplifies it greatly in comparison with Protein Explorer.
FirstGlance does enable hiding any portion(s) of the structure, or isolating any single component
(by hiding everything else in a single click).
Also, it enables selection of any portion(s) and will then display atomic contacts and
non-covalent interactions with the selected portion(s). All color schemes are pre-defined (and
color keys are displayed automatically).
Proteopedia and FirstGlance complement each other.
Proteopedia.Org, developed initially by Jaime Prilusky, Eran Hodis, and
Joel Sussman at the Weizmann Institute (Rehovot, Israel),
offers complete customization of interactive molecular scenes in Jmol
(later JSmol), and conveniently
became available as FirstGlance was initiated. The customization capability of Proteopedia,
implemented in straightforward menus and forms (no command language needed), thus complements
FirstGlance. And vice versa, the informative canned views in FirstGlance complement
what Proteopedia offers.
Presentations. In 2016, FirstGlance offered a mechanism to
capture presentation-ready static images or animations
(rocking or rotating) of any view it offers. The initial implementation
was problematic, so in 2018, with the help of
Jaime Prilusky,
it was re-implemented using an external server, becoming
simpler to use, and much more reliable.
A complete list of
changes between versions of FirstGlance
is provided.
Technical information for software developers is available
in several documents listed at the end of
All About FirstGlance in Jmol.
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