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".
Forerunners. I stumbled upon
RasMol in 1995, thanks to Amherst College biochemistry professor
Patrick Williamson.
I had been a cell biologist and immunologist for 30-some years,
since completing my PhD in Biology from Johns Hopkins University in 1963.
Although I had no formal training in protein crystallography or structural
bioinformatics, the mesmerizing world of protein
molecular structure fascinated me so deeply that by 1997 I gave up "wet lab research"
to pursue applied development of free, open-source software designed to make
protein structure more accessible to students, educators, and researchers.
This mid-career change of fields was enabled because I had tenure at the University of
Massachusetts, Amherst. With the blessing of Roger A. Sayle, the creator of RasMol
(see
Sayle's Short History of RasMol),
I created the first website for RasMol in November, 1995 -- still the dawn of the Internet
and the World Wide Web.
There I offered tutorials, reference materials, and downloads of the RasMol program.
Its enormous popularity was gratifying.
Later that site became the
RasMol Classic Site.
As the World Wide Web progressed, the fact that RasMol was a stand-alone program that
could not operate within a web browser became RasMol's main limitation. This was overcome
when Tim Maffett,
a brilliant employee of MDL Information Systems, along with Bryan van Vliet
and others,
converted RasMol into a web browser
plug-in named Chime (for Chemical MIME), and further extended its command language
and capabilities (see
MDL's Chime, 1996).
Inspiration.
I applied for a grant from the US National Science Foundation, Division of Undergraduate
Education, to teach college faculty in the NorthEast to use RasMol to show DNA and proteins
in 3D in their classes. I got the grant on the first try, quite unlike my experiences
with research grants. After two days of learning to use
RasMol command language at my home campus, the University of Massachusetts at Amherst,
the faculty returned to their campuses. A year later, they came back
to report their experiences in their classes. Few could remember the basics of the command
language. They could no longer see how many chains were in a protein oligomer, find the ligands,
visualize surface charges or hyrophoobic cores, etc.
It became obvious that even for smart and motivated people, if they do molecular
visualization only a few times a year, command language is too difficult to remember.
This experience was the main inspiration for me to design Protein Explorer.
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.
It was also widely used by pharmaceutical companies.
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".
Protein Explorer was also offered by the RCSB (Research Collaboratory for Structural
Bioinformatics) Protein Data Bank under the guidance of Phil Bourne, starting in 1999.
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).
I am grateful to Joel Sussman, who as head of the Protein Data Bank, and later the
Israel Structural Proteomics Center,
encouraged and supported development of Protein Explorer and FirstGlance in Chime, and later
in Jmol.
I am also grateful for the advice and insights of Frieda Reichsman,
MoleculesInMotion.Com, which
were important in making the user experience of Protein Explorer and FirstGlance
simpler and more user friendly.
I am grateful to Jaime Prilusky who, at my request,
kindly created essential tools to identify categories of PDB
files needed to expand and test the capabilities of FirstGlance.
I am also grateful to Keiichi Namba who supported numerous opportunities
for me to teach with Protein Explorer and later FirstGlance in Jmol in Japan, and to learn
more about structural biology.
Usage.
From 2006-2025, FirstGlance has been used to visualize molecules
more than 1.8 million times. In the
calendar year 2024, molecules were displayed on average 265 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.
A good strategy is to use FirstGlance to understand a protein molecule, and then use
Proteopedia to share customized views that illustrate your understanding.
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.
In calendar year 2024, 1,014 animations were generated (about one for every 95 molecules loaded).
Growth and Maintenance.
Since 2005 when FirstGlance was first made available, new, enhanced versions have been released
nearly every year to the present (2025). Often, several new versions were released in
a single year.
A complete list of
changes between versions of FirstGlance
is provided.
In 2025, FirstGlance offers
many unique capabilities absent from other
popular packages such as PyMOL, ChimeraX, iCn3D, and Mol*. FirstGlance is also much easier
to use, for most purposes, than are its free competitors.