Jmol: Open-source molecular visualization and analysis

Jmol: Open-source molecular visualization and analysis

Robert M. Hanson (St. Olaf College), Egon Willighagen (Cologne University Bioinformatics Center), Nicolas Vervelle (Jmol Project), Timothy Driscoll (molvisions), and Miguel Howard (Jmol Project)

Introduction to Jmol

Jmol is a free, open-source molecule viewer for chemistry and biochemistry. It works on multiple platforms, including Windows, Mac OS X, and Linux/Unix systems. The software consists of three parts, all written in the Java programming language: the Jmol applet, the Jmol application, and the Java development toolkit, JmolViewer. The Jmol application is a standalone Java application that runs on the desktop. JmolViewer is a set of Java “classes” that can be integrated into other Java applications to provide molecular visualization and analysis of chemical structure. While interesting in their own right, in this paper we will focus on the third component of the triad, the Jmol applet, as it is the component that can be integrated into web pages.

Jmol has many features to offer in the fields of chemistry and biochemistry. We will highlight many of them in this paper. Screen shots illustrating the broad variety of applications of Jmol are shown in Figure 1. For example, Jmol supports rendering of secondary structures of proteins and nucleic acids, it can produce animations of chemical reactions and conformational changes, and it can help visualize vibrations of small molecules based on quantum mechanics or molecular mechanics calculations.

Figure 1. Some Examples of Jmol.

click on an image to open a new window using Jmol.

Recent work has added many new capabilities (Figure 2), including the ability to select specific groups of atoms based on connectivity and to modify bonding patterns. Jmol can now display orbitals and other surfaces, including planes and axes that can help in the visualization of symmetry. Most recently, Jmol can now depict a wide range of polyhedral structures. These and many more capabilities will be highlighted in this paper.

Figure 2. Recent additions to Jmol functionality.

click on an image to open a new window using Jmol.

Jmol supports many of the common input and output formats, and new file reading capabilities are added on an as-needed basis (Table 1). Compressed files are automatically uncompressed in the browser for faster downloads.

Table 1. File formats read by Jmol (April, 2006)
CIF	Crystallographic Information File
mmCIF	Macromolecular Crystallographic Information File
CML	Chemical Markup Language file
CSF	Fujitsu CAChe chemical structure file
CTFile	Elsevier Molecular Design chemical table file
GAMESS	General Atomic and Molecular Electronic Structure System output file
Gaussian	Gaussian, Inc. output file
HIN	HyperChem native file
Jaguar	National Center for Supercomputing Applications Jaguar output file
MM1GP	Ghemical molecular mechanics file
MOL	Elsevier Molecular Design structure file
MOLPRO	Molpro output file
MOPOUT	MOPAC (public domain) output file
NWCHEM	Pacific Northwest National Laboratory NWChem output file
PDB	Research Collaboratory for Structural Bioinformatics Protein Data Bank file
QOUT	Q-Chem, Inc. output file
SHELX	SHELX output file
SMOL	Wavefunction, Inc. Spartan data file
XYZ	Minnesota Supercomputer Institute XMol file format
XYZ+vib	XYZ format files with added vibrational vector information (source unknown)
XYZ-FAH	Folding@home XYZ file

The Problem of Molecular Visualization on the Web

Chemistry is often referred to as the “molecular” science. As such, students of chemistry early on are introduced to molecules as three-dimensional objects, and many sorts of wooden or plastic or even paper molecular models are used in the teaching of chemistry. To this day, many students in organic chemistry are still required to purchase molecular model “kits” that allow the construction of a limited set of molecular structures. These kits help students “see” the symmetries and structural factors involved in chemical geometry and reactivity.

RasMol[1] was a key development in the history of computer-based molecular

visualization. Roger Sayle began developing it in 1989 as a system for

rendering 3D molecules on raster displays. He spent several years in the

early 1990s improving performance and porting to various systems. With the

help of the growing user community, he continued to add functionality,

much of it related to PDB files and biochemistry. In 1993 he released the

One of RasMol’s most intriguing aspects was (and still is) that it has a

scripting language which can be used to control the visual representation

of the molecule. One could develop lists of operations to be carried out

on the molecule in order to showcase important aspects of the molecular

structure such as alpha helixes, beta-pleated sheets, and hydrogen bonds.

RasMol is a stand-alone program that requires downloading and

installation. In the mid 1990s, with increasing interest in graphical web

browsers on the internet, there was growing demand among

chemical/biochemical educators and researchers for a method of conveying

the three-dimensional aspect of molecules on the web. Using the RasMol

public domain source code as a basis, Molecular Design Inc. created a

plug-in for the Netscape web browser. The Chime Netscape plug-in was

introduced to the chemical community at the 211th ACS National Meeting

almost exactly 10 years ago, in April of 1996.[2] Chime’s primary use was

for visualizations within MDL’s proprietary chemical inventory database

system, but it was also made freely available to the public.

Chime was an enabler for educators, providing widespread availability to a

web-based scriptable “virtual” molecular model kit along the lines of

RasMol. Chime was quickly adopted by educators as a valuable tool for

displaying molecules and demonstrating concepts. Thus, with the

introduction of Chime, virtual molecular visualization took a big step

into the general chemistry, organic and biochemistry classroom.

Chime was based upon browser plug-in technology, and therefore inherited a

set of technical complexities associated with plug-ins. A problem for

end-users was that the plug-in required manual installation on individual

user machines. At the university level in particular this was a problem,

as students might be using campus-wide public computing resources largely

out of the control of the professor or the designer of the web site.

A set of larger problems was caused by the fact that plug-in behavior was

different across browsers and operating systems. Netscape and Microsoft

did not implement plug-ins in the same way. The MSFT Internet Explorer

plug-in mechanism was different from the Netscape Navigator plug-in

mechanism and Netscape on Windows behaved differently from Netscape on

Macintosh. At times this made it difficult for content developers to build

portable web pages that would reliably run on different web browser

platforms.

In the long run, this inconsistent plug-in behavior had an even more

significant impact on MDL and on the future of Chime. Porting and

maintaining Chime on different platforms represented a significant ongoing

software development cost to MDL. These costs became increasingly

difficult to justify, particularly after the internet “bubble” burst. MDL

ultimately made the decision to stop porting to new systems and to put

Chime in “maintenance mode”. Consider these notes at MDL's Chime support web site:

When will you have a version of Chime for Macintosh OS-X or Linux?

We don't have any current plans for an OS-X version of Macintosh or a Linux version.

Why doesn't Chime work with Netscape 6 and 7?

Chime has been tested on a number of platforms, including certain versions of Netscape and Internet Explorer. The fully tested browser and operating system combinations are listed under the Requirements link. Other combinations of operating system and browser may work partially or not at all. Unfortunately, we don't have the resources to test Chime on every new browser and operating system.

The Jmol Solution

This potential crisis for chemical educators who were developing web-based content using Chime was diffused by the timely development of Jmol.

The Java programming language[3] was designed as a modern programming environment for the web. Cross-platform support and safe execution of downloaded code are fundamental to the design. Because the Jmol applet is written in Java, most of the cross-platform porting, maintenance and installation issues associated with the Chime plug-in do not exist. Jmol development regularly occurs on Linux, Mac OS X and Windows systems. When a user visits a web page containing the Jmol applet,

the program is automatically downloaded and executed on the client’s browser without requiring installation.

Dan Gezelter started writing Jmol in the late 1990s with the intention of building a replacement for XMol, an early program distributed by the Minnesota Supercomputer Center (now the Minnesota Supercomputer Institute).[4] Dan, then assistant professor at the University of Notre Dame, had started the OpenScience Project to promote open-source scientific software. Although Dan has not been directly affiliated with Jmol for a number of years, his early contributions as project founder were very important.

Egon Willighagen joined the project in 1998, contributing support for CML files and other file formats as well as other new functionality. In 2002 he became Jmol project leader and oversaw a number of public releases. Egon also has responsibility for maintaining the interface between the Chemical Development Kit software library and Jmol.

Miguel Howard joined the project in late 2002, with the explicit goal of building Jmol into a viable replacement for the Chime plug-in. His first major contribution was an interpreter for the RasMol/Chime scripting language. In the spring of 2003 Miguel began designing and implementing a software-based graphics engine that would provide cross-platform high-performance 3D functionality. He subsequently redesigned and re-implemented the core architecture to support efficient rendering of macromolecules with hundreds of thousands of atoms.

An extended testing period began at the end of 2003. Through 2004 a small set of users around the world made significant contributions to the Jmol project by testing Jmol releases and explaining scripting behaviors of RasMol and Chime.

Tim Driscoll, because of his extensive experience with Chime, was particularly helpful during this process. He helped resolve a number of issues associated with macromolecules, including definitions of protein/nucleic predefined sets and schematic rendering of secondary structures.

Bob Hanson also got involved during this time, developing an interactive web site providing Jmol script documentation and examples. Feedback and contributions from Bob and other JavaScript experts led to the development of the Jmol.js JavaScript library, which makes introducing Jmol into web pages almost trivial.

Jmol version 10.00, a fully functional replacement for the Chime plug-in, was released in December 2004.

As the Jmol community grew, requests for new functionality came in. Through 2005 a number of new scripting, rendering and file format features were introduced into the development version of Jmol. Notable additions included support for polyhedra representations and isosurfaces.

Nicolas (Nico) Vervelle joined Jmol because of his interest in the Folding@home

project. He contributed the file reader for folding@home’s files and added expressions for substructure searching using SMILES syntax. Nico then took over responsibility for managing internationalization and localization efforts.

Another official release, Jmol version 10.2, was made in April 2006. It included language localizations for Catalan, German, Spanish, Estonian, French, Dutch, and Portuguese. In the spirit of open source development, localizations were contributed and maintained by Jmol users from different countries.

Jmol development continues along a variety of paths, and the Jmol community continues to grow, with increasing involvement and interest from educators and scientists around the world.

What follows is a discussion of the use of Jmol in education in a variety of chemical and biochemical contexts. The discussion highlights web sites that have utilized Jmol, general capabilities of the current version of Jmol, and a few sneak peeks of some of the more experimental features of Jmol not yet publicly released. This list is by no means comprehensive. Most of these examples were taken from the extensive list at the Jmol wiki, which also includes examples of the use of Jmol in research.

Jmol for General and Inorganic Chemistry

In the area of general chemistry, Jmol has been used primarily to illustrate the various common three-dimensional molecular shapes. Some representative sites are shown in Table 2.

WebElements utilizes Jmol for the display of crystal structures of the elements. The 3Dchem.com site illustrates how easy it is to add a structure to any web page. This can be seen by taking a peek at the source for one of these pop-up windows. Explain it with Molecules uses Jmol to help explain everyday questions with the aid of 3D models. The CoolMolecules site illustrates a novel feature of Jmol – the ability to create a 3D model of a structure on the fly – with no actual structure file on the server. Instead, the data for all of the structures are stored in a compressed fashion in one single file, which is delivered to the user’s browser upon page loading. John Gutow’s VSEPR tutorial and Mark Winter’s Introduction to VSEPR are both excellent examples of the integration of Jmol into an online lesson in bonding theory and its association to molecular shape and electronic configuration. Richard Spinney (Ohio State) has developed an amazing site, “Dr. Spinney’s World of Chemistry” that employs Jmol in a wide variety of creative ways. Several web sites use Jmol to depict atomic and molecular orbitals in terms of probability, using Jmol “atoms” to represent positions around the nucleus. Finally, the University of Bristol maintains a Molecule of the Month site that features user-contributed articles, many of which involve Jmol applets as part of the illustrations.

The issue in inorganic chemistry for which Jmol has provided a general solution is the description of symmetry. An example can be seen in a recent contribution at the Journal of Chemical Education’s WebWare site, a component of the JCE Digital Library, which is a Collection within the National Science Digital Library (NSDL). We expect to see additional applications of Jmol within this area in the future as Jmol develops and the newer features involving symmetry planes, rotational axes, internal axis rotation, and internal coordinate referencing become more widely known.

Table 2. Representative Uses of Jmol in General and Inorganic Chemistry

WebElements (sulfur shown)

http://www.webelements.com/ “WebElements aims to be a high quality source of chemistry information on the WWW relating to the periodic table. Coverage is such that professional scientists and students at school interested in chemistry and other sciences will all find something useful.”

Access to the Jmol structures is via the “elemental properties – Crystal structure” link on each element page.

3Dchem.com

http://www.3dchem.com “Showing the world of chemistry and nano science in beautiful interactive imagery. This web site highlights areas of the chemical world and illustrates the structures behind the words. It also provides background information about the science of the chemicals.”

When the user clicks on any image of a molecule, a Jmol applet appears in a pop-up window. Controls are provided.

Explain it with Molecules -- Interactive Molecules (ice shown)

http://www.edinformatics.com/interactive_molecules “Explain it with Molecules -- Interactive Molecules-- is about "real interactivity"! All you need is to be java enabled. The Jmol Applet used with these molecular structures will allow you to view molecular structures in 3-D. Images can be viewed as wire-frame, ball and stick or CPK. As with the Chime plug-in, it is also possible to measure distances and angles.”

CoolMolecules

http://www.stolaf.edu/depts/chemistry/mo/struc “All of the 962 structures in the full database are actual, experimentally-determined structures. They are displayed TO SCALE (100 pm = 1 cm on my screen). You can rotate them around to see them from different angles, and you can double click on them to check bond lengths and angles right on the model itself.”

Structures are delivered to the browser as JavaScript arrays and then sent to the applet using Jmol’s applet.loadInline() function.

VSEPR tutorial

http://www.uwosh.edu/faculty_staff/gutow/
VSEPR_TUTORIAL/VSEPR.html “This set of web pages is intended as a tutorial on estimating the shape of a molecule once you have determined the molecule's Lewis Structure. The model used is often called the VSEPR (Valence Shell Electron Pair Repulsion) model, and descriptions of it may be found in almost all introductory chemistry texts.”

Introduction to VSEPR

http://winter.group.shef.ac.uk/vsepr “By arrangement with the publisher (Oxford University Press), this introduction to VSEPR is a hypertext version of Chapter 4 in my book on Chemical Bonding, one of the Oxford Chemistry Primers.”

Dr. Spinney’s World of Chemistry (atomic orbital page)

http://undergrad-ed.chemistry.ohio-state.edu/

An extensive site covering many popular topics in general and organic chemistry. Uses of Jmol at this site in the area of general chemistry include the displaying of atomic orbitals based on Monte Carlo methods, a visual guide to VSEPR theory, and an introduction to chemical bonding.

Orbitron

http://winter.group.shef.ac.uk/orbitron/ “The Orbitron: a gallery of atomic orbitals and molecular orbitals on the WWW.”

This site, like the previous one, uses Jmol to depict atomic orbitals as probability.

Orbital

http://www.stolaf.edu/people/hansonr/orbital/ “ORBITAL.EXE is a Visual Basic 3.0 program that runs under Microsoft Windows 9x. It allows students and presenters to produce probability-based three-dimensional representations of the atomic orbitals of the hydrogen atom. The orbitals are produced using a Monte Carlo technique and saved as XYZ files. These files are suitable for uploading to web sites and are displayed automatically using the default browser using the Jmol molecular viewer applet.”

Atomic and Molecular Structure

http://www.steve.gb.com/science/atomic_structure.html

This page goes one further and used Jmol to depict sigma and pi molecular orbitals in terms of probability.

Molecule of the Month

(Feb 2004 shown)

http://www.chm.bris.ac.uk/motm/motm.htm “Each month a new molecule will be added to the list on this page. The links will take you to a page at one of the Web sites at a University Chemistry Department or commercial site in the UK, the US, or anywhere in the world, where useful (and hopefully entertaining!), information can be found about a particularly interesting molecule.”

Molecules can be displayed using a number of formats; the Java “JM” option selects Jmol as the display applet.

An Animated Interactive Overview of Molecular Symmetry

http://www.jce.divched.org/JCEDLib/WebWare/
collection/reviewed/JCE2005p1742WW

“An Animated Interactive Overview of Molecular Symmetry is a series of web pages designed to help instructors teach molecular symmetry. These pages combine interactive images and instructional text that allow students to examine and explore the operations and elements that give rise to molecular symmetry.”

Jmol for Organic Chemistry

We cannot hope to present in this paper more than a small glimpse of the extensive use of Jmol that has appeared in the area of organic chemistry. A recent Google search of “jmol organic” returned “about 18,400” hits. In Table 3 we give only a small sampling the many excellent sites on the Web, just as a way of illustrating some of the variety of uses of Jmol. Topics cover a wide range, primarily because so much of organic chemistry relies upon a visual understanding of molecular structure and reactivity.

Table 3. A Few Representative Uses of Jmol in Organic Chemistry

Virtual Textbook of Organic Chemistry

(butane conformers)

http://www.cem.msu.edu/~reusch/vtxtindex.htm “An interactive textbook covering the usual topics treated in a college sophomore-level course. Links are offered to advanced discussions of selected topics.” This understated description accompanies the most extensive online discussion of organic chemistry ever produced. It is, in fact, a complete, online textbook involving hundreds of utilizations of Jmol.

Dr. Spinney’s World of Chemistry (symmetry page)

http://undergrad-ed.chemistry.ohio-state.edu/ Uses of Jmol at this site include the displaying of atomic orbitals based on Monte Carlo methods, VSEPR theory, molecular orbitals, animated reaction animated spectra, symmetry. The page shown on the left shows use of the Jmol pmesh capability to illustrate symmetry planes.

Mol4D

http://cheminf.cmbi.ru.nl/wetche/organic/ “The WeTChe.NL tutorials are an initiative of the Faculty of Science, University of Nijmegen. The goal is to develop web based supplementary material for courses in Chemistry, at all levels. The largest part of 'molecules in four dimensions' is (at least at this moment) devoted to organic chemistry.”

Spectral Zoo

http://web.centre.edu/muzyka/organic/organic.htm “This site includes Jmol-enabled tutorials to allow students to better understand difficult organic chemistry concepts such as conformations, sterics, and stereochemistry. There are also Jmol-enabled animations for substitution and elimination reactions. The Spectral Zoo is a set of combined spectra which serve as practice problems.”

Jmol/JSpecView

http://wwwchem.uwimona.edu.jm/spectra/JSpecView/ msanim/dodecaneJ/dodecane.html “JSpecView is a viewer for spectral data in the JCAMP-DX format. Examples of the combination of spectra and molecular graphics to show the interpretation of simple IR, MS or NMR using JspecView and Jmol are available.” This page uses several innovative aspects of Jmol, including “designer” planes and the use of “show file” to transmit the contents of the model file to JavaScript for further processing – in this case, determining the masses of the fragments selected by the user.

DCU Molecular Viewing Gallery

http://webpages.dcu.ie/~pratta/jmgallery/JGALLERY.HTM “The DCU Molecular Viewing Galleries currently contain over 400 molecules, organised alphabetically and viewable in pairs in adjacent viewing frames.”

Jmol for Biochemistry and Molecular Biology

Following the precedent of Chime and RasMol, Jmol has been utilized in the area of biochemistry and molecular biology in a variety of applications both in research and in education. Highlighted in Table 4 are selected applications of particular interest to educators that are employing Jmol, including web-accessible databases (Research Collaboratory for Structural Bioinformatics Protein Data Bank), structure explorers (FirstGlance, JenaLib), tutorials focusing on specific biomolecules and biological pathways (the Online Molecular Museum, Libmol, y Apuntes de Biología Molecular), and media tools for instructors (Molecules in Motion, MolSlides).

Table 4. Representative Uses of Jmol in Biochemistry and Molecular Biology
RCSB PDB (1d66 shown)	http://www.rcsb.org/pdb “The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. The RCSB is a member of the wwPDB, whose mission is to ensure that the PDB archive remains an international resource with uniform data. This site offers tools for browsing, searching, and reporting that utilize the data resulting from ongoing efforts to create a more consistent and comprehensive archive.” Jmol is one of the five viewers recommended by RCSB.
FirstGlance in Jmol (1blu shown)			http://molvis.sdsc.edu/fgij “FirstGlance in Jmol is a simple, free tool for macromolecular visualization. The initial display is Cartoon plus Ligands+. Click on the links and buttons above to see different aspects of the molecular structure.” Buttons show informative views of any macromolecule available on-line. Help, including color keys, appears automatically and is always in view. Hyperlinks show a molecule in one click. It is designed to be useful both to novices and to specialists.
JenaLib (1ash shown)		http://www.imb-jena.de/IMAGE.html “The Jena Library of Biological Macromolecules (JenaLib) is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. It provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). In addition, basic information on the architecture of biopolymer structures is available.”

The Online Molecular Museum		http://www.callutheran.edu/Academic_Programs/ Departments/BioDev/omm/gallery.htm “The Online Macromolecular Museum (OMM) is a site for the display and study of macromolecules. The OMM is part of a collaborative effort by faculty and students interested in macromolecular structure-function relationships.” Older exhibits are rendered in Chime; Jmol exhibits are indicated in red.
Libmol (1ag2 shown)		http://www.librairiedemolecules.education.fr Librairie de molecules “La librairie de molécules a pour but d'améliorer le transfert des connaissances de la recherche vers l'enseignement. Elle propose des modèles moléculaires sélectionnés à partir des banques de données des chercheurs par des enseignants pour les enseignants. Tout utilisateur peut contribuer à l'enrichissement de la librairie en proposant de nouveaux modèles et de nouvelles applications pédagogiques.”
Apuntes de Biología Molecular			http://av.bmbq.uma.es/bma/apuntes/index.htm “Con esta asignatura pretendemos enseñar las características físico-químicas de las macromoléculas que condicionan todo el funcionamiento celular así como mostrar que la estructura de las moléculas viene guiada por las distribuciones electrónicas de los átomos que las componen. También esperamos que quede claro que en la conformación y en los cambios conformacionales de las moléculas reside su función biológica y su regulación. Con ello queremos dejar claro que es mucho más lo que se desconoce que lo que se conoce sobre la biología molecular, por lo que animamos a la búsqueda y al análsis crítico de la bibliografía y los medios para acceder a la información molecular.”
Molecules in Motion	http://www.moleculesinmotion.com/ This site demonstrates two entertaining Jmol-based “movies” entitled “What is a Protein?” and “DNA Structure (with a little RNA thrown in)”.
MolSlides (1d66 shown)		http://www.umass.edu/microbio/chime/ my_molecules/molslides/bundled “MolSlides are annotated slides of rotating 3D views molecular structure. They are created with Protein Explorer. MolSlides can be saved from PE with a few mouse clicks. No text editing of disk files is involved. No knowledge of Chime command scripts or programming is needed.”

Jmol for Mineralogy and Crystallography

Jmol has found use in displaying the structure of minerals. Sites utilizing Jmol are listed in Table 6. The recently added connection and polyhedra capabilities of Jmol are expected to expand this use considerably.

Table 6. Representative Uses of Jmol in Mineralogy and Crystallography

Mineralogy Structure Index (perovskite shown)

http://webmineral.com/jmol/index.shtml “This mineral database contains 4,442 individual mineral species descriptions with links and a comprehensive image library.” Mineral Structure Index: “Click on mineral name in the Index of Mineral Structures for a large interactive display (Jmol Applet) of the chemical structure.”

The Virtual Museum of Minerals and Molecules

http://virtual-museum.soils.wisc.edu “The Virtual Museum of Minerals and Molecules™ is a web-based focal point and resource for 3-D visualizations of molecules and minerals designed for instructional use.”

This website is organized along the lines of a typical museum with “wings” and “galleries” all devoted to the structure of minerals.

WebEMAPS (FeS2 shown)

http://emaps.mrl.uiuc.edu

Web Electron Microscopy Applications Software

With this website you can enter crystal data from CIF files or manually based on symmetry or choose from a list of crystal structures already on the server. After specifying the number of unit cells, the structure is displayed using Jmol.

Molecular Origami (zircon shown)

http://www.stolaf.edu/people/hansonr/mo

Molecular Origami

The recent addition of “collapsed polyhedra” to Jmol (prototype version) has allowed the use of Jmol to produce realistic-looking virtual equivalents of the precision scale models created from paper.

Jmol in Textbooks

An exciting development has been the utilization of Jmol by several publishers for mostly biochemistry-related textbooks as the viewer of choice for their web site ancillary material. Those we know of are listed in Table 5.

Table 5. Textbooks Utilizing Jmol
Voet, Voet, and Pratt: Fundamentals of Biochemistry: Life at the Molecular Level, 2nd Edition	New to this edition: “Upgraded and re-designed web-based media program to accompany and complement the text includes Interactive Exercises, Guided Explorations, Animated Figures, as well as Kinemages. Media resources have been upgraded to take advantage of the most recent, web-friendly 3D visualization tools, eliminating the need for the Chime plug-in, which has proven to be problematic.”
Campbell and Heyer: Discovering Genomics, Proteomics and Bioinformatics, 2/E	“The Second Edition has been thoroughly revised and updated to incorporate the latest scientific findings on popular topics such as disease-causing organisms and genetic defects. Case study chapters have been placed throughout the book to tie real-life scenarios into the concepts that follow. Two of the book’s key pedagogical features, Discovery Questions and Math Minutes, have also been updated and expanded. The interactive companion website has been reprogrammed with JMOL, the latest 3-D software used to view DNA structures.”
Brooks-Cole General, Organic, and Biochemistry Chemistry Textbooks	New to this edition: “Organic and Biochemistry OWL content takes advantage of the latest technological advances in online computer modeling using Jmol and Marvin Sketch. MarvinSketch, a Java applet for viewing and drawing chemical structures, enables OWL to grade chemical structures that the students draw and is used extensively in the content for the Organic and Biochemistry chapters. Jmol, an interactive molecule viewer, enables students to rotate molecules, to change the display mode (ball and stick, space fill, etc.), and to measure bond distances and angles.”
Lehninger: Principles of Biochemistry	Future edition will incorporate Jmol.
Stryer: Biochemistry 6/e	Future edition will incorporate Jmol.

Jmol in the Hands of Instructors and Students

Examples of individual instructors involving students in the use of Jmol are starting to appear on the Web. For example, the online homework system, webassign, has recently added a Jmol template. Jmol has also been integrated into the OWL system. Students at the University of Arizona in an honors introductory biochemistry course were asked to explore the structure of brazzein for one of their homework assignments during the Fall of 2005.[5]

Conclusions -- Future Directions for Jmol

Jmol development relies solely on the volunteer contributions of scientists, educators, and programmers. Nonetheless, it is expected to be rapid during 2006. Areas currently under active development are listed below. Links open experimental pages that illustrate implementation of these goals within the very latest prototype “trunk” of the development tree (trunk). We welcome your comments, and we encourage you to get involved by joining the jmol users list if you are interested in contributing to the discussion or the Jmol developers list if you are interested in contributing at the developer level.

[after-notes added 2/23/2007]

· The introduction of solvent-accessible surfaces and surface mapping. [see isosurface]

· The ability to apply crystallographic symmetry and view multiple unit cells. [see load]

· The calculation and display of dipole moments and bond dipoles. [see dipole]

· Drawing points, lines, and planes based on atom positions or {x y z} coordinates. [see draw]

· Rotation and spinning around internal axes. [see rotate]

· Making multiple measurements all at once and providing running measurements in animations. [see measure]

· The ability to extract calculational and structural data from files. [see mo]

· The ability to probe the applet for a wide range of status messages as a replacement for callback functions. [callbacks found to be superior to polling -- see callback]

· Easier integration into wikis such as MediaWiki.

· Support for multiple file loading and independent manipulation. [see invertSelected]

· Further development of the application programming interface (API), which allows Jmol to “talk” to other applications and applets. [see AJAX]

Clearly, Jmol has come a long way during the past few years and is rapidly becoming one of the most popular Java applets in chemistry. Its strength is in its speed of rendering, its flexibility in file reading, its broad applicability in both small-molecule and macromolecule applications, and its ease of use. Applications range from general chemistry to computational chemistry, from inorganic chemistry to molecular biology to mineralogy and crystallography. The applet is fast becoming far more than simply a tool for putting a “gee-wiz” three-dimensional model of a molecule on the web. New capabilities allow it to be an investigative tool as well, allowing the web designer/user to gain access to information such as atomic charges, dipoles, vibrational frequencies, space group symmetries, and molecular orbitals contained in data-rich formats such as CIF, CDX, CML, and SMOL. Most importantly, as an open-source project, the Jmol discussion lists have become valuable forums for the discussion of important molecular visualization and data analysis ideas among an energetic and dedicated group of scientists and educators from all over the world.

References