What Is FirstGlance in Jmol?

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What Is FirstGlance in Jmol?

Purpose

What Can It Do?

What Should Beginners Use?

What Is The Competition?

Comparisions with PyMol, Protein Workshop, QuickPDB, WebMol, and KiNG.

Where Do The Molecules Come From?

How Does It Work?

Purpose: FirstGlance in Jmol is the easiest way to look at the 3D structures of proteins, DNA, RNA, and their complexes. It works within a web browser, and was designed to enable the readers of scientific journals to see the main features of newly published 3D models in a few clicks, without installing anything, and in all popular web browsers and computer platforms. It is in use by Nature Structural and Molecular Biology (see the 3D View links there), and the ConSurf Server (which automatically colors amino acids by evolutionary conservation), among others (see Adoptions).
What Can It Do? FirstGlance in Jmol can display major structural features of the molecule with one click each. Initially, each chain is given a different color, making it easy to see how many protein or nucleic acid chains are present. Clicking on something identifies it. One-click options display secondary structure, amino and carboxy (or 3' and 5') termini, composition (protein, DNA, RNA, ligands, and solvent), the distributions of hydrophobic, polar, and charged amino acids, salt bridges and cation-pi orbital interactions for amino acids. Non-standard residues and missing sidechains are flagged automatically. Examples can be seen in the Snapshot Gallery.

A Find.. dialog makes it easy to locate amino acids by name, sequence number, or a range of sequence numbers. Any chain, residue, or atom can be hidden by clicking on it in the Hide.. dialog, and remains hidden in most views until explicitly re-displayed.

The Contacts.. dialog shows the non-covalent interactions to any moiety you select (by clicking on it). The non-covalent interactions are automatically divided into seven categories: hydrogen-bonded water, water bridges, hydrogen-bonded non-water, hydrophobic interactions, salt bridges, cation-pi orbital interations, and metal and miscellaneous interactions. Checkboxes control whether or not each category is displayed. Examples can be seen in the Snapshot Gallery.

More Views.. includes coloring by uncertainty (B-factor, temperature factor), and display of the unit cell, axes, or bound box.

Links to external resources show specific oligomers, further information about the molecule and the quality of the model, and locate any gaps in the model.
What Should Beginners Use? FirstGlance in Jmol was designed for readers of scientific journals who are already familiar with the principles of protein structure. Therefore, it lacks the extensive help, and guidance in understanding, interpreting and evaluating 3D macromolecular models that is built into Protein Explorer (see Comparison). Protein Explorer was designed for students, educators, and beginners as well as more experienced users. It is considerably more powerful, making it easy to customize views from menus and buttons, and to create MolSlides.

However, Protein Explorer requires the free Chime plugin, which limits full functionality to the Firefox browser on Windows, and precludes it from working in Mac OS X (except in a Windows virtual machine or alternate boot; More..). In the future, it is planned to port Protein Explorer to use Jmol, instead of the Chime plugin, which will remove these limitations.
What Is The Competition?

Ease of Use. FirstGlance in Jmol was designed to enable viewing a molecule in one click, in all popular web browsers and computer platforms -- without installing anything. Several other java-based applications that meet these criteria are offered by the RCSB Protein Data Bank. Generally, these lack the ease of use, automatically-displayed context-sensitive help and color keys provided by FirstGlance in Jmol, and offer a less complete set of one-click molecular overview options. While FirstGlance in Jmol is designed to be "obvious" with labels clear to non-specialists that avoid crystallographic jargon, the other viewers often use the latter. Touching controls in FirstGlance in Jmol raises explanatory "tool tips", absent in the other viewers. For those interested, most terms in FirstGlance in Jmol are carefully defined (e.g. "metal", "carbohydrate", "non-standard residue") while other viewers typically leave such terms undefined.

Power. None of the other viewers offer an easy method to show all non-covalent interactions to any arbitrary moiety, comparable to the Contacts.. dialog of FirstGlance in Jmol.

However, aside from the general limitations noted above, each of the in-browser java-based viewers offered by RCSB has its special strengths:
- QuickPDB has a nice sequence-to-structure interface. At the outset, QuickPDB shows a one-letter code sequence, and when you touch (not click) any residue, it labels that residue in the 3D view. FirstGlance in Jmol lacks a sequence listing at this time, but you can use its "Find.." interface to enter a sequence number or range to locate them in the 3D view. And FGiJ has a PDB-code-specific link to RCSB for a sequence listing, and also a "Gaps" link to the SEQRES to Coordinates (S2C) listing from Wang and Dunbrack. However, QuickPDB (in late 2006) did not show nucleic acids at all.
- WebMol does dot surfaces including cavities (full molecule dot surface rotates very slowly; FirstGlance in Jmol lacks cavity viewing). It has very nice interactive distance matrix and Ramachandran displays. However, in order to run it, the user must approve an invalid digital signature. The initial view is uninformative wireframe (like RasMol). Touching a residue reports amino acid but not nucleotide identities. It has a wire-thin backbone trace which is not smoothed, and it offers no ribbons view.
- KiNG (Kinemage New Generation) shines for specialized applications such as showing clashes at the MolProbity Server, but has many idiosyncracies that limit its usefulness for general viewing by novices.
Image Quality. FirstGlance in Jmol's image quality is better than any of the other in-browser, java-based viewers offered at the Protein Data Bank. Nevertheless it does not provide the "publication quality" images of PyMol or the stand-alone Protein Workshop java application (see below).

Protein Workshop, also offered by the RCSB PDB, is a stand-alone java application spawned by the web browser (not an in-browser view). When tested in late 2006, this was unacceptably slow to rotate ordinary-sized proteins, but has much more beautiful rendering than does FirstGlance in Jmol.

Viewers Not Offered by RCSB. There are numerous, excellent stand-alone 3D molecular viewing applications (most listed at The World Index of Molecular Visualization Resources). PyMol, in particular, has become widely popular among structural biologists in recent years, including for making publication-quality images.
Where Do The Molecules Come From? FirstGlance in Jmol usually obtains the molecules it displays (atomic coordinate PDB files) from the US Branch of the Worldwide Protein Data Bank (PDB), which makes freely available all published macromolecular 3D structure data. In order to display functional biological assemblies (specific oligomers), theoretical models, and other data files not available from the PDB, FirstGlance in Jmol can obtain molecules from any web server (More..).
How Does It Work? Technically, FirstGlance in Jmol is a user interface to the Jmol java applet. FirstGlance in Jmol is written in javascript and HTML, while Jmol is written in java. FirstGlance in Jmol makes the visualization power built into the Jmol java applet accessible to users who do not have the time to learn the Jmol command language, or how to embed Jmol in web pages. Jmol is developed separately by its own open-source volunteer team. FirstGlance in Jmol has been developed largely by Eric Martz (author of Protein Explorer), but others are free to get involved since it is an open-source project. FirstGlance in Jmol has a very permissive Creative Commons Attribution license, while Jmol itself uses the GNU Lesser General Public License.

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