What Is FirstGlance in Jmol?
Updated May, 2016.

Purpose How Does It Work? What Should Beginners Use? Your "First Glance"! What Does It Tell You? What Can It Do? What Can't It Do? How Good Is The Competition? Where Do The Molecules Come From? How Does It Work? (Technical)

- 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 has been in use by Nature since 2007, as well as Nature Structural and Molecular Biology (see their 3D View links), Proteopedia.Org, the OCA Structure Browser, and the ConSurf Server (which automatically colors amino acids by evolutionary conservation), among others (see Adoptions).
- How Does It Work? FirstGlance in Jmol is a user-interface to the preeminent free molecular visualization program named Jmol (more at jmol.org). Jmol is very powerful, but in order to access that power, you either need to learn a complicated command language, or use a wrapper (user interface) such as FirstGlance in Jmol. FirstGlance makes much of the power inherent in Jmol accessible to people who don't have the time or inclination to learn Jmol's command language. More..
- What Should Beginners Use? FirstGlance in Jmol was designed to be easy for beginners and non-specialist researchers. Help is displayed automatically, with links to further information about structural biology terms and concepts. Yet FirstGlance in Jmol has ample power for researchers and structural biologists. It is not uncommon for it to show structural biologists features of a model that they did not appreciate before.

  Initial view of Hin recombinase protein bound to DNA double helix (1ijw).

- Your "First Glance"! The initial view is designed to be maximally informative. Each protein or nucleic acid chain is assigned a different pastel color, so it is easy to distinguish chains. Disulfide bonds are evident. The initial secondary structural schematic "cartoon" display makes alpha helices and beta strands obvious. All atoms or compounds that are not standard protein or nucleic acid residues ("ligands") have spacefilling atoms so they are obvious. A clickable list of ligands in the Molecule Information Tab (see below) gives their full names, and locates them. Touching or clicking on any atom in the 3D view identifies it. Regions with missing residues are marked with "empty basket" icons . Residues with incomplete sidechains are marked S-, and non-standard residues are marked X.
- What Does It Tell You? The control panel for FirstGlance is separated into five Tabs: Molecule Information, Views, Tools, Resources, Preferences. The Molecule Information Tab digests information in the PDB file, presenting it in readable form: Title of study/name of molecule, year of publication, method of structure determination. For X-ray structures, resolution and free R are "graded" to interpret them for non-specialists. The number of models is given for NMR results, and viewing all models superimposed is one click away. A clickable list of chains gives the total number, shows which are sequence-identical, and locates each in the 3D model. For each chain is given the number of missing residues, and missing positive and negative charges. A clickable list of ligands and non-standard residues gives their full names, counts, and locates each in the 3D model. The abstract of the primary publication, and other publications, are linked.
- What Can It Do?

  Potassium channel (1R3J) showing membrane surface planes. Obtained (from OPM) via Resources tab in FirstGlance.

  - Save Images and Animations: Any molecular view in FirstGlance can be saved with a few clicks. It can be saved as a static image at any size desired (up to 5,000 pixels across). Or it can be saved as a rocking or spinning animation. Animations can be dropped into a slide (in Powerpoint, Google Slides, Libre Office, etc.), or displayed in web pages such as the example at right. Here are more examples of animations from FirstGlance:
    - Download Example Animations in Powerpoint.
    - View Example Animations Online in Google Slides.
  - Views Tab: Major structural features of the molecule are revealed. Explanatory help is shown automatically for each view. 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, charged amino acids, and local uncertainty (B factor/temperature). Non-standard residues, missing residues, and incomplete sidechains are clearly indicated. Centering, slab and zoom buttons make an uncluttered closeup examination easy for any moiety of interest. Examples can be seen in the Snapshot Gallery.
  - Tools Tab: A Find.. tool makes it easy to locate short sequences, and amino acids (or nucleotides) by name, sequence number, or a range of sequence numbers. A Hide.. tool hides any chain(s), residue(s), or atom(s) that you click. They remain hidden in other views until explicitly re-displayed. An Isolate.. tool, in one click, hides everthing except one residue or chain, and this persists in all views until isolation is undone.

    | Contacts & Non-Covalent Interactions: Anti-Alzheimer's drug analog (*) hydrogen bonds to tyrosines in acetylcholinesterase (1gpk).

    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 interations, and metal and miscellaneous interactions. Checkboxes hide categories, simplifying the display.
    Disulfide bonds are shown in the initial view, but here, a disulfides/S/Se tool highlights and counts disulfide bonds, sulfur, and selenium atoms (and counts cysteine, methionine, selenocysteine, selenomethionine). A salt bridge and cation-pi interaction tool highlights these. Distances and angles are easily measured with mouse clicks. Crystal contacts and the unit cell can each be displayed with a single click.
  - Resources Tab: Explanations with illustrated step-by-step guides provide visualization of biological units, evolutionary conservation, atomic clashes, lipid bilayer boundaries for integral membrane proteins, as well as help predicting intrinsically disordered segments of a protein chain, and sharing customized molecular views in the Proteopedia wiki.
  - Preferences Tab: You can specify whether links to FirstGlance will use Java or not, whether the molecule should spin at the beginning of a session, etc.
- What Can't It Do?
  Customized Views. FirstGlance is designed to show you important structural features as easily as possible. Views (renderings and color schemes) are "canned" for ease of use. FirstGlance does not let you customize a view beyond its "canned" options. If you wish to customize the rendering and colors, we recommend Proteopedia.Org, which has Molecular Scene Authoring Tools. Proteopedia is the easiest place to customize a molecular scene. Scenes that you create will be immediately online for sharing with anyone. Any scene in Proteopedia can be saved as a presentation-ready animation by FirstGlance (see instructions).
  FirstGlance has not yet been adapted to display mmCIF format atomic coordinate files. (Jmol has already been adapted for mmCIF files.) This means that FirstGlance cannot display some extremely large models, since the older PDB format is limited to 99,999 atoms per model, or a maximum molecular mass of about 1,400,000 Daltons. In May, 2016, approximately 500 (0.4%) of the entries in the Protein Data Bank are too large for FirstGlance.
- How Good Is The Competition?
  There are numerous molecular visualization software packages available. Sometimes a particular package is best suited to the job at hand. When comparing FirstGlance with another package, ask yourself whether the other package:
  - Shows an equally informative initial view (cartoon ribbons, each chain a different color, ligands obvious).
  - Displays an explanation and color keys for every view or operation that you perform. Has tool tips on every link and button.
  - Alerts you to missing residues, listing them on request. About 80% of X-ray entries in the PDB have missing residues (15% of NMR entries; percentages determined May, 2016). Labels residues with incomplete sidechains. 38% of X-ray entries have them. Most of the time users don't realize that anything is missing.
  - Displays key information from the header of the PDB file in readable form, with extensive explanations (the Molecule Information Tab in FirstGlance).
  - Alerts you to the quality of the model by objectively grading free R as better than average, average, worse than average, or unreliable, and explaining why free R is crucial and how it is graded.
  - Tells you the sequences of the crystallized fragment and of the full-length protein, and which chains in the model are identical in sequence. And you can label each residue by sequence number and/or residue name, or click on it to report the number and name.
  - Gives the full name of each ligand or non-standard residue. Clicking locates each in the model.
  - Has one-click renderings and color schemes to show you secondary structure (with statistics), solid (spacefilling van der Waals) renderings, the amino and carboxy termini (or 5' and 3' for nucleic acids), distribution of hydrophobic/polar residues on the surface and in the core of the protein, and distribution of charges with counts and resources for calculating pI and net charge at various pH's. (Views tab.)
  - Displays disulfide bonds, sulfur-containing residues, selenium-containing residues and statistics. Salt bridges and cation-pi interactions. (Tools tab.)
  - Offers a tool to see all atoms/residues contacting any moiety you choose -- including all non-covalent interactions. (Tools tab.)
  - Shows you Crystal contacts with examples of how they might affect the conformation of the protein in the crystal. Also the unit cell. (Tools tab.)
  - Enables you to find anything of interest in the 3D model: sequence motifs, sequence numbers or ranges, particiular amino acids or nucleotides, etc. etc.
  - Lets you isolate any single chain, residue, or ligand in one click, for closer examination. Also you can hide chains, residues, ligands easily by clicking on them.
  - Gives you easy access to the biological unit (functional quaternary assembly). In FirstGlance, it takes only 4 clicks to see it. Many users don't realize that they are not looking at the functional biological form of the molecule, but rather the crystallographic asymmetric unit.
  - Provides a link to view the abstract of the publication at PubMed.
  - Provides a Practical Guide to Homology Modeling. (Main page and Resources tab.)

    |  | Enolase ( 4enl; a glycolytic enzyme) evolutionary conservation from ConSurf. Catalytic pocket is highly conserved. More..

  - Provides an Introduction to Evolutionary Conservation as well as guidance for those with experience. FirstGlance can directly display proteins colored by evolutionary conservation (in collaboration with the ConSurf Server). This enables you to see the conservation of residues contacting ligand, involved in protein-protein interactions, as well as identifying functional regions based on their high level of conservation.
  - Offers assistance for using external resources to see atomic clashes (MolProbity), predict intrinsically disordered protein, see lipid bilayer boundaries on integral membrane proteins (Orientations of Proteins in Membranes). (Resources tab.)
  - Alerts you to unusual chemical elements in the model, and locates them.
  - Provides a master index where you can find how to access a particular tool or capability.
  - Defines and explains the technical terms it uses (such as "metal", "carbohydrate", "non-standard residue", "biological unit", "asymmetric unit", "free R").
- 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..), or you can upload your own model data.
- How Does It Work? (Technical) Technically, FirstGlance in Jmol is a user interface to the Jmol java applet (or alternatively to the JSmol application which does not use Java). FirstGlance in Jmol is written in HTML, javascript and Jmol command language. Jmol is written in Java. JSmol is a javascript version of Jmol produced by machine translation from the Jmol java code. As mentioned above, FirstGlance in Jmol makes the visualization power built into the Jmol accessible to users who do not have the time to learn the Jmol command language, or how to embed Jmol in web pages. When you request a particular view in FirstGlance in Jmol, the Jmol commands to produce that view are generated dynamically (with javascript) and sent to Jmol. The user may be unaware of this, simply seeing the desired view.
  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 uses the Creative Commons Attribution-Noncommercial-Share Alike 3.0 License, while Jmol itself uses the GNU Lesser General Public License.

For more details, see All About FirstGlance in Jmol.

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