|
| Initial view of Hin recombinase protein bound to DNA double helix (1ijw). |
.
Residues
with incomplete sidechains are marked S-, and non-standard residues
are marked X.
|
| Potassium channel (1R3J) showing membrane surface planes. Obtained (from OPM) via Resources tab in FirstGlance. |
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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:
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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.
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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 chain or ligand molecule,
and this persists in all views until isolation is undone.
The Ends.. tool lists the ends of chains, telling whether they are charged, missing,
or blocked. Clicking on one end zooms in and shows all its contacts and non-covalent interactions.
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, or, using Find.., by name, sequence numbers, etc.). 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.
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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 the molecule should spin at the beginning of a session, etc.
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 March, 2020, approximately 0.8% of the entries in the Protein Data Bank are too large for FirstGlance.
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. Background information about terms
and concepts is provided through links to articles in
Proteopedia.Org.
- 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.)
- Tabulates an analysis of alternate locations and occupancies
with links to view subsets of interest.
(Molecule Information 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").
Jmol is developed separately by its own open-source volunteer team. FirstGlance in Jmol has been developed largely by Eric Martz, with much-appreciated help from many others. 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.