Unique Capabilities: FirstGlance in Jmol
offers the following powerful/convenient features absent from the viewers offered by the
Protein Data Bank (2025: Mol*, basic Jmol, Molmil2)
as well as others such as PyMOL, ChimeraX, iCn3D:
-
Each molecular view is explained, with an adjacent color key,
and with illuminating cases for comparison with yours.
Terminology is less technical, and
terminology is explained in detail, either
within FirstGlance,
or via links to
articles in Proteopedia.Org.
Buttons and links have tool tips. All
methods are detailed.
-
Missing residues are obvious in the initial view as empty baskets,
with details available
(example).
About 90% of X-ray crystallographic models have missing residues, but users are
often completely unaware, since PyMOL, ChimeraX, Mol*, and iCn3D make
missing loops much less
obvious, and don't alert you to missing ends at all
(see comparison snapshots).
It is crucial to be aware if you are interested in the shape,
distribution of charges,
intrinsically disordered regions, etc.
Without the empty baskets, how long would it take you to realize that 75 amino acids
are missing in
1F1J?
Or that there are 15 within-chain gaps of missing residues in
6QJ4?
- Incomplete Sidechains occur in about 70% of empirical models:
residues
modeled without some terminal sidechain atoms.
These are labeled S- in FirstGlance, but are not indicated at all in
PyMOL, ChimeraX, Mol* or iCn3D
(see comparison snapshots).
Example:
6QJ4.
(These labels are
easily hidden.)
- Atom counts and molecular mass are shown, and all chemical elements present
are listed.
-
Resolution is interpreted with one of
8 non-technical descriptions.
Further explanation with examples is provided.
- Reliability of
X-ray diffraction models is interpreted objectively with one of
5 grades,
from Much Better Than Average
to Unreliable.
You are not left to interpret Rfree on your own.
- Full chemical names of ligands are listed
(example).
Clicking on one highlights its position(s) in
the structure, and shows a
diagram of its chemical structure.
- The most reliable chain, when more than one copy is in the
asymmetric unit,
is indicated in a table summarizing average
temperatures per chain.
Example.
-
The appropriate Color Key is always displayed next to the current molecular view
(example). (iCN3D does this for several color schemes.)
- Contacts to any selected ("target") moiety (non-covalently and covalently bonded atoms)
are visualized,
one type of non-covalent bond at a time, with Contacts & Non-Covalent Interactions
(Tools tab). They can also be listed, spreadsheet-ready.
Powerful and easy target selection methods are provided: ligand, residue, helix, domain, chain,
etc.
Example 1: Visualization of nicotine bound to protein.
Example 2: Two Ig domains in an antibody.
-
Assigning one color to each group of sequence-identical chains is an option
of the Solid View
(Example 1;
Example 2).
(Mol* appears to provide this as "Illustrative", but it is not
explained, and with huge assemblies such as virus capsids, at PDBe, it freezes the browser.)
- You will be alerted when unusual Protein Crosslinks, such as isopeptide bonds,
are present.
Six types are detected.
(Detection methods.)
Clicking on one bond automatically zooms in and shows it in detail:
11.5 Minute MOVIE.
Another tool highlights and counts the more common Disulfide Bonds
(Example).
- Ends of chains can be tabulated indicating whether the terminal
residue is missing, charged, blocked, or a phosphorylated 5' nucleotide
(blocked example;
5' phosphorylated example.)
Clicking on one chain-end in the table automatically zooms in and shows it in detail.
- All Salt Bridges or Cation-Pi Interactions can be visualized with one click
in the Tools tab.
Snapshot (1ZMS).
1ZMS in FirstGlance.
- You can get Spreadsheet-Ready Lists
(including conservation levels from
ConSurf)
of
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