Snapshot Gallery
for FirstGlance in Jmol


A look through these snapshots from FirstGlance in Jmol will give you an overview of what it can to. Clicking on any of the four character PDB identification codes below (such as 1D66) will enable you to explore that molecule in FirstGlance




Each of the views in the next three tables is achieved with one click of the mouse.
When actually using FirstGlance, the molecular views are much larger .

Initial view (Cartoon plus Ligands+) of Gal4 transcriptional regulator (DNA-binding domain only) bound to DNA (1D66). Each chain is a different color.
Secondary Structure view of Gal4 with alpha helices as "rockets" (1D66). Compare with another molecule below showing a beta sheet.

N->C Rainbow view of Gal4:DNA showing Amino/5' and Carboxy/3' termini. (1D66).
Composition view of Gal4:DNA indicating Protein, DNA, and Water (1D66).


Hydrophobic/Polar view of Gal4:DNA indicating Hydrophobic and Polar residues on the surface. (1D66).
Charge view of Gal4:DNA indicating Hydrophobic, Polar uncharged, Cationic (+), Anionic (-), and Backbone atoms on the surface. (1D66).
Atomic detail is available in Vines.. views. The Slab.. option (not pictured) hides atoms distant from the point of interest. (1D66).


Secondary Structure view of Streptococcal protein G (1PDB) indicating beta-strands, alpha-helices and turns.



Begin Contacts.. Section

The Contacts.. tool of FirstGlance produced the following views.
The snapshots below are much smaller than the actual views when using FirstGlance.

Contacts.. enables you to see how the chains (each a different color) touch each other. (View obtained with 1 click.) Optionally, you can select a target (by clicking on chains, groups, or atoms) in order to display the putative non-covalent bonds to the target. (1D66)
Clicking on one protein chain (green) marks it as the target with a black asterisk (magnified in inset) on each atom. (View of 1D66 obtained with 2 clicks.)
Only the atoms that contact the green target chain are now shown. (View obtained with 3 clicks; 1D66). These contacts can be shown in great detail, in seven subsets of different kinds of non-covalent bonds, as shown below.


Contacts 1: non-water hydrogen bonds. (Definition.) At left, target Gal4 protein atoms (larger balls, bottom, marked with white asterisks) are shown within hydrogen-bonding distances of DNA atoms (smaller balls, top). These hydrogen bonds are to a specific sequence of bases. The DNA sequence recognized by Gal4, CGG (in chain E), can be visualized here. Atoms represented as sticks are too distant from the protein to be hydrogen-bonded, but are shown for context. (View of 1D66 obtained with 6 clicks, plus additional double-clicks for each distance measurement.)

Double-clicking atoms reports distances or angles. More..
In this view (and many views below), atoms are colored by element:

C H O N S P
(more elements..)


Contacts 2 view of 1D66: putative hydrogen bonds to water. (Definition.)
Contacts 3 view of 1D66: putative water bridges, a subset of hydrogen bonds to water. One putative bridge from 1D66 is shown above. (Definition.)
Clicking on any atom reports its identity to the lower left of the molecule, as shown above. ("NH2" means Nitrogen, Eta2. More..)


Contacts 4 view of 1D66: van der Waals (hydrophobic) interactions. (Definition.) Here, the target chain atoms are spacefilled to van der Waals radii, while the contacting atoms are small balls.
Contacts 5: protein salt bridges. (Definition.)
Contacts 6 view of 1BL8: protein cation-pi orbital interactions. (Definition.)


Contacts 7: metal and misc. interactions. Here the interactions of iron in heme are shown (from 2HHD). (Definitions.)



Begin Hide.., Find.. Section



This potassium channel (1BL8) is a homotetramer (four identical chains). This view is obtained with one click on Contacts...
Here, the Hide.. dialog of FirstGlance has been used to hide the front two chains (3 more clicks). Now we can see three potassium ions, and one water molecule. (View of 1BL8).
Hydrophobic/Polar shows that most of the surface of this molecule is hydrophobic (gray), consistent with its transmembrane location. (View of 1BL8 obtained with 1 click.) Compare with the same view for Gal4.
The Find.. dialog of FirstGlance was used to locate all tryptophan residues (yellow clouds). Clearly, they sit at the lipid-water boundaries. (View of 1BL8 obtained with 2 clicks plus typing "TRP".)



Begin Structural Bioinformatics Resources Section


FirstGlance has numerous links to structural bioinformatics servers and resources.
One of the most important is the link to Probable Quaternary Structure:

Here is 1K28 Notice the implausible folding of the left end, which suggests that some of the chains are missing in this model, (the asymmetric unit). (View obtained with 1 click.)
Might this molecule have formed specific oligomers, with more chains, in the protein crystal? The answer is provided by a visit to the Probable Quaternary Structure (PQS) server of the European Bioinformatics Institute.

In FirstGlance, simply click on

Indeed, PQS reports that the molecule existed in the crystal as a hexamer, rather than a dimer. The hexamer is formed from three dimers by symmetry operations. A link to FirstGlance at PQS displays the above specific oligomer.
What is this amazing molecular machine? To find out, view 1K28 in FirstGlance, and click on either or .

Crystallographic models often have portions missing -- regions where the molecule was disordered ("blurry") in the crystal. To find out, in FirstGlance, click on . Nearly 50 amino acids are missing from the asymmetric unit (so nearly 150 from the specific hexamer)!

In addition to the structural bioinformatics resources mentioned above, FirstGlance offers links, under More Views.., to:
  • Assessment of model quality by All Atom Contact Analysis at the MolProbity server
  • List of energetically significant cation-pi orbital interactions at the CaPTURE server.
  • The Jmol console and command language.
  • Protein Explorer: more information for beginners, and more power for advanced users, compared to FirstGlance in Jmol.
  • Visualize evolutionary conservation with the ConSurf server.
  • And more.



Begin More Views.. Section



Within FirstGlance, More Views.. offers a display of all protein salt bridges throughout the molecule. Here, all salt bridges in an SH3 domain 1B07 are shown. (View obtained with 2 clicks.)
When the same view is colored by chain, it is easy to see that one of the salt bridges is between two chains. (View obtained with 1 additional click.)
The same dialog displays all protein cation-pi orbital interactions throughout the molecule. (View obtained with 2 clicks.)


More Views.. has a checkbox to highlight (as ball and stick) non-standard amino acids or nucleotides. Here, phospho-serine (SEP) is indicated in 1BKX (View obtained with 2 clicks.)
More Views.. also offers to color the molecule by uncertainty (crystallographic "temperature" or "B factor"). The positions of the red atoms in Gal4:DNA model above have the least certainty. (View of 1D66 obtained with 3 clicks.)
More Views.. also offers to show the atomic coordinate axes, the unit cell, or the boundbox (in any combination). Above, all three are shown for Gal4:DNA (1D66). (View obtained with 4 clicks.)


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