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Small molecules
Reactions, vibrations, etc.

Small molecules

Jmol screenshot Acetic acid using CPK colors and spacefilled atoms.
Jmol screenshot A shaded rendering of caffeine, with some measurements shown (distance, angle, dihedral).
Jmol screenshot Display of bounding box and axes of coordinates space. Note the transparency of the yellow halo around selected atoms.
Jmol screenshot The electrostatic potential of allene mapped onto a translucent surface. (submitted by Nick Greeves)
Jmol screenshot Two translucent planes (pMesh) illustrating symmetry planes for water molecule. (prepared by Bob Hanson)


Jmol screenshot A few residues with backbone in blue and vdw dots surface.
Jmol screenshot Hemoglobin with backbone trace colored by chain and spacefilled hemes.
Jmol screenshot Crystal structure of an H/ACA box RNP from Pyrococcus furiosus (PDB CODE: 2HVY)
Cbf5p    Gar1    Nop10    L7AE    RNA
A nucleotide of the RNA helix is flipped out into the active site formed by the protein complex.
(submitted by Wayne Decatur)
Jmol screenshot Biotin (cpk color, spacefilled) inside its binding pocket in a streptavidin subunit (cyan translucent surface) and capped by a portion of the neighbour streptavidin subunit (yellow translucent surface).
(submitted by Angel Herráez)
Jmol screenshot A fragment of transcription factor TFIIIA forming three consecutive zinc finger motifs (cartoons), bound to a stretch of DNA (spacefilled). (submitted by Angel Herráez)
Jmol screenshot Highlighting two salt bridges in hemoglobin tetramer (hemo group as sticks at bottom-right). (submitted by Angel Herráez)
Jmol screenshot Eubacterial 70S Ribosome from Thermus thermophilus (PDB CODES: 1jgo and 1giy)
On the right is the small subunit and on the left is the large subunit.
In between the subunits: mRNA A-site tRNA P-site tRNA E-site tRNA (submitted by Wayne Decatur)
Jmol screenshot Illustrates the variable translucency, in preparation for Jmol 11.2. (prepared by Bob Hanson)


Jmol screenshot Display of quartz crystal structure, filling 2x2x2 unit cells. The unit cell boundbox is drawn and the unit cell data are shown on upper left. (prepared by Bob Hanson)
Jmol screenshot Network of aluminate-silicate tetrahedra and the volume available for absorption. (submitted by Alan Hewat)


Jmol screenshot The 4f-orbitals (submitted by Nick Greeves)
Jmol screenshot Cartoon p-orbitals of benzene together with the corresponding translucent molecular orbital. (submitted by Nick Greeves)

Reactions, vibrations, etc.

Jmol screenshot An SN2 reaction animation with the distance measured between the chlorine and carbon atoms
Jmol screenshot Vibration animation of benzene with vectors shown as yellow arrows and list of vibration frequencies.
Jmol screenshot Periodic table showing atomic, van der Waals and ionic radii for all elements with their unique colors. (submitted by Angel Herráez)

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