Jmol help

Jmol help

Jmol default colours


Hover over any element to see more information (Atomic Number, Symbol, Element Name)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
H He
s-block p-block
Li Be B C N O F Ne
Na Mg d-block Al Si P S Cl Ar
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
Cs Ba * Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
Fr Ra ** Lr Rf Db Sg Bh Hs Mt Ds Rg Cn
* La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb
** Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No

Biological macromolecules

Primary structure

Amino acid residues
Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val Asx Glx Xxx
Nucleotide base residues

Secondary structure

α helix 310 helix π helix β strand (β) turn other DNA RNA other carbohydrate other
Nucleic acids

Tertiary structure

Polypeptides and nucleic acids
N-terminal or 5’- C-terminal or 3’-

A reverse rainbow gradient (bgyor) is used to color according to position of the corresponding groups or residues (for example, amino acids or nucleotides) along a chain.

Jmol mouse control

Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux), or wheel mice.

Action Main (left) button Middle button Secondary (right) button
Jmol menu Ctrl + click   Click
Rotate X,Y Click & drag    
Translate X,Y Shift + double-click & drag Double-click & drag Ctrl + click & drag
Rotate Z Shift + click & drag horizontally Click & drag horizontally Shift + click & drag horizontally
Zoom Click & drag vertically near right-hand edge
or Shift + click & drag vertically
Click & drag vertically
or mouse wheel
Reset & centre Shift + double-click (away from molecule) Double-click (away from molecule)  

Jmol measurements

For further information see: