Jmol help

Jmol default colours

Elements

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
			f-block
		*	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

Polypeptides

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

Distance (2 atoms):
1. double-click on the starting atom
2. to fix a distance measurement, double-click on second atom

Angle (3 atoms):
1. double-click on the starting atom
2. click on the second atom (central atom in angle)
3. to fix an angle measurement, double-click on third atom

Torsion angle or dihedral (4 atoms)
1. double-click on the starting atom
2. click on the second atom
3. click on the third atom
4. to fix a dihedral angle measurement, double-click on fourth atom

In all cases:
- move pointer over destination atom in order to see measurement results without leaving a permanent measurement
- move outside the window in order to cancel the measurement
- make the same measurement again in order to delete the measurement

For further information see: http://jmol.sourceforge.net