Jmol Help

Help with using the Jmol_filter

Jmol mouse control

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

Action	Main (left) button	Middle button	Secondary (right) button
Jmol menu	Click on Jmol logo or 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	Shift + click & drag vertically	Click & drag vertically or mouse wheel
Reset & centre	Shift + double-click (away from molecule)	Double-click (away from molecule)
Resize Jmol	Click & drag bottom-right corner

Jmol measurements

• Distance between 2 atoms:

1. double-click on the starting atom
2. to fix a distance measurement, double-click on second atom

• Angle between 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 between 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

Jmol default colours

Elements: CPK colour scheme

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
Li	Be											B	C	N	O	F	Ne
Na	Mg											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	*	Hf	Ta	W	Re	Os	Ir	Pt	Au	Hg	Tl	Pb	Bi	Po	At	Rn
Fr	Ra	**	Rf	Db	Sg	Bh	Hs	Mt	Ds	Rg	Cn
	*	La	Ce	Pr	Nd	Pm	Sm	Eu	Gd	Tb	Dy	Ho	Er	Tm	Yb	Lu
	**	Ac	Th	Pa	U	Np	Pu	Am	Cm	Bk	Cf	Es	Fm	Md	No	Lr

Biological macromolecules

Primary structure

Amino acid residues: Amino colour scheme

Ala

Arg

Asn

Asp

Cys

Gln

Glu

Gly

His

Ile

Leu

Lys

Met

Phe

Pro

Ser

Thr

Trp

Tyr

Val

Asx

Glx

Xxx

Amino acid residues: Shapely colour scheme

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: Shapely colour scheme

A

G

I

C

T

U

Secondary structure

Polypeptides, nucleic acids and carbohydrates

α helix

310 helix

π helix

β strand

(β) turn

other

DNA

RNA

other

carbohydrate

other

Tertiary structure

Polypeptides and nucleic acids

N-terminal or 5’-

C-terminal or 3’-

More

For further information see:

Jmol

Jmol Wiki

Jmol Scripting Reference