Jmol Help

Help with using the Jmol_filter

Jmol default element colours

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

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

*

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

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	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 (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

More

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