How to Manipulate JSmol Structures

Mac/PC Instructions: Practice commands on the ethane model below.

Place the cursor over the structure of ethane.

Rotate: click mouse, move mouse.

Zoom: depress SHIFT, click mouse, move mouse.

Translate: depress SHIFT. double click, move mouse. [PC: depress CNTRL key and then click and hold right button of mouse to translate structure.]

Measurements:

  • Bond Length: Place the cursor over the center of an atom (hydrogen in ethane). The type and number of the atom will appear. Double click. A plus sign appears. Place the cursor over the attached carbon. The bond length appears in magenta nanometers. Double click. The bond length appears permanently in white.
  • Bond Angle: Place the cursor over an atom as described above (hydrogen in ethane). Double click. A plus sign appears. Place the cursor over the attached carbon. The bond length appears in magenta nanometers (1 Angstrom = 0.1 nm; Angstroms can be set in Menu/Measurements). Single click. Move the cursor to either the carbon or the attached hydrogen. The bond angles appear in magenta. Double click to display the bond angle permanently in white.
  • Dihedral Angle: Follow bond angle instructions for four atoms (H-C-C-H).
  • Menu: Place the cursor over the JSmol logo located at the lower right of the ethane molecule. Click. The menu can be dragged on the screen. The menu has more functions than are needed and some functions are not operable. After selecting a function from the menu you may have to refresh (Mac: command R) the screen to return to the original structure.
JSmol menu

 

 

Ethane (larger view)