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IUMSC   Indiana University Molecular Structure Center

The JaMM 2.1 applet gives the user several options for examining the molecular structure.

General Layout

General Layout of JaMM applet

The JaMM applet contains three principal screen elements:

  1. a model-rendering area
    The model-rendering area is the heart of JaMM. Here the model is displayed and manipulated.

  2. a control bar to select drawing modes and options
    The control bar sets various rendering options and contains buttons for generating ORTEP and ray-traced images, and for resetting the view orientation.

  3. a scrollable output area
    The output area displays messages from the applet, such as distances and angles and status information.
    The output area displays messages from the applet, such as distances and angles and status information.

Keyboard Controls

+ Brighten the model background - Darken the model background ? or F1 Display the help file

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Mouse Operations

  1. Manipulating the model
    • Rotate the molecule by holding down the left mouse button and dragging the mouse.
    • Rotate about the axis perpendicular to the screen by holding down the control key while dragging as described above.
    • Scale the model by holding down the alt key while dragging.
    • Translate the model by holding down the shift key while dragging.

  2. Selection and measurements
    • Select a single atom by clicking on it in "Atom" output mode. The atom label and current 3D coordinates are displayed in the text output area.
    • Select an interatomic distance in "Distance" output mode by selecting first one atom then the other. (No need for a bond to be present.) The atom labels and interatomic distance is displayed in the output area.
    • Select an interatomic angle in "Angle" output mode by selecting three atoms in sequence; the second selected is the vertex of the angle. (No bonds need be present among these atoms.) The atom labels and interatomic angle is displayed in the output area.
    • Any selected atoms are labelled in the drawing area with a bold version of their label, whether or not atom labels are turned on for the other atoms in the options area.

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The examples of the various options

1. Ball-and stick representation Ball-and stick representation
2. Space-filling representation Space-filling representation
3. Stereographics view using Left-Right option Stereographics view using Left-Right option
4. Stereographic image using Red-Green option
(requires red-green glasses)
Stereographic image using Red-Green option
5. When distance mode is selected, the designated atoms are labeled and the vector corresponding to the distance highlighted. The distance is shown in the window at the bottom of the applet. Image when distance mode is selected
6. The ORTEP or rendered image file will be drawn in the same orientation as the molecule in the applet. Note the difference in quality between the space filling representation in the applet and the output of the rendered image. The ORTEP and Create Image options submit a job to the server, and are not performed by the applet itself. The ORTEP or rendered image

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