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[Atoms Menu]

This menu allows the user to select atom types from each molecule that is displayed. In the system illustrated above, an atom panel appears that allows for changing the display characteristics of atom types "C" and "H" are selected with the mouse. Changes only take effect when the "SAVE" button is selected.

The "C" atom panel is shown below:


[C Atom Panel]


The items on the left side of the panel control atom display. They are:

  • POINT Does not display this atom type.
  • CIRCLE Draws a circle of appropriate radius about the atomic center.
  • LINESPHERE Draws a "Beachball" structure (circles transformed around two axes) with an appropriate radius about the atomic centers.
  • LIGHTSPHERE Draws a lighted sphere about the atomic center. The position and characteristics of the light source are fixed.
  • TRANS_SPHERE Draws a transparent sphere with an opacity chosen by the user (see below) about the atomic center.
  • DOTS Draws a sphere as a surface of dots. The button to the left allows you select the density of the dots.
  • LABEL Labels the atoms
  • UNLABEL Turn off labeling for this atom type



    • The sliding panel controls the atoms radius. The user may either move the cursor with the mouse or type in a specific value.



    The COLOR button brings up the color panel which is common to atom types, bonds,surfaces, vectors, and background color.


    [Color Panel]


    Each slider changes the value of the red, green and blue color components. Specific values ranging from 0 to 1 may be typed in as well. The intensity for each component appears to the right and the composite value on top. The "alpha" value controls the opacity of the object if transparent rendering is selected. The color change takes effect when the SAVE button is selected


    The "ALL:1" menu item brings up an atom panel where the changes effect all atoms in molecule "1". The ALL:Si's menu item brings up a panel where the changes effect all Silicon atoms in the system. The "ALL" menu item produces changes in all atoms in all molecules. Selecting the "BACKGROUND" item brings up a color panel that changes the background color.