Program Operation.

The Chem-Ray program is runs under Windows 95, but program control varies a bit from conventional Windows 95 programs. In particular the mouse is used for manipulating the molecule according to special rules.

Mouse Control. Three axes of rotation have been defined. The x axis is horizontal, the y axis is vertical. Normal mouse movement with the left button down controls rotations about these two axes. The z axis comes out of the screen toward the user. Mouse movement with the right button down controls rotations about the z axis.

With the control key down, mouse movement with the left button controls the scale of the molecule, zooms in or zooms out are both possible. With the control key and the right mouse button down, the molecule can be translated or moved within the window.

Finally with the shift key down the Molecular Window can be resized. This is an unconventional Windows procedure. With the shift key down just point the cursor at the furthest extent desired for the Molecular Window and depress the left mouse button.

Commands.

Normal Operations. Under normal operations the primary function of the program is simply drawing molecules using one of the available Styles selected from the Styles menu. If a static image is drawn then new colors can be selected from the color menu (found under the options header). Several colors can be changes at once. Then the Update button should be pressed to implement the color changes.

Auto Rotation. When the Auto Rotation command is selected, the following buttons appear:

These buttons control the axis of the auto rotation of the molecule. The Molecule in the Molecular Window will rotate continuously about the selected axis until the stop button is pressed. Tumble is a special option in which the axis of rotation constantly changes. The Tumble option should be used with care, since it has been know to drive the operator crazy. Auto Rotation operations only work for Dynamic Styles.

Geometry Inquiry. When the Geometry Inquiry command is selected, the following buttons appear.

This option is used for determining geometric parameters within the structure displayed in the Molecular Window. There are three inquiry buttons, Atom, Dist, and Angle. When the Atom button is pressed then the user should select any single atom using the mouse and the left mouse button. Once an atoms has been chosen, a list of all bond distance and bond angles about the chosen atom will appear in the dialog box. If the Dist button is pressed, two atoms should be chosen. The distance between the two atoms, bonded or non-bonded, will appear in the dialog box. If the Angle button is pressed then three atoms should be chosen. The angle between the atoms, assuming the second choice to be the central atom, will be listed in the dialog box. When any of the these three buttons is pressed the molecular image will be frozen and will no longer be movable under mouse control. If the Move button is pressed then the image will be unfrozen and the mouse will again control molecular movement (assuming a dynamic style has been selected.) The Quit button returns the program to normal operation.

Select Atoms. When the Select Atoms command is selected, the following buttons appear.

This option is used to select atoms for deletion or for labeling. To select atoms press the Atom button and use the mouse and left mouse button to select individual atoms. The selected atoms will be listed in the dialog box. If the Mol. button is pressed then entire molecules can be selected instead of individual atoms. Once a selected atom list has been created the Delete button will delete the selected atoms from subsequent images drawn in the Molecular Window. The Restore button will bring deleted atoms back. The Clear button can be used to clear the selected atom list.

The Select Atoms option can also be used to selectively label atoms. To do this go to the Labels option of the Option menu and choose the Selected Atoms option. With this option only the selected atoms will appear with labels. When either the Atom or Mol. button is pressed the molecular image will be frozen and will no longer be movable under mouse control. If the Move button is pressed then the image will be unfrozen and the mouse will again control molecular movement (assuming a dynamic style has been selected.) The Quit button returns the program to normal operation.

Relection/Inversion.

This option is used to convert the molecule to its enantiomer by changing the sign of one of the three principal coordinates (reflection) or of all three coordinates (inversion). Simply select one of these four options from the submenu.

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Last Update - March 24, 1997