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viewing molecules
Attachments
center_camera_molecule.png
(59136 bytes)
center_group_atoms.png
(62212 bytes)
center_molecule_button.png
(740 bytes)
center_molecule_menu.png
(2768 bytes)
center_select_atom.png
(37343 bytes)
move_group_atoms.png
(83116 bytes)
translate_buttons.png
(3145 bytes)
translate_selected_atom.png
(34600 bytes)
zoom_buttons.png
(1669 bytes)
viewing molecules
translating molecule on screen
Molecule can be translated by using buttons with green arrows in zom/translation expander,
or arrow keyboard keys. Combination of shift keyboard button and arrow keyboard buttons makes larger translations. The nature of translation depends on the option selected in the menu from zoom/translation expander.
Move camera causes movement of the image of molecule across the screen and move molecule option causes change in atomic coordinates, along vectors, parallel to the screen.
In the figure below, the selected atom was moved across the pyrene surface. In order to translate selected atom parallel to the pyrene surface, pyrene must be oriented parallel to the screen.
The same principle can be used for moving a group of atoms. In that case the group of atoms must be defined by marking them.
centering molecules on screen
There are two different actions for centering molecule: moving camera and moving molecule.
These options can be accessed from the menu in zoom/translation expander.
Actions are executed by clicking on a center button in zoom/translation expander.
The first option moves the geometrical center of the molecule to the center of the screen and the second option brings the geometrical center of the molecule to the (0,0,0) coordinate. Please note that the second option changes molecular coordinates and saving them after this action saves changed coordinates. The difference between these two actions can be seen if coordinate axis is shown.
This action can be used to center molecule to the selected atom. In that case the molecule will be translated in order to bring the selected atom to (0, 0, 0).
In the same way, a bond can be centered if two atoms are selected. The geometrical center of group of atoms can be brought to (0,0,0) by marking the group of atoms and aplying center with move molecule selected.
zooming molecules
Zooming can be done with zoom buttons in zoom/translation expander.
The middle button changes zoom to the original value. The easiest way for zooming in or zooming out is by dragging mouse while the middle mouse button is pressed.
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