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Graphical interface


Four Panels

The main program window is divided into four panels.

The central (main) panel has the usual multiple document interface with the windows showing three-dimensional molecular models. The graphical windows are conventional overlapping windows, which can be controlled by mouse and toolbar buttons . In addition, active window can be selected by special tabs under the toolbar showing abbreviated filename. These tabs become convenient when a considerable number of files are open.

The left, lower, and right panels control the program. These slide panels can be immediately expanded or collapsed by dragging their side edges. When several windows are open in a panel, only the active one is visible. Other ones can be accessed using tabs under the panel.

 

Three-Dimensional Graphics

Three-dimensional graphical visualization is controlled by the left mouse button and the keyboard. When the left mouse button is down, dragging the mouse cursor rotates the "camera" around the model about the X and Y axes. Pressing the space bar sets the rotation point to the center of the model. Simultaneously, the camera moves to the model center at a distance making the whole model visible. For rotation about the Z axis, place the mouse cursor to any corner of the graphical window and drag it outside the window and around it in the desired direction. Dragging the mouse while holding the Shift key brings the camera closer or further from the model. Dragging the mouse while holding the Ctrl key moves the camera about to the XY plane. The origin of the model is shown as a small yellow globule.

 

 

Information Panel

The information panel can be useful to check the validity of the generated model. The panel can be accessed via the Analyze menu (Information entry) or the button on the toolbar.

Check the Boundary conditions, Force Field, and charge of each molecule type in the Model section; fractional charge values for the molecule are indicative of certain errors.

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Copyright 1996, 1999, 2005, 2007 by: Alexander Lyubartsev, Aatto Laaksonen, Alexey Nikitin.
Department of Physical Chemistry, Stockholm University.
All rights reserved.

Copyright 2006, 2007 Agile Molecule.
All rights reserved.