3. Running VEGA ZZ
VEGA ZZ can be started in several ways:
selecting VEGA ZZ item in the Windows Start Menu;
double-clicking the VEGA ZZ icon on the Desktop;
double-clicking the molecule/trajectory files associated to VEGA ZZ;
using the Context Menu Send To item shown clicking with the right mouse button on a file;
typing VEGAZZ without arguments in the command prompt;
typing in the command prompt:
VEGAZZ <FILE_NAME>
with this syntax, VEGA ZZ starts loading and showing the specified
molecule.
If you need operate in command line mode without the graphical output, you must type VEGA instead of VEGA ZZ in the command shell. For the complete command syntax, click here.
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In the Window title bar are shown
the VEGA ZZ version, the communication port number, the active workspace number
and the name of the workspace that is corresponding to the molecule name. The
communication port number is important to identify the VEGA ZZ session to witch
send the script commands. You can start more than one VEGA ZZ and so with the
communication port number that is different for each session, you can redirect
the script commands to the window in witch they must have effects.
The Menu bar allows the access to the software main functions. It's
dockable component and it can be placed at top, left, right or outside the main
window. It can't be closed. For more information about the Main menu, click
here.
Tool bar 1 and Tool bar 2 are classic tool bars that replicate
some main menu commands for a fast-easy access. They can be moved as the Menu
bar and can be closed. To reopen them, you must use the View -> Tool
bars item in the Main menu.
The Workspace controls are useful to manage the multiple workspaces. A workspace
is a separated area that can contains molecules, surfaces and trajectory
analysis without interferences between the other workspaces. In other hands,
it's a bin and each bin can be separately managed.
To add a new workspace, you must open the context menu clicking the Workspace
controls box with the right mouse button and selecting the New item.
To change the current workspace, you can click on its name in the list or use
the Q (previous) and W (next) keys.
To remove a single workspace, you must click it and select Remove in the
context menu. If you want remove all workspaces, you must choose Remove all.
Please remember that the first (0) workspace can't be removed.
The Graphic view shows the 3D representations of molecules, surfaces, etc
and the Console displays
the text information only (calculation progress, results, etc). In this window you can type
directly the commands of the menu and the extended
commands in order to control VEGA ZZ without the GUI. To explore the command
history, you must use the cursor
arrows and the Pg. Up/Pg Down keys . The Console can be moved from its
docking position and can be closed also clicking on the button placed at the
top-left corner. It can be docked at main window bottom only and you can use the
View -> Console menu item to show or hide it.
The Status bar shows the current mouse mode (Rotate, Translate and
Scale), the object that are subjected to the mouse 3D transformations (All,
Molecule, Segment and Residue) and the mouse measurement mode (Atom, Rotation center,
Distance, Angle, Torsion and Angle between two planes). For more
information about the mouse controls, click here.