4. Mouse, keyboard and joystick

 

4.1 Mouse

The mouse can be used to manage the 3D objects trough rotation, translation and scale operations, changing the mouse mode with the context menu and/or the M hotkey (see hotkeys section). To change a 3D property, you must drag the mouse from left to right and vice versa pressing the left mouse button. To apply a Z transformation (rotation or translation), you must drag the mouse holding the middle button or the left button and the shift key at the same time. The mouse wheel, if present, has some functions on the basis of the current mouse mode: it can rotate around Y axis, translate along the Z axis and zoom. To change the mouse settings, see the configuration of the human interface devices (HID).
In the main window, you can select some functions with the context menu, pressing the right mouse button:

 

Item Subitem CmdName Description
Mouse mode

                          

Rotate mMouseRotate

Switch the mouse into the rotation mode.

Translate mMouseTrans

Switch the mouse into the translation mode.

Scale mMouseScale

Switch the mouse into the scaling mode.

Move All mMoveAll

Connect the mouse and the 3D controls to the world

Molecule mMoveMol

Connect the mouse and the 3D controls to a specified molecule or segment or residue. Holding down the Control key, it's possible to switch temporally from the specified object to the world.

Segment mMoveSeg
Residue mMoveRes
Measure Reset picking mPickReset

Restart the atom selection from the beginning.

Remove monitors mPickRemMon

Remove all monitors.

None mPickNone

With these items, you can enable/disable the mouse atom picking in order to change the rotation center and/or to show the atom information and/or perform a measure between 2 (distance), 3 (angle), 4 (torsion) and 6 atoms (angle between two planes). The result of each pick/measure operation is shown in the console window.

Center item allows you to change the rotation center.

Atom mPickAtom
Center mPickCenter
Distance mPickDistance
Angle mPickAngle
Torsion mPickTorsion
Plane angle mPickPlaneAngle
Hydrogen bonds mHbonds

Calculate the H-bond energy and highlight them in the main window.

E/Z geometry mEzGeom Show the E/Z geometry of the double bonds.
Bump check mBumpCheck

Perform the manual bump check. The collisions are shown by stippled lines which color can be changed in the Color settings dialog. The number of collisions is printed in the console and the monitors can be removed through Remove monitors menu item.

RT bump check mBumpCheckRT

Enable/disable (default = enable) the real time bump check when you move molecules, segments and residues. If the computational power of your CPU isn't enough, disable this feature and use the manual bump check (see above).

Joystick enabled   mJoyEnable

Enable/disable the joystick control.

Select    

See the Select item in the main menu.

Display Wireframe mShowWire

Switch the current display mode to Wireframe, Van der Waals dotted, Van der Waals vectorized, Van der Waals solid, CPK with vectors, CPK solid and liquorice.

VdW Dotted mShowVdwDot
VdW mShowVdwWire
VdW Solid mShowVdw
CPK mShowCpkWire
CPK Solid mShowCpk
Liquorice mShowLiquorice
Settings mShowSettings

Show the display settings dialog box.

Window 320x240 -

Change the window size. Only the sizes compatible with the current screen resolution, are shown in the this submenu.

640x480 -
800x600 -
1024x768 -
1280x1024 -
1600x1200 -
Center   mCenterView

Center and zoom the current atom selection.

Reset   mResetView

Reset the current view, changing to default the rotations, the translations and the scale factor.

Stop calc.   mStopCalc Stop the current calculation.
Power off the system    

When you check this item and a calculation is finished, the system is automatically switched off. The PC is not switched off immediately, but a count down dialog is shown in which you can press Abort button to terminate the procedure.

Please note that the CmdName column contains the command name, that must be used with SendVegaCmd program to activate the menu functions in batch files (click here for more information).

 

There are other menu items that are sensible to the context and are shown if you click an atom or a bond by the right mouse button, as shown in the following table:

 

Object to change Item Subtem Description
Atom

 

Residue

 

Chain

 

Segment

 

Molecule

Select   Show the object.
Hide   Hide the object.
Label Off Switch off all labels of the object.
Name Show the atom labels by name.
Element Show the atom labels by element.
Number Show the atom labels by atom number.
Type Show the atom labels by atom type (force field).
Charge Show the atom labels by atom charge.
Chirality Show the R/S chirality of the asymmetric atoms.
Fixing val. Show the atom labels by fixing value (constraint).
Residue Show the residue labels with name, number and chain.
Residue name Show the residue name labels.
Residue number Show the residue number labels.
Color By atom Color the object by atom.
By residue Color the object by residue.
By chain Color the object by chain identificator.
By segment Color the object by segment.
By molecule Color the object by molecule
By H-bond Color the object by property to accept or donate H-bonds.
By charge Color the object by atomic charges.
By constraints Color the object by constraint values.
Selection Color the object by selected color (a graphic submenu is shown).
Display Wireframe

Change the display mode of the object to wireframe, CPK dotted, CPK wireframe, CPK solid, ball & stick wireframe, ball & stick solid, stick wireframe, stick solid, trace and tube.

CPK dotted
CPK wire
CPK solid
Ball & stick wire
Ball & stick solid
Stick wire
Stick solid
Tube
Trace
Add Hydrogens Add the hydrogens to the object.
Change   Change the object
Remove   Remove the object.

 

The following table includes the specific options to change a bond.

 

Object to change Item Subtem Description
Bond
Label Off Switch off all labels of the bond.
Length Show the bond length.
Name Show the atom labels by name.
Element Show the atom labels by element.
Number Show the atom labels by atom number.
Type Show the atom labels by atom type (force field).
Charge Show the atom labels by atom charge.
Chirality Show the R/S chirality of the asymmetric atoms.
Fixing val. Show the atom labels by fixing value (constraint).
Color By atom Color the bond by atom.
By residue Color the bond by residue.
By chain Color the bond by chain identificator.
By segment Color the bond by segment.
By molecule Color the bond by molecule
By H-bond Color the bond by property to accept or donate H-bonds.
By charge Color the bond by atomic charges.
By constraints Color the bond by constraint values.
Selection Color the bond by selected color (a graphic submenu is shown).
Change Single Change the bond type to single, double, triple and partial double.
Double
Triple
Partial double
Remove   Remove the bond.

 

4.2 Keyboard

When the main window is active, some commands can be executed directly from the keyboard, like shown in the following table:

Key Description
A

Turn on/off the animation mode.

ESC

Close VEGA.

L

Switch on/off the light.

Q Go to the previous workspace.
R Enable the mouse rotation mode.
S Enable the mouse scale mode.
SPC

Reset view and eventually stop the animation.

T Enable the mouse translatiopn mode.
V

Change the current display mode in Wireframe Van der Waals dotted Van Der Waals vectorized Van der Waals solid CPK with vectors CPK solid Liquorice (see the main menu section).

W Go to the next workspace.
Arrows
Up, Down

Rotate the molecule around the X axis.

Arrows
Left, Right

Rotate the molecule around the Y axis.

Pg. Up
Pg. Down

Rotate the molecule around the Z axis.

 

4.3 Joystick

To enable the joystick operation, you must check the Joystick enabled menu item present in the the context menu. The keyboard and the mouse are kept full operative. To change the joystick settings, see the configuration of the human interface devices (HID).

 

4.4 Interactive controls

Another way to control the VEGA 3D visualization, is the use of the 3D control window. It can be shown clicking View 3D controls.

3D Controls   

The window contains seven dynamic buttons to control rotation, translation and scale factor. The bottom slider sets the sensitivity of the dynamic buttons. As an example, when you click X Translation button, the direction is due by the clicking point: if you click the left part of the button, the molecule is translated to left and clicking the right part, the it's translated to right. The translation speed is higher clicking the button extremities, but it's lower clicking the button center.
The controls are connected to the selected object (world,  molecule, segment, residue). To transfer temporally the controls to the world, you can hold down the keyboard Control button (Ctrl). In this way, you can switch easily from word to molecule and vice versa.