BALLView Documentation: Scene

Index

3D View

The Scene widget provides the three-dimensional visualization of the loaded molecules.
All activated Representations are shown here.

The 3D View has several distinct modes:

Rotate Mode (Hotkey CTRL-R)
Picking Mode (Hotkey CTRL-H)
Move Mode
Editing Mode

The user can switch between the different modes, either by selecting the according menu entries in the "Display" menu, or use of the hotkeys. Switching between the last and the current mode is done by using the "Escape" key.

While the mouse cursor is over the 3D View, also the keys Q,W,E,R can be used to switch to the individual modes.

Rotate Mode

In the Rotate Mode, the user can zoom, rotate or translate the view by pressing the mouse buttons and moving the mouse:

Mouse Button	Effect
Left	Rotate left/right and up/down
Middle or Wheel	Zoom in and out
Right	Translate up/down and left/right
Left + Right (first keep one button pressed, than additionally the other)	Rotate (counter) clockwise
Double Left Click	Show information for object under cursor (e.g. Atom)

Special key combinations are recognized to allow all the operations described above on systems with one- or two-button mice. Just hold the respective keys on the keyboard and press the (left) mouse button:

Mouse button + key pressed	Effect
Left	Rotate left/right and up/down
Left + Shift	Zoom in and out
Left + Control	Translate up/down and left/right
Left + Shift + Control	Rotate (counter) clockwise

Picking Mode (Identifying parts of molecules)

The Picking mode is designed to identify parts of molecules or to select them for special tasks. Once you entered the picking mode the cursor will change to a cross. Now you are able to select single items. Multiple items are selected using a selection rectangle (hold left-mouse-button while moving the mouse over the area you want to select). Any selected objects become instantly colored (normally yellow, see image above). In the structure window, the checkboxes for the entries of these items become checked. The user can also deselect picked objects by using the right button (or for users with only one mouse button, by using the left mouse button and the Shift-modifier).

Mouse button + key pressed	Effect
Left	Select geometric objects, e.g. for atoms
Right (or Left + Shift)	Deselect geometric objects
Left double click OR Middle	(De-)Select the parent of the object under the cursor (e.g. the Residue of an Atom)

There is also an other alternative available for identifying atoms: BALLView can show popup informations about the molecular entities under the mouse cursor. To enable this, switch into the Rotate mode and double click on any bond or atom.

Move Mode

In the Move mode, selected atoms can be moved by using the mouse. It can also be used to position Clipping Planes (select Move in the context menu of the Clipping Plane in the Representations list).

Mouse button + key pressed	Effect
Left	Move objects in X and Y direction
Middle (or Left + Shift)	Move objects in Z direction
Right (or Left + Control)	Rotate objects

Edit Mode

Since version 1.2 BALLView supports editing of molecules: The 3D view offers a special mode to create and delete atoms / bonds and change bond orders:

Mouse button + key pressed	Effect
Left click on empty space	Create a new atom
Left click on atom and drag	Move atom in X and Y direction.
Left click on atom and drag + Shift	Move atom in Z direction
Double click on atom	Set the atom's element
Double click on ring bond	Make whole ring aromatic
Double click on bond	Cycle through bond orders
Middle (or Left + Control)	Create bond
Right	Context Menu for items under cursor
Mouse wheel	Zoom in or out

Key pressed	Effect
H,N,C,O,P,S	Select the element for the next atom
D	Delete atom under cursor
Backspace	Delete bond under cursor

The middle click in the edit mode can either create bonds between existing atoms, or if the mouse button is released while not pointing at an existing atom, a new atom is created along with the new bond.

The editing mode allows the creation of new molecules or to modify existing ones. Bonds can be created and deleted, bond orders and formal charges can be set. Furthermore it is possible to saturate molecules with hydrogen atoms and to perform a quick optimization of the currently highlighted System (using the MMFF94 force field).

When a user creates a new bond or wants to move an atom, BALLView by default only looks for matching atoms in the currently highlighted AtomContainer (e.g. an highlighted Molecule or Residue). This enable users e.g. to create ligands in their binding pocket, while keeping the receptor untouched. To modify this behavior, the Editing Setting in the Preferences can be used. New atoms are always created in the highlighted AtomContainer.

To ease access to its features, the editing mode also provides some entries in the toolbar list:

	Choose the element for the next atom
	Saturate the molecule with hydrogens
	Perform a quick optimization

The editing functionality is optional, it is realized in the class EditableScene. To obtain a slimmer application without the editing functionality, use the class Scene.

Selection Color

The color for selected objects can be changed in the model properties dialog.

Background Color

The background color can be changed in the preferences dialog under the point "Display"-"Main".

Setting the Light Sources

BALLView supports multiple light sources, which can also be freely configured, this can be done in the entry "Lighting" in the preferences dialog. Lights can either be set to a static position or they can move along with the camera, when zooming, rotating etc.

For static lights the position is set in means of absolute cartesian coordinates.
Relative light sources obtain their position relative to the position of the camera, the right-, up- and view vector. The example below means, that the light source is positioned 20 Å behind the observer and 4 Å units over him. The direction of the light source is set to the view vector.