There are some key concepts that are helpful for understanding how to interact
with VIDA. Individual objects in VIDA can be in various states,
including Focused, Visible, Locked, Marked, and Selected. Each of
these states carries some special behaviors which are described below. These
states also provide a way to refer to specific molecules or sets of molecules.
For example, one could apply a coloring scheme or rendering style to all
Marked objects, or to the Focused object.
VIDA’s “Scope” determines which objects will be affected by operations
within the program, based on their states, and is discussed in the “Scope”
The Focused state is a property of a single object in the application;
there can be only one Focused object at any given time. Being
Focused indicates that that particular object is the current object of
interest and is therefore the primary focus of all relevant windows. If the
Focused object is not already Visible (see below), it will behave as if
it were Visible for as long as it remains Focused.
In addition, when a molecule is the Focused object, its SMILES
representation is displayed in the application’s status bar (which can be found
at the bottom of the application window). If any of the molecule’s atoms are
selected, that selection will be indicated in the SMILES display by the
coloring of relevant atoms. Selected atoms are colored using the current
selection color (the default is orange) and are also in a bolded font while
all of the unselected atoms will be displayed in their usual normal black font.
For large molecules (>100 atoms in this case), no SMILES representation is
displayed as it would not fit in the status bar.
The Visible state is an indicator of whether or not the associated
object is drawn in the 3D display. Multiple objects can be Visible
simultaneously. If VIDA is operating in tiled mode (see
Tiled Display), each Visible object will be displayed in its own
If the 2D display is also shown and VIDA is in
tiled mode, Visible molecules will be drawn in the 2D display as well as
the 3D display.
The Locked state is essentially the same as the Visible state
except in the situation
where the application is in tiled mode, in which case each Locked object
will be displayed in every pane of the 3D display. However, a Locked
object can also be simultaneously Visible and/or Focused in which case it will be
displayed in its own individual pane as well as every other pane in the 3D
The Marked state is simply an indicator of user interest in the
associated object. The Marked state can be used to help filter data as
well as to specify the desired input to application functions. For instance,
the Marked state can be used to specify which molecules out of a large
list are saved. Finally, when certain operations generate too many results to
be displayed at one time, the Marked state can be used to indicate the
results of those operations.
The Selected state is a special property of the Visible state. Only objects
that are Visible, Focused, or Locked can be Selected. Much like the
Marked state, the Selected state is an indicator of interest and provides an
input set to application functions. Unlike, the Marked state, the Selected
state is more transient and is easily cleared. The act of selection is
usually performed in either the 3D or 2D display. Selected objects are usually
indicated by a change of color (the default is orange) in the 2D display, and
by a colored outline in the 3D display. More
details on the actual process of selection can be found in the chapters on 3D
and 2D displays.
Scope is a state of VIDA, and indicates which objects the application
should operate on. The default application scope is Focused which means
that all of the application functions will operate on the Focused object.
Scope Order of Precedence
However, as seen in Figure: Scope Order of Precedence,
if there is anything currently Selected, the
selected set will take precedence over the current scope i.e. the action will apply
only to the selected atoms/objects. Furthermore, in
Focused scope, if there is no Selected set and no Focused object, the
Focused scope defaults to behaving as if it were the Visible scope.
The Visible scope operates on all objects that are currently Visible,
Locked, and/or Focused.
The Marked scope operates on all objects that are currently Marked.
The All scope operates on every object currently loaded in the
application. Operating on the All scope can be a very lengthy process,
and as such, its progress is displayed in the progress bar in lower right hand
corner of the application. Operations performed on the All scope can
be halted if desired by clicking on the Stop button immediately to the
left of the progress bar.
The current scope is displayed in and can be modified from the main application
toolbar as seen in the figure below.
The layout of the application should be relatively familiar to most users.
VIDA provides a menu bar with many standard as well as specific menus, a
toolbar for common operations, a central main window, and a number of
peripheral windows. An example of the layout can be seen in
Figure: Docked Layout.
The layout including the position and visibility of the main and peripheral
windows is saved on exit and will be restored the next time the application is
run. The layout of the windows can be changed by clicking on the title bar of
the individual window and dragging it to the desired location. A placeholder
window will appear when the mouse is over an area where the dragged window can
be placed as seen in Figure: Dragging Windows.
Furthermore, multiple windows can be tiled on top of each other into a tab
controlled area as can be seen in the bottom window in
Figure: Docked Layout. This example shows tabs for
“Spreadsheet” and “Scripting Window”.
In addition to manually changing the layout, there are a number of predefined
layouts which are accessible via a drop down button on the toolbar as can be
seen in Figure: Custom Layouts. The colored icon
associated with each option indicates
which peripheral windows will be shown and where. Hovering the mouse over any
given option for about one second will generate a preview image of the
resulting layout. The “Save” option allows for the creation and storage of
custom layouts. The “Organize” option enables the reorganization of the
ordering of the layouts.
The main window is the window that occupies the central area of the
application on the screen. At any given time, there can be only one main
window; however, there are multiple windows which are capable of being the
main window if desired. The choice of main window can be controlled by
selecting the desired option from the “Main window” submenu in the top-level
Windows menu. In
Figure: Docked Layout, the 3D display (see
3D Display) is serving as the main window.
Currently, there are three different main window options: the 3D display,
the 2D display, and the spreadsheet. More details about
the individual windows can be found in their relevant chapters.
In addition to the standard layout described above, the main window can
optionally be displayed in fullscreen mode, by selecting the “Fullscreen”
option in the top-level View menu. Pressing the “Esc” key will exit
fullscreen mode (please note that clicking the mouse on the screen may be
required before hitting the “Esc” key in order to ensure that the key press is
When in fullscreen mode, the main menu bar and status bar are hidden by default.
However, they can be toggled on or off by hitting the “F1” and “F2” keys
The 3D display normally contains popup toolbars around the edge of the window.
These toolbars remain when in fullscreen mode to allow for easy access to
display functionality. For more details on these toolbars see
In addition to the main window, there can be multiple peripheral windows docked
around the edges of the main window or as separate floating top level windows.
Furthermore, multiple windows can be placed on top of each other in a tabbed
Currently, multiple peripheral windows (including the potential main windows)
- 2D Display
- 2D Preview
- 3D Viewer
- List Window
- Scripting Window
- Style Control
The display of peripheral windows is controlled by toggling the desired
window options in the Windows menu. Currently visible windows are indicated
by the presence of a check mark next to their names. Peripheral can also be
hidden by clicking on the ‘X’ in the upper right hand corner of the window.
As mentioned above, the layout of the peripheral windows can be controlled by
dragging the individual windows to their desired locations (see
Figure: Dragging Windows).
Undo / Redo
VIDA provides multi-step undo and redo functionality for almost all
operations. Operations can be undone by selecting the “Undo” option in the
Edit menu, clicking on the undo button in the top 3D toolbar, or by hitting
Ctrl+Z on the keyboard. Any of these actions will undo the last operation
performed. This can be done repeatedly or the undo history can be viewed in
the “Undo History” option the Edit menu which allows selecting how far back
into the undo history to go. Please note that while this menu only displays the
10 most recent operations, the undo history can be much greater, so feel free
to revisit the “Undo History” option to go back further.
Operations that were just undone can be redone by selecting the “Redo” option
in Edit menu, clicking on the redo button in the top 3D toolbar, or by
hitting Ctrl+Y on the keyboard. Any of these will redo the last operation
undone. This can be done repeatedly or the redo history can be viewed in the
“Redo History” option in the Edit menu which allows selecting how far into
the redo history to go. Like the undo history, this menu only displays the 10
most recent undone operations, but the redo history may be much greater and can
be revisited to go further.
User interaction in the 3D display is primarily performed using the mouse. The
following table details the available functions as well as the mouse actions
required to perform those functions.
||Move mouse with Middle button
||Move mouse with Left + Right buttons
||Move mouse with Left button
|Rotate around Z axis
||Move mouse with Left button + Alt key
|Translate in XY plane
||Move mouse with Left button + Shift key
|Translate in Z plane
||Scroll wheel with Alt key
||Click Left button
||Move mouse with Right button
||Click Left button with Ctrl or Shift key
||Double click Left button
|Select add grow
||Double click Left button Ctrl or Shift key
|Select rectangle and add
||Move mouse with Right button and Ctrl or Shift key
|Change clipping plane
||Scroll wheel with Ctrl + Shift key
|Change far clipping plane
||Scroll wheel with Alt + Ctrl key
|Change near clipping plane
||Scroll wheel with Alt + Shift key
||Scroll wheel with Ctrl key
||Click Right button
|Adjust contour level
||Scroll wheel with Shift key
||Move with Ctrl key
Special Builder Mouse Actions
When a molecule is in Editing mode, the Rotate and Translate in XY
plane actions above can be applied exclusively to the molecule being
edited by holding down the Ctrl key (Command key on a Macintosh) while rotating or translating.
VIDA stores user specific information in a user writable local directory
on the computer running the application. Contained in this directory are the
user’s application settings (VIDA.ini), preferences (preferences.oeb),
journal file (journal.py), and a cached copy of the license file
The location of the user directory is specific to the operating system, the
details of which are listed below:
Linux / Unix
Mac OS X
Microsoft Windows Vista / Windows 7 / Windows 8
The user directory can be accessed from within VIDA by clicking on the
“Open User Directory” option within the Help menu.
Help with VIDA can be found under the Help menu in the main menubar as
well on the OpenEye website: http://www.eyesopen.com. The Help menu
provides an About option, access to documentation,
licensing utilities, access to Examples, access to the User Directory, as
well as the ability to file a bug report.
The About box provides extensive details about the running version of
VIDA as well as the system on which that VIDA is running. It also
provides licensing information and direct access to the license file in use.