 |
 |
 | VIDA
User Manual | ||||
 |
 |
 |
 |
||||
The primary interface mechanism to the 3D display is the mouse which is discussed in detail in Section 5.1.1. However, there are a large number of potential operations that can be performed in the 3D display which necessitates an additional mechanism of interaction besides the simple use of mouse buttons and popup menus. For this reason a separate peripheral window (see Section 3.3.2) is provided to access these operations. This window is called the ``Style Control" and is discussed below in Section 5.1.2.
As described above, the mouse is considered to be the primary interface mechanism to the 3D display. The details of how to use the mouse to interact with the 3D display are listed here. A three (or two) button mouse is recommended for use; however, support for a single button mouse is available. Holding down the Ctrl key while clicking or pressing the mouse button will emulate using the Right mouse button on a three button mouse.
For users not comfortable or familiar with the mouse interactions described below, VIDA can be made to emulate the mouse behavior of many other applications including: Coot, Insight, Maestro, MOE, O, Quanta, PyMol, RasMol, and Sybyl. The desired mouse map can be set in the application preferences in the 3D Display section. Please note that not all the functionality described below is available in the emulated mouse modes, nor is all of the functionality of the emulated applications available in VIDA.
Objects in the display can be selected by clicking on them using the Left mouse button. The selection is cleared between button clicks (or by clicking in the background) unless the Shift or Ctrl key is also held down when clicking. If a single vertex on a surface has been selected, holding down the Shift key and selecting an second vertex will select the shortest path of vertices between the two selected end points.
Double-clicking using the Left mouse button expands the current selection to the next logical grouping. For instance, double-clicking on a selected atom in a protein will expand the selection to include all of the atoms in the same residue as the original selected atom. Double-clicking on the selected set again will expand the selection to include either the entire chain if there are multiple chains, otherwise it will include the entire molecule.
Selection can also be performed using a lasso style selection method by holding down the Right mouse button and moving the mouse in the window to define a selection rectangle (a dotted rectangle will be displayed on the screen as you do this). Releasing the Right mouse button will select all of the atoms and bonds inside of the rectangle. The previous selection will be cleared unless the Shift or Ctrl key is also held down while moving the mouse. Lasso style selection of surfaces and grids is not currently supported.
Additional methods of selection are available in the Selection pane of the Style Control (see Section 5.1.2).
The scene can be rotated in three dimensions by holding down the Left mouse button and moving the mouse in the window. These movements will emulate rotation using a trackball.
The scene can also be rotated around just the Z axis by holding down the Alt key and the Left mouse button simultaneously.
Using the mouse, the scene can be translated in the XY plane by holding down the Shift key and the Left mouse button simultaneously. Translation along the Z axis can be performed by holding down the Alt key, Shift key, and the Left mouse button simultaneously. The scene can also be translated along the Z axis by holding down the Alt key while using the mouse wheel.
Using the keyboard, the scene can be translated horizontally in the display by pressing either the A key or D key which translate to the left and to the right respectively.
The scene can be scaled (or zoomed) by holding down the Middle mouse button, the Left and Right mouse buttons together, or by using the mouse wheel. Any of these three modes will scale the scene. Multiple modes are provided for convenience and to accommodate the many varied mouse configurations in existence.
The scene can also be scaled using the W and S keys on the keyboard.
The scale of the text displayed in the scene can be controlled by using the mouse wheel while holding down the Ctrl key.
The position of the near and far clipping (or slabbing) planes can be controlled using the mouse wheel while holding down both the Ctrl and Shift keys. Both planes are moved simultaneously and mirror each others' positions. It is important to note that slabbing must already be enabled for these operations to actually be performed.
The contour level of the grids in the default scope can be adjusted using the mouse wheel while simultaneously holding down the Shift key. Each incremental turn on the mouse wheel corresponds to an increase or decrease in the contour level by 0.1.
Informative labels can be displayed about atoms and bonds (as well as surfaces and grid contours) underlying the current mouse position if the Ctrl key is pressed while moving the mouse (no mouse button need be depressed) on most platforms. On the Mac, this behavior is obtained by holding down the Alt key instead of the Ctrl key.
Additional methods of labeling atoms and bonds are available in the Style pane of the Style Control (see Section 5.1.2).
A context sensitive popup menu can be generated by clicking in the window while holding the Right mouse button down. This menu will contain operations that can be performed on those objects associated with the context when the popup menu was generated.
The Style Control is a separate peripheral window (see Section 3.3.2) which is provided to enable additional interactions with the 3D display. The Style Control is a vertical window consisting of many individual panes. Each pane provides its own set of functionality. The display of the individual panes can be toggled by clicking on the title bar of the pane of interest. In addition, individual panes can be ``torn off" to act as top-level windows by clicking on the ``+" icon in the top right of the title bar. When the pane is torn off the ``+" icon becomes a ``-" icon which when clicked hides the ``torn off" window. The specific details of the individual panes are listed below.
VIDA provides a wide array of coloring options as can be seen in the color pane (see Figure 5.1). The first button (with the color wheel icon) prompts the user to select a specific color which will be applied to all of the objects in the current scope. The second button (with the molecule overlayed on a color wheel) prompts the user to select a specific color that will be applied to all molecules in the current scope. In addition, this button contains a drop down menu of molecule specific coloring schemes which can be applied. Detailed information about the individual color schemes can be found in Section 5.9.2. The third button (with the surface overlayed on a color wheel) prompts the user to select a specific color that will be applied to all surfaces in the current scope. In addition, this button contains a drop down menu of surface specific coloring schemes which can also be applied. Detailed information about the individual color schemes can be found in Section 5.11.2. The fourth button (with the grid overlayed on a color wheel) prompts the user to select a color that will be applied to all grid contours in the current scope. The fifth button (with the ``U" icon overlayed on a color wheel) assigns a unique color to every object in the current scope. The last button restores the original color of all the objects in the current scope. More details about the specific coloring schemes can be found below.
 |
Beneath the buttons is a slider which can be used to adjust the transparency of surfaces (see Figure 5.2(a)) and grid contours. The slider values range from 0 (completely opaque) to 100 (completely transparent). The specified transparency value is applied to all surfaces and grid contours in the current scope. However, if a part of a surface is selected, the transparency will only be applied to the selected region as can be seen in Figure 5.2(b).
[Partially transparent surface]
 |
The simplest mechanism to perform a selection is to click on the object of interest in the 3D display using the mouse as described in Section 5.1.1. However, a number of addition selection mechanisms are available in the selection pane as can be seen in Figure 5.3.
 |
In the top row of the selection pane, there are seven individual buttons. The first button with the ``A" icon selects all of the currently visible molecules. The second button with the partially selected molecule icon performs a selection based on a substructure query. Clicking on this button will launch a query dialog which allows the user to specify a substructure query. The substructure can be entered as a SMARTS pattern, selected from a large number of predefined patterns, or can be specified using a common or IUPAC name which will be converted to a structure using OpenEye's Lexichem toolkit. All atoms in the current scope matching the specified pattern will be selected. If the current scope is set to All and more than 50 molecules match the pattern, the user will be prompted as to whether to Mark the matching structures instead of selecting them, as being selected would make them visible.
The third button inverts the current selection, unselecting everything that was selected and selecting everything that is currently visible but was not previously selected. The fourth button selects everything within a defined radius of the current selected set (the default is 5 Angstroms). The fifth button selects everything within a user specified radius of the current selected set. This radius is specified by the slider in the bottom row of the pane. The sixth button selects everything outside of the same user specified radius of the current selected set. It is important to note that these distance based selection mechanisms expand their selected sets to include entire residues in the event that only a portion of a residue is included within the radius.
The last button contains a drop down menu which has different options based on the current selection. If a molecule is selected it contains the following options: ``Hide Outside", ``Hide Inside", and ``Restore". Selecting one of these options will hide all of the atoms and bonds outside the current slider specified radius, hide all of the atoms and bonds inside the current slider specified radius, or unhide any previously hidden atoms and bonds respectively. If a surface is the options are: ``Crop Outside", ``Crop Inside", and ``Restore". Selecting one of these options will crop away the unselected portion of the surface, crop away the selected portion of the surface, or restore the surface to its original state respectively. Examples of cropped surfaces can be seen in Figure 5.5.
In the bottom row, there is one button adjacent to a slider and a numeric display. The button is a toggle that controls whether or not unselected atoms and bonds are shown based on their distance to the selected set. The cutoff distance is controlled by the adjacent slider (and the actual value in Angstroms can be seen in the numeric display). This state of this button is ignored when a surface is selected. When a vertex (or a line of vertices) is selected, the slider can be used to flood out from the original selected set to include many more adjacent vertices. The different types of surface selections can be seen in Figure 5.4.
[Line of vertices selected]
[Region of vertices selected]
 |
[Selected region removed]
 |
The style pane of the Style Control is divided into two distinct areas as can be seen in Figure 5.6. The area above the dividing line contains a row of four buttons which control the display style of the various different types of objects that can be visualized in VIDA. The area beneath the dividing line is a collection of buttons whose functionality is specific to just molecules.
 |
In the top area, the first button (with the molecule icon) contains a drop down menu of the available molecule display styles: ball and stick, CPK, stars, stick, wireframe, and hidden. Selecting one of these options will change the display style of all the atoms and bonds in the current scope. For more details on these individual styles, see Section 5.9.1.
The second button (with the surface icon) contains a drop down menu of the available surface display styles: solid, mesh, and points. Selecting one of these options will change the display style of all the surfaces in the current scope. For more details on these individual styles, see section 5.11.1.
The third button (with the grid icon) contains a drop down menu of the available grid display styles: solid, line, and cloud. Selecting one of these options will change the display style of all the grid contours in the current scope. For more details on these individual styles, see Section 5.10.
The fourth button contains a drop down menu of the supported grid types in VIDA: Electrostatic, ET, FRED, Generic, Difference Map, and Regular Map. Selecting one of these options will change the grid type of all the grids in the current scope. A grid's type determines how it is visualized in VIDA including the default number of contours (and their levels) and the display style as well as the color of those contours. For more details on the individual grid types, see Section 5.10.1.
In the bottom area, there are three individual rows of buttons. In the first row, the first three buttons turn on the display of electrostatic grids, molecular surfaces, and accessible surfaces respectively. These specific grids and surfaces are considered display properties of their associated molecules and therefore are not displayed in the List Window (see Chapter 8). Independent (non-property) versions of these can be created from the relevant options in a right-click menu (see Section 5.1.1). The next two buttons turn on the display of protein ribbons and c-alpha traces respectively (for more information about these protein specific displays, see Section 5.9.3). The next button turns on the display of hydrogen bonds by making all of the molecules in the current scope to be hydrogen bond targets. Being a hydrogen bond target means that when it is visible, it displays any hydrogen bonds made between it and any of the other molecules that are also visible. The last button in the row toggles whether or not internal (intramolecular) hydrogen bonds are shown.
In the second row, the first three buttons turn off the display of electrostatic grids, molecular surfaces, and accessible surfaces respectively. The next two buttons turn off the display of protein ribbons and c-alpha traces respectively. The next button makes all of the molecules in the current scope no longer hydrogen bond targets. The last button in the row toggles whether or not external (intermolecular) hydrogen bonds are shown.
In the last row, the first button allows the user to specify and turn on atom and bond labels. The second button turns off all of the atom and bond labels in the current scope. The third button toggles the display of non-bonded atoms in the scene. The remaining three buttons control the hydrogen style for the molecules in the current scope. The first of the three turns all hydrogens on, the second buttons shows only polar hydrogens, and the last button hides all hydrogens.
[Advanced View]
 |
The contour pane of the Style Control is used to control the number and level of the individual grid contours as can be seen in Figure 5.7(a). When the current application scope is set to Focused there will be a pulldown menu in the top left of the window containing a list of all the current grid contours. If the scope is not set to Focused, the scope will be displayed in place of the pulldown menu to remind users that all operations in this window apply to more than just the Focused grid. Next to this area is a numeric display which displays the current contour level. Next to this display are two buttons, one with a ``+" icon and one with a ``-" icon. These two buttons allow for the creation and deletion of individual grid contours. Please note that these options are disabled for both Electrostatic and ET grids as they can have only two contours: positive and negative. Furthermore, the contour levels of the positive and negative contours are coupled together and so changing one will change the other (but with the opposite sign).
At the bottom of this window is a slider which allows for direct control over the contour level. To the right of the slider is an Advanced button (with the equalizer icon) which will expand the pane to show a number of advanced options (see Figure 5.7(b)).
In the advanced section, there are two adjustable parameters (Radius and Resolution) and one button. The parameters control how contours of Reentrant grids are displayed according to their symmetry. The Radius parameter specifies how far out from the center of the scene (in Angstroms) VIDA should look in the grid in order to generate of the isocontour. The Resolution parameter specifies the resolution (in Angstroms) of the sub-grid used to generate the isocontours.
The single button (with the check icon) to the right of the Radius parameter converts the current grid contour into a fixed surface independent of the grid. This can be particularly useful when generating state files as a single surface can take up considerably less disk space than an entire grid.
The graphics control pane in the Style Control provides an additional level of control over and interaction with the the 3D display (see Figure 5.8). It is particularly useful for users without mouse wheels.
 |
At the top of the graphics pane are three check boxes: ``Depthcue", ``Slabbing", and ``Mirror". The first two check boxes toggle the use of their associated properties respectively. The ``Mirror" check box is only enabled when slabbing is on and controls whether the front and back slabbing planes move together (mirrored around the center of the scene) or independently.
Beneath these check boxes is an interactive control which allows the user easy control over both depthcueing and the clipping planes. Displayed in the control is a top-down view of the current scene in the 3D display. The front of the scene is at the bottom as indicated by the label.
When depthcueing is enabled, two red lines will appear in the control which indicate the start and the end points in the depthcueing calculation. These lines can be moved by clicking on the triangular tab at the right of the lines and dragging them to the desired location. The 3D display will update dynamically as these lines are moved.
When clipping (or slabbing) is enabled, two yellow lines will appear in the control which indicate the position of the near and far clipping planes. These can be moved by simply clicking on the triangular tab at the left of the lines and dragging them to the desired location. The 3D display will update dynamically as these lines are moved.
In the center of the control is a small white dot that corresponds to the center of scene that the camera is pointing at. The position of the center can be changed in the Z plane by dragging the dot in the vertical plane. The position of the center can be changed in the X plane by dragging the dot in the horizontal plane.
Beneath this control is a slider which controls the scale of the text drawn in the 3D display. The 3D display will update dynamically as the slider is adjusted.
Beneath the slider are three radio buttons which control the mode of stereoscopic visualization. The default behavior is ``Off". The ``Hardware" option is only enabled on machines which are capable of performing 3D hardware stereo-in-a-window. This capability is determined by the computer's graphics card. For more details on stereo display, please see Section 5.3.
Each of the individual custom views available in VIDA can also provide their own individual panes which can be inserted into the Style Control to further enable task specific operations. These panes appear when a specific custom view is selected and disappear when the ``X" icon is clicked or when another custom view is loaded. For more details on the individual custom views available, see Section 5.12.
|
|
| VIDA
User Manual | ||||
|
|
|
|
||||