Maestro User Manual

Chapter 2: The Maestro Main Window

Schrödinger Software Release 2015-2 

28

Table 2.2. Selection shortcut menu items.

Menu Item

Action 

Background Color

 

Set the Workspace background color to black, white, gray, or blue. 

Workspace 

Feedback

 

Set up entry properties to be shown at the top left of the Workspace (“feed-

back”). Opens the 

Preferences

 panel at the 

Feedback – Entry

 section.

Invert Selection

Select the unselected atoms and deselect the selected atoms. 

Expand Selection

Expand the selection to include atoms or residues within a specified distance, 

or to select only these atoms. (Workspace)

Select Matching 

Atoms By

Select all atoms that match any of the currently selected atoms by 

Color

, 

Rep-

resentation

, or 

Element

 (which you choose from the submenu). For example, 

if the selection has red and green atoms, all red and green atoms are selected.

Representation

 

Set the molecular representation to wire frame, ball and stick, CPK, tube, or 

thin tube. 

Color Scheme

 

Apply the color scheme from the submenu to the selected atoms. 

Labels

 

Apply the label from the submenu to the selected atoms. 

Highlights

 

Add a highlight of a particular type with the default settings or manage high-

lights. (Workspace)

Display

 

Display the entire molecules or residues containing the selected atoms. This 

action is useful if part of the molecule or residue was previously undisplayed. 

Also, display residues within a given distance of the selected atoms.

Display Only

 

Display only the selected atoms. (Workspace)

Undisplay

 

Undisplay the selected atoms. 

Delete

 

Delete the selected atoms. 

Switch Alternate 

Positions

 

For atoms with partial occupancy, switch between the alternate positions. 

(Workspace)

Display Alternate 

Positions

 

For atoms with partial occupancy, display all positions. The alternate positions 

are displayed as ghosts. (Workspace)

Set Element

 

Change the selected atoms to atoms of the element chosen from the submenu. 

(Workspace)

Insert Gap

 

Insert a gap to the left of the selected residue. Opens a dialog box in which you 

can specify the number of residues to insert. (Sequence viewer) 

Mutate Residue

 

Change the residues that contain the selected atoms (or the selected residues) 

to the type chosen from the submenu. 

Rotamers

 Open 

the 

Rotamers

 dialog box to select one of the standard rotamers for the 

selected residues.

---

Chapter 2: The Maestro Main Window

Maestro 10.2 User Manual

29

Create Project Entry

Create a project entry. Opens the 

Create Project Entry 

dialog box, in which 

you can provide a title for the entry, and choose whether to use the selected 

atoms, the displayed atoms, or all atoms. (Workspace)

Exclude Entries

Exclude the entries that contain the selected atoms from the Workspace. 

Select Project 

Entries

Select the entries that contain the selected atoms in the Project Table. The sub-

menu allows you to choose whether to add the entries to the current Project 

Table selection, or to replace the selection. 

Fit to Workspace

 

Fit the displayed structure to the Workspace and reset the center of rotation. 

Clip

 

Clip the display to the selected atoms. Moves the clipping planes. (Workspace)

Center Electron 

Density

 

Center the displayed electron density map on the centroid of the selected 

atoms. Used for PrimeX. (Workspace)

Transform

 

Perform a local transformation. (Workspace)

Align Centers of 

Mass

 

Translate the entries so that the centers of mass of the selected atoms in each 

entry coincide. (Workspace)

Help

 

Open the Shortcut Menus help topic.

Table 2.3. Bond shortcut menu items.

Menu Item

Action

Order

 

Set the bond order to zero, one, two, or three. 

Measure

 

Measure the bond length and display it. The measurement is added to the list in the 

Measurements

 panel. 

Adjust

 

Adjust the bond length or the dihedral angle around this bond. 

Delete

 Delete 

the 

bond. 

Table 2.4. Tiling items on shortcut menus.

Menu Item

Action

Apply Zoom to All Tiles

 

Apply the zoom value from the current tile to all tiles. 

Apply View to All Tiles

 

Apply the view (rotation, translation, zoom) from the current tile to all 

tiles.

Reset Tile 

Reset the view of the current tile to its initial value. 

Pick Tiles to Move

 

Turn on or off picking to move tiles. When enabled, picking selects tiles 

which can then be moved to a new location. The location is marked with a 

vertical line between tiles as you move the mouse to the desired location.

Table 2.2. Selection shortcut menu items. (Continued)

Menu Item

Action 

---