Menu Bar

The File menu contains project and structure management actions. See Maestro Projects for an overview of projects in Maestro. The File menu in the Project Table Panel and in the main window are the same.

New Project (Ctrl+N / ⌘N)

Create a new, empty project. The project is temporary until you give it a name (Save Project As).

Open Project (Ctrl+O / ⌘O)

Open an existing project. See Opening a Project for more information on opening projects.

Save Project As

Save the current project with a new name. See Saving and Copying Projects for more information.

Close Project (Ctrl+W / ⌘W)

Close the current project, and open a new scratch (temporary) project. See Closing a Project for more information on closing projects.

Import Structures (Ctrl+I / ⌘I)

Import structures into the current project from structure files. Opens the Import Dialog Box. See Importing Entries for more information.

Import Recent Structures

Import structures into the current project that have been recently imported. See Importing Entries for more information.

Import From

Import structures from another project (see Import from Project Dialog Box) or from a LiveDesign instance (see LiveDesign to Maestro Import Panel). See Importing Entries for more information.

Merge Project

Merge the entries from another project into the current project. See Merging Projects for more information on merging projects.

Get PDB

Import a structure from the PDB. Opens the Get PDB File Dialog Box.

Export Structures

Export structures to a file. Opens the Export Dialog Box.

Export to LiveDesign

Export structures to a LiveDesign instance. Opens the Maestro to LiveDesign Export Panel

Send to PyMOL

Send entries and data to a PyMOL session. Opens the Export to PyMOL Panel.

Change Working Directory

Change the directory that is used by default to read and write files. See Changing the Working Directory for more information.

Save Workspace Changes

Save changes made in the Workspace to the project entries. You might want to do this when making multiple changes to structures, to save a particular state of the changes.

Back Up Project

Save a copy of the project in its current state as a separate zipped project, in the same directory as the current project. See Backing Up and Restoring Projects for more information on backing up projects.

Restore From Backup

Restore a project to the state of a selected backup (which must be in the same directory as the project). See Backing Up and Restoring Projects for more information on restoring projects from a backup.

Save Checkpoint

Save a copy of the project in its current state inside the project folder, as a checkpoint. See Checkpointing a Project for more information on project checkpoints.

Revert to Checkpoint

Revert the current state of the project to the state stored in the checkpoint. See Checkpointing a Project for more information on project checkpoints.

Quit (Ctrl+Q / ⌘Q)

Close the Maestro session. You may be prompted to save changes to structures or projects. See also Quitting Maestro settings.

The Edit menu contains actions related to changing structures and entries, as well as preferences.

Undo (Ctrl+Z / ⌘Z)

Undo the last action.

Redo (Ctrl+Shift+ Z / ⌘⇧Z)

Redo the last undone action.

History

Submenu with a list of the most recent actions performed. Selecting an action restores the project and Workspace to the state it was in when the action was performed.

Cut (Ctrl+X / ⌘X)

Remove the selected atoms from the Workspace structure and place them in the paste buffer (in Maestro and SMILES format). See Copying and Pasting Structures for more information.

Copy (Ctrl+C / ⌘C)

Copy the selected atoms from the Workspace structure into the paste buffer (in Maestro and SMILES format). See Copying and Pasting Structures for more information.

Copy As

Copy the selected atoms to the paste buffer in SMILES or SMARTS format, according to the choice from the submenu. This allows you to paste the SMILES or SMARTS into an external application. See Copying and Pasting Structures for more information.

Paste (Ctrl+V / ⌘V)

Paste a structure into the Workspace, either from previously cut or copied Workspace structures, or an external structure in SMILES format or on Windows, ChemDraw or IsisDraw format. See Copying and Pasting Structures for more information. Atoms cut or copied from the Workspace are pasted at the coordinates they had when they were cut or copied.

Paste Special

Submenu with options to control how atoms are pasted into the Workspace. If they are 3D, you can place the centroid by picking a point in the Workspace (By Placing option); if they are 2D, you can choose to convert them to 3D before pasting (As 3D option). See Copying and Pasting Structures for more information.

Delete Atoms (Del)

Remove the selected atoms from the Workspace structure. If Workspace changes are automatically synced with the project, the atoms are also removed from the corresponding project entries.

3D Builder

Open the 3D Builder Panel to build or edit the Workspace structures.

2D Sketcher

Open the 2D Sketcher Panel to draw or edit a structure in 2D.

Add Hydrogens

Add hydrogen atoms to atoms where the valence is incomplete. See Drawing Structures for more information

Minimize

Perform a short force-field minimization of the Workspace structure.

Move Atoms (Ctrl+G / ⌘G)

Move the selected atoms as a rigid body. See Moving Atoms for more information.

Adjust

Submenu with items to adjust the geometry of the Workspace structure. See Adjusting Structures for more information.

Rapid Torsion Scan

Perform a scan of geometries around a selected dihedral angle in a small molecule. Opens the Rapid Torsion Scan Panel.

Rotamers

Select rotamers of a structure such as a protein. Opens the Rotamers Dialog Box.

Assign

Submenu with properties that can be assigned to structure components or from analysis of the structure. See Changing Atom and Residue Properties for more information.

Crystal Mates

Add atoms to a crystal structure from neighboring cells or asymmetric units. Submenu with choices of distance options for adding atoms, saving the result and removing the crystal mate atoms. See Adding Atoms from Crystal Mates for more information.

Centroids

Create a "dummy" atom at the centroid of a set of atoms. See Centroids Panel for more information.

Symmetrize Workspace

Adjust the positions of the atoms in the Workspace so that the structure has a chosen point group symmetry. Opens the Symmetrize Workspace Dialog Box.

Update Coordinates

Update the coordinates of the Workspace structures to match the coordinate system of the view (performing rotation and translation on the original coordinates as needed).

Star Included Entries (*)

Add a star to the Stars property of the Workspace entries. Useful for identifying and manually ranking interesting entries in the project.

Mark

Set or remove the Mark property of the entries chosen from the submenu. Useful for identifying entries.

Preferences (Ctrl+, / ⌘,)

Set preferences for the behavior of many Maestro features. Opens the Preferences Panel.

The Select menu contains actions related to atom selection. See Selecting Atoms for more information and links to detailed topics on selection.

Set Pick Level

Set the type of substructure that is selected when picking atoms in the Workspace ("selection scope"). See Selecting Atoms by Picking in the Workspace for more information.

Pick to Select

Submenu with items for the way the picked atoms change the selection, and for how to select of multiple atoms by dragging.

Quick Save (within session)

Save the current selection (in terms of atom numbers in the Workspace) in one of ten memory locations, for use within the current Maestro session. See Saving the Selection for more information.

Restore Quick Save

Apply the atom selection from one of the ten memory locations.

Exclude Nonpolar Hydrogens

Toggle for including or excluding nonpolar hydrogens when selecting atoms.

All (Ctrl+A / ⌘A)

Select all atoms.

Visible

Select only the displayed atoms. (Some of these atoms might not be in the Workspace view, but they are still selected.)

None (Ctrl+U / ⌘U)

Clear the selection (no atoms are selected).

Protein

Select the protein atoms.

Ligand

Select atoms belonging to ligands. See Ligand Detection Preferences for more information on the definition of ligands.

Solvent

Select solvent objects. These are usually small molecules that are dissolved in the main solvent (e.g. water), and modify the properties of the main solvent.

More Objects

Opens a pane that presents a larger variety of structural objects that can be selected.

Invert

Invert the selection: selected atoms become unselected, unselected atoms become selected. See Inverting the Selection for more information.

Expand

Submenu to expand the selection to include atoms that are with in a chosen distance of any selected atom.

Previous

Select the atoms that were selected before the last selection action. This is essentially a one-step undo action on the selection.

Define

Define the atoms to be selected using the Atom Selection Dialog Box.

Find (Ctrl+F / ⌘F)

Select atoms with particular properties by finding them in the Workspace. Displays the Find Toolbar at the top of the Workspace.

Previous Residue (P)

Select the previous residue in a chain.

Next Residue (N)

Select the next residue in a chain.

Actions related to Workspace contents. Also includes appearance settings.

Save Image As

Save an image of the Workspace in a chosen format. Opens the Save Image Dialog Box.

Animate

Animate the view of the Workspace structure with a rocking or spinning motion. See Animating the View for more information.

Animation Settings

Make settings for animation of the Workspace structure. Opens the Animation Settings dialog box. See Animating the View for more information.

Create Project Entry (Ctrl+Shift+ N / ⌘⇧N)

Create a project entry for the Workspace structure. Opens the Create Project Entry dialog box, to set the entry title and choose the atom set to save to the new entry.

Clear Workspace

Remove all structures and other objects from the Workspace, so that it is empty.

Measure

Measure distances, angles, and dihedrals in the Workspace. Displays the Measure banner. See also Measurements Toolbox, which lists all the Workspace measurements.

Surface

Submenu for creating, displaying, importing, and managing surfaces. See Creating and Displaying Surfaces for more information.

Preset Style

Submenu for defining and applying style presets. See Changing Structure Styles for more information.

Fonts

Change the font size of Workspace text, or set preferences for the fonts used.

Add Caption

Add a caption to the Workspace in a box. Opens the New Caption/Edit Caption Dialog Box. See Adding Captions to the Workspace for more information.

Highlights

Add highlights to the structures. Opens the Manage Highlights Panel.

Bond Labels

Compose labels from bond properties, and pick bonds to apply the labels. Opens the Bond Labels Panel.

Project Scenes

Create, display, and manage project scenes. See Project Scenes for more information.

Configure

Configure various aspects of the Workspace. Opens the Workspace Configuration Toolbox.

Customize Mouse Actions

Customize the actions performed for different mouse types and for a trackpad. Opens the Customize Mouse Actions Panel. See Mouse Interaction and Settings for more information.

Access point for user-defined scripts and KNIME workflows.

Manage

Manage the installed scripts. Opens the Manage Scripts Panel.

Install

Install scripts onto the menu. Opens the Install Scripts Panel.

Actions for changing camera view, saving views, changing screen display.

Fit

Fit the Workspace view to all atoms, selected atoms, or ligand atoms in the Workspace. Also has options for automatic fitting on Workspace changes. See Zooming and Fitting for more information.

Rotate

Rotate the Workspace through 90° around X or Y axes, or in small increments around X, Y, or Z axes. See Rotating the Workspace View for more information.

Translate

Translate the Workspace by small increments in the X, Y, and Z directions. See Translating the Workspace View for more information.

Zoom In (K)

Zoom in on the Workspace structure by a small factor. See Zooming and Fitting for more information.

Zoom Out (J)

Zoom out on the Workspace structure by a small factor. See Zooming and Fitting for more information.

Move Clipping Planes

Change the location of the planes at which the structure is clipped for display. See Adjusting the Clipping for more information.

Reset All

Reset the Workspace view to its default.

Align View

Align the Workspace view to orient it to an axis or a plane. Opens a banner to perform the action. See Aligning the View to the Structure for more information.

Save Camera View

Save the camera view to the project with a name so you can reapply it. Opens the Save View dialog box to name the view. See Saving and Restoring the View for more information.

Restore Camera View

Restore the camera view to the chosen saved view. The submenu lists the available views, as well as items for stepping through the views.

Manage Camera Views

Add or remove, export or import, animate and record a movie of animated views. Opens the Manage Views Panel.

Tile (Ctrl+L / ⌘L)

Display each Workspace entry in a separate tile in the Workspace area. See Tiling the Workspace for more information.

Stereo (Ctrl+S / ⌘S)

Display the Workspace structure as two stereo images that can be viewed with a stereo device.

Full Screen (Ctrl+= / ⌘=)

Toggle viewing of the Maestro main window in full screen mode.

The Window menu contains access points for floating windows, panes and gadget toggles.

Project Table (Ctrl+T / ⌘T)

Open the Project Table Panel, to view the list of project entries and their properties.

2D Viewer

Open the 2D Viewer Panel, to display 2D structures for entries in the Project Table in a tiled view.

Multiple Sequence Viewer

Open the Multiple Sequence Viewer/Editor Panel, for performing tasks with multiple sequences.

Project History

Open the Project History Panel, which displays text about the actions taken on the project.

Job Monitor

Open the Job Monitor Panel to monitor the status of jobs.

Clipping Planes

Display the clipping planes in the Workspace. See Adjusting the Clipping for more information.

2D Overlay

Display the 2D Overlay in the Workspace, showing the 2D structure of small molecules in the Workspace.

Command Input Area (Ctrl+ Shift+ E / ⌘⇧E)

Display the Command Input Area in the Workspace, for entering Maestro commands.

LiveDesign Connection

Display the widget for connection to a LiveDesign instance.

Entry List / Structure Hierarchy (Ctrl+E / ⌘E)

Open the Entry List / Structure Hierarchy panel , docked in the Workspace.

Workspace Properties

Show or hide entry properties in the Workspace. See Displaying Entry Properties in the Workspace for more information.

Sequence Viewer

Display the Sequence Viewer in the Workspace.

Status Bar

Display the Status Bar in the Workspace.

Command Script Editor (Ctrl+D / ⌘D)

Open the Command Script Editor Panel to view command history and create scripts from Maestro commands.

Message Console

On Windows, display a panel that contains the console messages.

Python Shell

Open the Python Shell Panel, to execute Python commands in a Maestro context.

Raise All

Raise all panels to be above any other windows.

Close All

Close all Maestro panels except the main window.

Cascade

Arrange the panels in a cascade from top left to bottom right.

Save Layout

Save the layout of the panels on the screen.

Restore Layout

Restore the panel locations on the screen to the saved layout.

Access to documentation, tutorials, general information etc. Also includes access to Contact Technical Support and Job Server registration dialogs.

Search All Documentation (Ctrl+H / ⌘H)

Search the documentation, including help, user manuals, command references, and tutorials. Opens the search page in your default browser.

Search Knowledge Base

Search the knowledge base on the web site.

Maestro Documentation

Open the documentation to the section on Maestro.

Applications Documentation

Open the documentation to the section on applications.

Tasks & Workflows

Open the documentation to the section on tasks and workflows, organized in the same way as the Task Tool.

Tutorials

Open the documentation to the tutorials section.

Sample Files

Import a sample structure file that is provided in the distribution.

Keyboard Shortcuts

Open the documentation at the page that describes the keyboard shortcuts.

About Maestro

Opens a pane that gives information about the Maestro version and access to information on the software environment on your machine.

New Features

Opens a web page that lists the new features in the software release.

Known Issues

Opens a web page that gives information on any known issues in the software release.

Legal Notices

Opens the page containing the legal notices, such as third-party software acknowlegements.

Register with Job Servers

Register with a job server instance for running jobs.

Contact Support

Opens a web page at a form to submit for technical support.