Key Concepts and Features of MS Maestro

Materials Science Maestro (MS Maestro) is Schrödinger’s interface for Materials Discovery and Analysis.

MS Maestro is a streamlined interface for atomic-scale structural visualization, cutting-edge physics-based computational modeling, and machine learning workflows for materials discovery and analysis. MS Maestro provides insights into the mechanisms and properties of materials and chemical systems in a wide range of technological applications such as catalysis, polymers, batteries, consumer packaged goods, renewable energy, and semiconductors to accelerate materials innovation.

MS Maestro is a customized form of the Maestro interface that is specially designed for materials science use. It inherits most of the capabilities of the Maestro interface, and it has features of its own.

If you prefer to use the standard Maestro interface, you can do so. Most of the capabilities of the Materials Science Suite are available from the Task Tool; however some features are only available in MS Maestro.

The following are some of the most important concepts and features for MS Maestro users to understand.

Click on the section label below to learn more about that section:

Maestro Projects

Maestro organizes all work into a project (.prj extension). The project is a collection of structures and data in Maestro. If there is no named project open, Maestro creates a scratch project to work from. Scratch projects are temporary, so we recommend saving the project.

Entry List (Entries)

Entries are imported or created structures and their associated data. The entry stores a collection of atoms; molecules (structures) grouped together and assigned an entry ID and a title. File types that can be imported include .pdb, .sdf, .smi as well as .mae files (native Maestro file type) among with many others (see a complete list of supported file types in the Import Dialog Box documentation).

The Entry List displays all the entries in the project, letting you choose which ones to view in the Workspace.

Workspace

The Workspace is the central area in the Maestro window. It is used for visualizing the entry structures in 3D, applying styles, and modifying the structures.

The Main Toolbar has a collection of selection, viewing, and styling tools. The selection tools make it easy to choose common objects and create more complex selections in the Workspace.

You can style each set of selected atoms with the Style Toolbox, or, style the entire Workspace quickly using the Preset Styles.

You can build and edit structures using the 3D Builder, which allows you to delete selected atoms and bonds, add fragments to them, or modify their properties.

The Periodic Structure Tool provides information on periodic structures and access to tools for display of periodic structures.

The Workspace Configuration Toolbar has toggles for showing or hiding commonly used objects in the Workspace: ribbons, interactions, clipping planes. Some toggles include a button to open respective menus.

The Status Bar shows information on the contents of the Workspace and individual atoms.

Project Table

The Project Table button opens the Project Table which contains all project entries and their properties. Use the Project Table and its menus to select specific sets of entries, import, generate, view and modify data, and create charts.

Jobs

Jobs are scientific computations set up and submitted via the panels that run on local and remote resources. The Jobs button shows the status of jobs started from the project, and gives access to the Monitor Panel to view running or recently completed jobs.

Tasks

Use the Tasks tool to open application panels and perform tasks. Tasks are organized by topics, methodologies, and application. Or, use the search field to find panels by name or function.

Periodic Structure Tool

In the Materials Science profile, Maestro has additional tools for working with periodic structures. The Status bar is customized to provide information on periodic structures and access to tools for display of periodic structures, with a section to the right side of the Status bar.

Other Important Features

Many but not all of the following features can be found on the image above. Click the links (where available) for more information.

Menu Bar—contains menus for various actions including the Window menu that can show important Workspace components such as the Find toolbar, the Clipping Planes window, and the Command Input Area among others.
Favorites Bar—buttons for tasks designated as favorites in the Task Tool. You can add items by clicking the pale star next to any action in the Task Tool, and remove items by right-clicking and choosing Delete.
Fitting Buttons—tools for zooming the view to specific content.
Clipping Planes—options to adjust the clipping.
Sequence Viewer—shows the sequences of the proteins and nucleic acids in the Workspace.
Command Input Area—text box for typing in Maestro commands.
LiveDesign Connection—the connection status to a LiveDesign server is indicated by the color of the icon: a green icon indicates that you are currently connected to a LiveDesign server, while a gray icon indicates you are disconnected. Click to open the Connect to LiveDesign Dialog Box

Some of the tools for biological systems are not present in the Materials Science profile:

Ribbons button on the Workspace Configuration toolbar
Crystal Mates and Alternate Positions buttons, under Workspace Toggles in the Workspace Configuration toolbox.
2D Overlay and Sequence Viewer buttons, under Workspace Gadgets in the Workspace Configuration toolbox.
Ligand-receptor and Intra-ligand options for hydrogen bonds in the Interactions toolbox.
Protein-related objects in the Select Objects pane.

In addition to the features in the Workspace Tools for Periodic Structures there are few other differences between the default Maestro interface and MS Maestro:

The mouse actions in the interface follow the PyMOL style (see Customize Mouse Actions Panel for information on customizing them).
The default working directory is the directory in which the Maestro project is located. This is called the "parent of the project directory", as the project itself is a directory (see Directories settings for information on customizing the default).
When you hover over a coarse-grained particle, the particle type is shown in the status bar instead of an element symbol.