Maestro User Manual

Chapter 2: The Maestro Main Window

Schrödinger Software Release 2015-2 

20

• Fragments toolbar—contains a small selection of molecular fragments for building. See

Section 5.1 on page 79

.

• Find toolbar—contains tools for finding various structural objects in the Workspace. See

Section 2.10 on page 36

.

• Proteins toolbar—contains buttons for various protein-related tasks. See 

Section 3.7

 of

the PrimeX User Manual.

• Periodicity toolbar—contains buttons for display of periodic structures. 

Section 7.5.3 on

page 152

.

• Favorites toolbar—contains no buttons by default, but is intended for you to customize.

The toolbar buttons for the default 

Project

, 

Edit

, and 

Workspace

 toolbars are described below.

Many of their features are described in later chapters.

2.4.1

The Project Toolbar

This toolbar contains buttons for the common project operations.

Open 

Open a project. Opens the 

Open Project

 project selector so you can select a project to open.

Menu equivalent: 

Project 

→

 Open

.

Save As 

Save a project by a different name.

Menu equivalent: 

Project 

→

 Save As

.

Import 

Import structures into the project as new entries. Opens the 

Import

 panel.

Menu equivalent: 

Project 

→

 Import Structures

.

Export 

Export structures from the project to file. Opens the 

Export

 dialog box.

Menu equivalent: 

Project 

→

 Export Structures

.

Table 

Open or close the 

Project Table

 panel.

Menu equivalent: 

Project 

→

 Show Table

.

2D Viewer 

Display 2D structures of the selected entries in a grid. Opens the 

2D Viewer

 panel.

Menu equivalent: 

Project 

→

 2D Viewer

.

Lig. Int. 

Display a simplified representation of ligand-receptor interactions. Opens the 

Ligand Interac-

tion Diagram

 panel.

Menu equivalent: 

Tools 

→

 Ligand Interaction Diagram.

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Chapter 2: The Maestro Main Window

Maestro 10.2 User Manual

21

2.4.2

The Edit Toolbar

This toolbar contains buttons for atom selection and editing structures, in addition to the usual

buttons found on Edit toolbars.

Get PDB 

Retrieve a structure from the PDB and import it into the project. Opens the 

Get PDB File 

dia-

log box. 

Menu equivalent: 

Project 

→

 Get PDB

.

Prep Wiz 

Prepare a protein for use in calculations. Opens the 

Protein Preparation Wizard

 panel.

Menu equivalent: 

Workflows 

→

 Protein Preparation Wizard

.

Select 

Select atoms in the Workspace. Double-click to select all atoms.

This button has a menu from which you can choose the type of structural unit you want to 

select. If you select a structural unit from the menu, the icon changes to reflect that structural 

unit (A for atoms, R for residues, etc.). You can expand the selection to include entire residues 

within a specified distance by choosing one of the distance options, and you can include or 

exclude the picked object in the final selection.

You can choose Select to open the Atom Selection dialog box and specify atoms to select.

Menu equivalent: 

Edit 

→

 Select Atoms

.

Undo/Redo 

Undo or redo the last action. The button icon and text changes, depending on the action.

Menu equivalent: 

Edit 

→

 Undo/Redo

.

Cut 

Delete the selected atoms from the Workspace and place them on the clipboard, in Maestro 

format and in SMILES format. 

Menu equivalent: 

Edit 

→

 Cut

.

Copy 

Copy the selected atoms and an image of the Workspace onto the clipboard. The selected 

atoms are stored in Maestro and SMILES format. The resolution of the image is the current 

screen resolution, so if you want a higher resolution, you should use the 

Save Image

 panel. 

Menu equivalent: 

Edit 

→

 Copy

.

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Chapter 2: The Maestro Main Window

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Paste 

Paste a structure from the clipboard into the Workspace. The structure can be a SMILES 

string, a structure from ChemDraw or Isis Draw (Windows) or a set of atoms previously cut or 

copied from the Workspace.

SMILES strings are converted into 2D structures, and added to the project as a new entries, 

with the SMILES string as the title. No attempt is made at 3D conversion. To paste it in 3D, 

choose 

Edit 

→

Paste Special 

→

 As 3D

.

Atoms that were cut or copied from Maestro are placed at the coordinates at which they were 

cut or copied onto the clipboard, as a scratch entry. You can paste atoms from one Maestro ses-

sion into another session. 

Menu equivalent: 

Edit 

→

 Paste

.

Delete 

Delete objects in the Workspace. The button menu has several sections: one for the current 

selection (

DELETE

), one for structural units to pick for deletion, one for other kinds of struc-

tural objects to delete, and one for markers and annotations. Double-click to delete the 

selected atoms.

Menu equivalent: 

Edit 

→

 Delete 

→

 Pick to Delete

.

Build 

Show or hide the 

Build

 toolbar and 

Fragments

 toolbar, or open the 

Build

 panel from the menu. 

Menu equivalent: 

Edit 

→

 Build.

2D Sketcher 

Sketch to edit or create structures in 2D. Opens the 

2D Sketcher

 panel. 

Menu equivalent: 

Edit 

→

 2D Sketcher

.

Add H 

Add hydrogen atoms to a structure that lacks them, to complete the valence. From the button 

menu you can choose the type of structural unit to pick for addition of hydrogens, open the 

Atom Selection

 dialog box to select the atoms, or choose a hydrogen treatment. Double-click 

to add hydrogens to the selected atoms.

Menu equivalent: 

Edit 

→

 Add Hydrogens

.

Transform 

Transform (rotate or translate) selected atoms in the Workspace. From the button menu you 

can choose to display hydrogen bonds, contacts, and bond lengths while transforming, choose 

a structural unit to pick the atoms to transform, or open the 

Advanced Transformations

 panel 

for more control over the transformation. 

Menu equivalent: 

Edit 

→

 Transform

.

Adjust 

Adjust the geometry of structures. From the button menu you can choose geometric parame-

ters to adjust: distances, angles, dihedrals or chirality; torsions, peptides, or side chains (rota-

mers); or choose to display hydrogen bonds and contacts while adjusting torsions.

Menu equivalent: 

Edit 

→

 Adjust.

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