Maestro User Manual

Chapter 2: The Maestro Main Window

Maestro 10.2 User Manual

39

Figure 2.5. The Quit Maestro panel.

If you are working in a scratch project and have not saved the project, you are prompted to do

so, if you have the preference 

Warn before closing a scratch project

 set, under 

Project – Closing

projects

 in the 

Preferences

 panel. If this preference is not set, the scratch project is discarded. 

To quit Maestro quickly, press 

CTRL+Q ENTER

 

(Q ENTER)

.

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Chapter 3

Maestro 10.2 User Manual

41

Maestro User Manual

Chapter 3:

Importing and Exporting Structures and 

Data

The primary place for reading and writing data from Maestro is a project. When you open a

project, the structures and data from that project are read into Maestro. As you modify struc-

tures and data they are automatically saved in the project (unless you have set a preference not

to do so). Projects are described in detail in 

Chapter 9

. In addition to reading and writing to

projects, Maestro can also read and write structural information in a variety of formats,

including its own native Maestro format, MacroModel, Jaguar, PDB, MDL SD, Sybyl Mol2,

and MCPRO zmat format. Structural information can also be obtained from the input and

output files of a wide variety of quantum chemical programs. 

Obtaining structures from a file in Maestro is called importing rather than reading because the

structures are imported into the current project. Any structures that do not exist as entries in the

current project are external to the project, and therefore must be imported. Similarly, the term

exporting is used instead of writing because a file is created for use outside the current project. 

Data that is associated with structures can also be imported and exported independently to

spreadsheet files. This capability enables properties that are created by Schrödinger software to

be read by a spreadsheet program, manipulated, and re-imported into the project. 

3.1

Importing Structures

The main means of importing structures is by using the 

Import

 panel. You can import data from

files in Maestro, MacroModel, PDB, Sybyl Mol2, MDL SD, and a range of other formats. If

the files contain multiple structures, such as the output of a conformational search, you can

select the structures to import. 

If you want to import structures from a file you have recently imported from, with the current

import settings, you can simply choose 

Project

 

→ 

Import Recent Structures

 

→ filename. 

When importing structures, Maestro places each structure into a separate, new entry in the

current project. For Maestro files, molecular representation information can be imported along

with a structure. In addition, Maestro adds two properties to the structures on import: the full

path to the file from which the structures were imported (

Source Path

), and the file name

without the path (

Source File

). If these properties already exist in the imported structures, they

are overwritten.

You can undo the import operation, but the changes made to the Project Table remain.

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Chapter 3: Importing and Exporting Structures and Data

Schrödinger Software Release 2015-2 

42

Figure 3.1. The Import panel.

To open the 

Import

 panel, do one of the following:

• Choose 

Project 

→

 Import

 

Structures 

in the main window.

• Press 

CTRL+I (

I

) with the pointer in the main window.

• Choose 

Table 

→

 Import 

→

 Structures

 in the

 Project Table

 panel.

• Click the 

Import 

button on the 

Project

 toolbar in the main window or the 

Project Table

panel.

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Chapter 3: Importing and Exporting Structures and Data

Maestro 10.2 User Manual

43

3.1.1

Selecting Files

Selecting a file type: Before you choose files, you must specify the file type by choosing a file

format from the 

Files of type

 option menu. The menu options are described below.

Common

Import one of the common file types, including Maestro, PDB, and SD. See the descriptions

below for these file types. 

Maestro

Import from Maestro structure files, which have a .mae extension (.mae.gz or .maegz if they

are compressed). Properties are imported as well as structures.

PDB

Import PDB files, which have either a .pdb, a .pdb.gz (for compressed files), or a .ent

extension. (See also 

Section 3.1.6 on page 48

.)

The PDB ID is used for the structure title, and the title from the PDB file is stored in a new

property, 

PDB TITLE

. 

Where multiple sets of coordinates (alternate positions) exist for atoms in a single PDB entry,

Maestro reads all sets by default. You can read the coordinates for the first set only by dese-

lecting 

Read alternate locations

 in the 

Import Options

 dialog box. Properties are imported as

well as structures. 

Note:

PDB structures that have varying number of atoms in different MODELs cannot be

imported.

Mol2

Import Sybyl Mol2 files, which have a .mol2 extension.

SD

Import MDL SD files, which have an .sd or.sdf extension for multiple structure files, an

.sdfgz

 or .sdf.gz extension for compressed multiple structure files, or a .mol extension for

files with a single structure. Properties are imported as well as structures. If you want to choose

a property from the SD file to use for the 

Title

 property in the Maestro project, you can do so in

the 

Import Options

 dialog box. The default is the SD molecule name. 

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