Maestro User Manual

Chapter 3: Importing and Exporting Structures and Data

Schrödinger Software Release 2015-2 

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3.2

Exporting Structures

Using the 

Export

 dialog box, you can write out structure files in Maestro, PDB, Sybyl Mol2,

MDL SD, and SMILES formats, and in various other formats available through the program

Babel. You can use the Workspace contents or selected project entries as input, and you can

append structures to an existing file and retain additional information when the file format

allows it. When exporting project entries, Maestro provides options for exporting each selected

entry to its own file, or placing all selected entries in the same file.

Project data is automatically saved, unless you are running in a non-automatic synchronization

mode. The structures from a project are saved in a Maestro-formatted file, along with other

data. If you want to save just the structures and their associated data, or if you want to save

structures in other file formats, you can export the structures. 

Figure 3.3. The Export dialog box.

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Chapter 3: Importing and Exporting Structures and Data

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53

To open the 

Export

 dialog box, do one of the following:

• Click  the 

Export

 button in the main window or in the 

Project Table

 panel. 

• Choose 

Project 

→

 Export Structures 

in the main window.

• Choose 

Table 

→

 Export 

→

 Structures

 in the 

Project Table

 panel.

• Choose 

Export Structures

 from the entry group shortcut menu.

The 

Export

 dialog box is laid out in a similar fashion to the 

Import

 dialog box, as a standard file

selector, with an 

Options

 button to display or hide the options for making export settings. The

options are displayed by default.

When you have made all the necessary selections, click 

Export

. A dialog box confirms that the

files were written. If a file by the specified name already exists, the 

Exporting-Overwrite?

dialog box is displayed and you must choose an action. 

3.2.1

Selecting a File

By default, structures are exported to a single file, which you can select as described below. It

is also possible to export structures to multiple files. 

Selecting a file format: To create a file, you must specify the file format. By default, the file

type is determined by extension, which means that you can enter the file name with its exten-

sion in the 

File name

 text box. You are warned if the extension is invalid. Otherwise, you can

select the type of file you wish to write from the types given in the 

Files of type

 option menu,

which include 

Maestro

, 

PDB

, 

Mol2

, 

SD

, 

MacroModel

, and a range of file types converted by

Babel. The file extension in most cases is determined by the file type. Maestro, PDB, and SD

files can be exported as compressed (gzipped) files. Default file extensions for the files in the

first section of the menu can be set under 

General 

→

 File extensions 

in the 

Preferences

 panel.

Properties from the Project Table are exported as well as structures to Maestro and SD files,

and any relevant properties are exported to PDB files. SMILES files are exported as plain text

files with the extension .smi. The SMILES string for each structure is written on a separate

line, followed by the title (if it exists), from which it is separated by a space. 

Selecting a directory: To specify the directory to export to, you can enter it in the 

File name

text box, or navigate to it using the standard locations, the navigation buttons, or the option

menu at the top of the panel. The path displayed in the option menu and the lists are then

updated for the chosen directory. 

Selecting a file: If the file exists, you can select it from the list of files or enter its name in the

File name 

text box. If you want to export to a new file, enter the name in the 

File name 

text

box, including an absolute or relative path if you want.

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Chapter 3: Importing and Exporting Structures and Data

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3.2.2

Selecting Export Settings

Once you have selected the file to export structures to, you can make choices about which

structures to export and how to export them. You can display the options for these choices by

clicking 

Options

. 

Appending or overwriting files: To append a structure to an existing file, select 

Append

. If

the file exists and you do not select 

Append

, it is overwritten. 

Maestro file format: If you want to export a Maestro file for use in an earlier release, you can

select 

Use v1 format (Suite 2012) when writing Maestro files

. The v2 format reduces the size of

the Maestro file by removing redundant space and information, so it cannot be used in earlier

releases. 

PDB file records: When writing a PDB file, you can include the SEQRES, HELIX, SHEET,

TURN, and SSBOND records in the file by selecting 

Write SEQRES, HELIX, SHEET, TURN,

and SSBOND information

. You can write out duplicate CONECT records to store information

on the bond order, by selecting 

Write multiple bonds as duplicate CONECT records

. If you

deselect this option, only one record is written per bond, regardless of bond order. 

You can also ensure that the atoms are written out in ascending order of residue number, by

selecting 

Reorder by residue number

. This option ensures that all the atoms from a given

residue are in a contiguous block in the PDB file. It is useful if atoms have been added to the

structure, as added atoms are placed at the end of the atom list and are not next to other atoms

from the same residue.

SD file format: If you are saving an SD file, you have the choice of writing it in V3000 format

by selecting 

Use V3000 format when writing SD files

. This is a a free-format version that allows

the writing of structures with more than 999 atoms. The default is to use the V2000 format for

SD files, which is fixed-format.

The property names in the SD file can be written out with names as they appear in the Project

Table (the display name), by selecting 

Use display names when writing SD files

. The default is

to write the internal names, which have prefixes that indicate the type and origin of the prop-

erty and spaces replaced with underscores. When an SD file from another source is imported,

the property names do not have type and origin information. The name in the SD file is used as

the display name, and an internal name is constructed that adds the type and origin prefixes, for

internal use in Maestro. If you are exporting a file for use in other applications, you should

select this option, particularly if you are transferring data between Maestro and other applica-

tions using SD files and want to maintain consistent naming.

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