Maestro User Manual

Chapter 3: Importing and Exporting Structures and Data

Maestro 10.2 User Manual

47

Mapping Maestro and SD properties: To map properties in an input Maestro file to different

properties in the project, select 

For Maestro files, modify property mapping

. This allows resolu-

tion of property types as well as creation of a single project property from multiple sources.

The 

Map Properties

 dialog box opens when you click 

Open

. In this dialog box you can select a

property from the project for each property in the input file (in the first structure). You can also

save and load property mappings, so you can use different mappings for different files or proj-

ects. Mapping of properties in SD files can be done similarly by setting a preference under

Project – Importing Structures

 in the 

Preferences

 panel—see 

Section 14.2.4 on page 343

. 

At the same time, you can select the properties to import, using the check boxes in the 

Import

column of the 

Map Properties

 dialog box. Properties that are not imported cannot be mapped.

Selecting structures to display: When you import structures from a file, you can set options

to control which structures to display, and whether the structures already in the Workspace are

cleared or not. If 

Replace Workspace

 is selected (the default setting), Maestro automatically

clears existing structures from the Workspace. To import new structures without removing the

Workspace contents, deselect 

Replace Workspace

. 

Other display options are available under 

Project – Importing Structures

 in the 

Preferences

panel—see 

Section 14.2.4 on page 343

. Some of these are described below.

• To specify which structures are to be included in the Workspace, choose one of the

options from the 

Include in Workspace

 option menu: 

No Imported Structures

, 

First

Imported Structure

, or 

All Imported Structures

. The default is 

First Imported Structure

. If

you choose 

No Imported Structures

 and 

Replace Workspace

 is selected, the Workspace is

cleared.

• Structures that are imported are not necessarily centered on the coordinate origin, and

might not be visible even though displayed. To ensure that the view is centered on the

structures and zoomed to display all atoms upon import, select 

Fit to Workspace following

import

. (This setting is persistent between Maestro sessions.) 

Opening the Protein Preparation Wizard: If you are importing a PDB file, you can select

Open Protein Preparation Wizard after importing PDB file

 under 

Project – Importing Structures

in the 

Preferences

 panel, to open the 

Protein Preparation Wizard

 panel automatically when the

structure is imported. You can then prepare the protein for use in various applications. 

Setting up pose viewing: If a pose viewer file is imported, you can perform the setup in the

Project Table automatically by selecting 

For pose viewer files, turn on pose viewing

 under

Project – Importing Structures

 in the 

Preferences

 panel. You can then immediately start

viewing poses—see 

Section 6.1

 of the Glide User Manual for more information. This option is

selected by default.

---

Chapter 3: Importing and Exporting Structures and Data

Schrödinger Software Release 2015-2 

48

3.1.3

Interacting with the Import Process

If the import takes more than a few seconds, or there are errors on import, the 

Import Progress

dialog box opens. The dialog box shows which file is being read and how many structures have

been read. It also shows whether there have been any errors or warnings on import, and shows

the related messages in a text area. You can show or hide these messages by clicking the

Details

 button. You can also copy and paste the messages into another application with the

usual key strokes.

You can suspend import by clicking the 

Pause

 button. This allows you to examine any

messages that were generated, and choose whether to continue with the import or cancel it. The

button changes to 

Resume

, so you can continue the import.

If you cancel the import, the structures imported successfully are kept. If you want to delete

these structures, click the 

Undo

 button or choose 

Edit

 

→ 

Undo

 in the main window.

When the import finishes, the dialog box remains open if there were any errors or warnings, or

if the messages area is displayed. The 

Cancel

 button changes to 

OK

 so that you can dismiss the

dialog box when you have finished examining the messages. 

3.1.4

Importing Structures from Another Project

You can import entries from another project, by choosing 

Project 

→

 Import from Project

. A

project selector opens, in which you can select the desired project. When you have selected the

project, the Import entries dialog box opens. This dialog box lists the title and the PDB ID for

the entries, which you can select for import. When you click 

OK

, the entries are imported,

along with all their properties and auxiliary data. The entries are selected, and the inclusion of

entries is governed by the options in the 

Import

 panel.

3.1.5

Importing Structures by Dragging onto the Workspace

You can import structures into Maestro by dragging one or more files from your window

manager’s file explorer onto the Maestro Workspace. The structures are imported in the same

way as using the 

Import

 panel, except that the first structure in the first file is added to the

Workspace, and the imported structures are added to the selection in the Project Table. Drag-

and-drop is supported for Maestro, SD, MOL2, XYZ, and PDB formats.

3.1.6

Importing Structures from the PDB Database

In addition to importing PDB files, you can import structures directly from the PDB database

or from a local copy of the PDB database. To do so, you can use the 

Get PDB File

 dialog box,

which you open from the 

Project

 menu. This dialog box runs the getpdb utility, which is

described in 

Section 2.3

 of the General Utilities manual, and which you can use directly from

---