Import Dialog Box

The Import dialog box allows you to import structures and their properties into the current project from Maestro files and a wide variety of other file formats, including PDB, MDL SD, Sybyl Mol2, ChemDraw, and MOE formats, files containing a list of SMILES strings, MacroModel and Jaguar input and output files, Desmond CMS files, FEP+ map files (FMP), Phase hypothesis files, crystallographic information (CIF) files; and from many other file formats supported by the OpenBabel file conversion utility. If you are importing structures from Maestro files, you can also import various settings. When the structures are imported, you can control which structures, if any, are displayed in the Workspace. You can import structures from multiple files at the same time. Multiple structures from any single file can be added as an entry group to the Project Table, with the group named after the file.

To open this panel, choose File → Import Structures or press Ctrl+I (⌘I).

  • Using
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Using the Import Dialog Box

To import structures from one or more files, you can either enter the file names directly into the File name text box or use the Look in tools to navigate to and select files.

Maestro opens and reads the files using the current settings, which are set in the Options section of the panel. To display this section, click Options. Maestro accepts both absolute (e.g. /home/joe/file1.mae) and relative (e.g. file1.mae) file names.

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 drag and drop Maestro, SD, PDB, XYZ, MOL2, and ChemDraw files from your window manager's file explorer onto the Workspace to import the structures in the file. When you do so, the first structure in the first file is added to the Workspace (rather than replacing it) and the new entries are added to the entry selection in the Project Table.

On Windows, you can double-click on Maestro, SD, PDB, and MOL2 files to import them into the most recent Maestro session, or a new session if Maestro is not running.

Files that contain SMILES strings are expected to be in CSV format, i.e. text lines in which the fields are separated by a standard delimiter (comma, space, or tab) and can have a header column. The file can have the extension .csv, .txt, .smi (with suffix .gz or gz for compressed .csv or .smifiles). If the file has only one column, this must be the SMILES string, and then the SMILES string is also used for the entry title. If the file has two columns, the SMILES string and the title property are automatically detected (either from the header or the first line). If the file has more than two columns, the Import SMILES Dialog Box opens, where you can choose the fields and decide whether or not to import any properties in the file. If you select multiple SMILES files for import, they must have no more than two columns: files with properties must be imported individually.

If the structures you want to import are in another project, you can import them by choosing File → Import From → Other Project. A project selector opens, so you can select the project, and then a dialog box opens that lists the entries in the project, displaying the title and the PDB ID.

If you want to import structures from a file that you have recently imported from, in the Project Table panel, choose File → Import Recent Structures → filename. The file is imported with the current import settings. This is especially useful when importing into a different project, as the list records all recent imports in any Maestro session or project. The number of files displayed on the list can be set in the General – History tab of the Preferences panel.

You can import structures by entering a text command in the Command Input Area in the main window. To import structures from a file, enter:

entryimport filename

including any appropriate option or path name.

Import Progress and Reporting

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. If the import is successful, a banner is displayed in the Workspace. The banner can offer further actions, depending on the file type: for, example, a Prepare link is present for PDB file import to prepare the structure with the Protein Preparation Workflow Panel.

Importing Compressed Files

Maestro can read a variety of compressed files in gzip format, and uncompress them while reading. It recognizes these files automatically by the extension, for example .maegz or .mae.gz for Maestro files. If Maestro does not read compressed files in some formats, you must uncompress them first, for example using gunzip on Linux, or one of the zip applications on Windows or Mac. If the compressed files do not have the appropriate extensions, rename them to include the proper extensions. This renaming step may be necessary particularly when downloading PDB files from internet sites.

Import Dialog Box Features

The Import panel has the standard file selection tools that usually appear in File Selectors, including a custom file filter. Options for display, structure selection, grouping of structures, and so on, are hidden by default, but can be displayed by clicking Options. The options are described below. Other settings for import are available in the Preferences panel. On Windows, you can choose to show the native file selector separately from the options—see File chooser dialogs (Windows only) options.

Import all structures option

Select this option to import all structures from the specified file. Deselect this option to specify the structures to import. To specify the structures, enter the starting index in the Start text box, and either select End to import to the end of file, or deselect End and enter the number of structures to import in the Total text box.

The start index is automatically reset to 1 when a different file is selected. These capabilities only apply to file formats that allow multiple structures, and not, for example, to PDB files.

Import associated data files option

If the structure file has other data associated with it, such as volume data for surfaces, the data can be imported into the project and associated with the relevant entries, by selecting this option. The mapping of the data to the entries is done in a file with the suffix .smap. This option is selected by default. If Maestro has features for visualization of the data, a button is added to the entry for the structure to provide access to these features. Some panels within Maestro can make use of associated data that is relevant to the panel task.

Replace Workspace option

Select this option to clear the Workspace before opening the new file, and display in the Workspace the structures specified with the Include in Workspace option menu. If this option is not selected, the new structures are added to the current project and the Workspace remains as it is.

For Maestro files, modify property mapping option

Modify the mapping of properties in the imported file to the properties in the project. This allows resolution 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.

For Desmond files, import only first structure option

When importing from a .cms file, import only the first structure. There is no need in this case to use the Start and Total text boxes.

For SD files, create titles from options

Specify the property to be used as the title in Maestro:

  • SD molecule name—This is the default, and corresponds to the first row in the CT block.
  • SD property—Select this option to use a specified property for the title, and enter the property name in the text box.
Create groups for option menu

When you import structures, they can be added to the Project Table as entry groups, named after the file. This option menu allows you to create a group for:

  • Each file with multiple top-level items—create a group for each file in which there is more than one structure or group in the file. If there is only a single item in any of the files being imported, i.e. a file contains only one structure or one group, a new group named after the file is not created. This prevents import of a single group from a file into another top-level group that contains nothing but the imported group.

  • Each file—create a group for each file, regardless of its content. This may result in import of a single group from a file into another top-level group that contains nothing but the imported group.

  • All files—create a single group for the items from all files, in a group named imported_structures. Structures and groups from all the files imported are placed in this group.

  • None—import structures or groups into the top level of the Project Table, i.e. without placing them in an entry group named after the file.

This choice applies whether you are importing from a single file or from multiple files.

Preserve groups within files option

If the file contains properties that classify the structures into groups and subgroups, use these properties to set up groups and subgroups in the project. These groups and subgroups are created underneath any group created due to a choice from the Create groups for option menu. The grouping properties are added to Maestro files when entries are exported, and when Phase hypotheses are generated. Phase hypotheses (.phypo, _phypo.maegz, _phypo.mae.gz) are always imported with preservation of groups, regardless of the setting of this option.

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