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Import Dialog Box |
The Import panel 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, and Sybyl Mol2 formats, files containing a list of SMILES strings, MacroModel and Jaguar input and output files, MCPRO input files, Desmond CMS 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 the Import dialog box, you can:
Choose Project → Import Structures in the main window.
Press Ctrl+I (⌘I) in the main window.
Click the Import button on the Project toolbar in the main window.
Choose Table → Import → Structures in the Project Table panel.
Press Ctrl+I (⌘I) in the Project Table panel.
Click the Import button on the Project toolbar in the Project Table panel.
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.dat) and relative (e.g. file1.dat) 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, and MOL2 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.
If the structures you want to import are in another project, you can import them by choosing Project → Import from 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, you can choose Project → 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.
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.
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.
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.
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.
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.
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.
Select this option to read alternate locations from a PDB file. If deselected, the coordinates for the atoms with the highest occupancy are read, and the rest are ignored. You can display alternate locations from the Workspace menu.
Specify the property to be used as the title in Maestro:
When you import structures, they can be added to the Project Table as entry groups. This option menu allows you to create a group for each file with multiple structures (the default) or for all files, to create a single group for all files, or to import structures without placing them in an entry group (None option). This choice applies whether you are importing from a single file or from multiple files. If you choose to create a single group for all imported files, you can provide a name in the Group name text box.
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.
Maestro can read compressed Maestro, SD, PDB, and SMILES files in gzip
format, and uncompress them while reading. It recognizes these files
automatically by the extension .maegz or .mae.gz for
Maestro files, .sdfgz or .sdf.gz for SD files,
.pdb.gz for PDB files, and
.smigz or .smi.gz for SMILES files. To read
compressed files in other formats, you must uncompress them first, for example
using gunzip on Linux, or one of the zip applications on
Windows. 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.
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