Exporting Structures

Using theExportpanel, you can write out structure files in Maestro, MacroModel, PDB, Sybyl Mol2, and MDL SD 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 panel.

To open theExportpanel, chooseExport Structuresfrom theProjectmenu on the main menu bar, or chooseStructures from the Export submenu of theTable menu in the Project Table

panel.

When you have made all the necessary selections, clickExport. 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 Export Settings

TheExportpanel is laid out in a similar fashion to theImportpanel, with the file and file type selection tools at the top, and various options under them.

Selecting a file format: To create a file, you must select the type of file you wish to write from

the types given in theFormatoption menu, which includeMaestro,PDB,Mol2,SD, Macro- Model, and a range of file types converted by Babel. The file extension in most cases is deter- mined by the file type. Default file extensions for the files in the first section of the menu can be

set in the File Suffix tab of 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.

Selecting a directory: To select a directory, you can enter it in thePathtext box, navigate to it in theDirectorieslist, or clickLaunch Directory or Working Directoryto select the directory from which you launched Maestro or the current working directory. The path and the directory and file lists are updated for the chosen directory.

Selecting a file: If the file exists, you can select it in theFileslist or enter its name in theFile

text box. If you want to export to a new file, enter the name in theFiletext box. You can specify an absolute or relative path in theFile text box in addition to the file name.

Appending or overwriting files: To append a structure to an existing file, selectAppend. If the file exists and you do not selectAppend, it is overwritten.

Saving graphical information: If you are writing a Maestro file, you can selectSave graph- ical information to store the molecular representation information for the structure you are saving. This option is ignored for other file types.

Specifying the source of the structures: The Exportpanel can be used to save structures directly from the Workspace or to write files containing structures associated with one or more project entries. To write out the contents of the Workspace to a file, selectWorkspaceunder

Structure source to be exported. This is equivalent to writing the included entries. If you only want the displayed atoms to be written to a file, selectDisplayed atoms only. To write out the entries that are selected in the Project Table to the exported file, selectSelected entries.

Exporting to single or multiple files: You can export entries to a single, multi-structure file,

or to multiple files that each contain a single entry. From theFilesoption menu, choose either

Export all entries to a single fileorExport each entry as an individual file. If you export struc- tures using one of the Babel-supported formats, you can only export a single structure to each file. In this case, you should not chooseExport all entries to a single file.

3.2.2

Exporting Multiple Files

If you want to save each entry to a separate file, you must specify how to name the files by choosing one of four naming schemes from the File Names Areoption menu. The naming schemes are described below.

Note: Because entry names are not unique, choosingFile name + entry nameor Just entry name does not guarantee that the file name is unique.

File name + entry name

If you chooseFile name + entry name, you must select a file or type in a file stem. The entry name and the file suffix are appended to the file stem. If you choose a file name, the suffix is the suffix of that file name. For example, if you are exporting the entries combination-3,

combination-4, and combination-5 in Maestro format, and you select the file

structure.mae, the new files are named

structure_combination-3.mae structure_combination-4.mae structure_combination-5.mae

If you typed in the file stemHIV, the following files would be written: HIV_combination-3.mae

HIV_combination-4.mae HIV_combination-5.mae

File name + entry ID

If you chooseFile name + entry ID, you must select a file or type in a file stem. The entry ID and the file suffix are appended to the file stem. If you choose a file name, the suffix is the suffix of that file name. For example, if you are exporting the entries with IDs 3, 4, and 5 in Maestro format, and you select the filestructure.mae, the new files are named

structure3.mae structure4.mae structure5.mae

File name + automatic number

If you selectFile name + automatic number, you must specify a filename. The files are given the same name and extension as the selected file, but numbers are added in sequence to the base file name. For the same example as above, if you select the filestructure.mae, the new files are named

structure_1.mae structure_2.mae structure_3.mae

Just entry names

If you chooseJust entry names, the file name is constructed from the entry name. For the above example, the new files are named

combination-3.mae combination-4.mae

combination-5.mae

and a dialog box confirms that the files were written to the desired directory.