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Export Dialog Box |
In the Export dialog box you can export (save) entries from the current project to a file or a number of files, in Maestro, PDB, Mol2, SD, or SMILES format, and to several other formats supported by Babel. You can create new structure files or append to an existing structure file.
To open the Export dialog box, you can:
Click the Export button on the Project toolbar in the main window.
Choose Table → Export → Structures in the Project Table panel.
Click the Export button on the Project toolbar in the Project Table panel.
Right-click in the entry selection or on an entry group in the Project Table panel or the Entry List panel and choose Export Structures.
To export structures to a single file, you can enter the file name directly into the File name text box. The file is exported with the current settings when you press ENTER or click Save. See below for descriptions of the settings. Maestro accepts both absolute (e.g. /home/joe/file1.mae) and relative (e.g. file1.mae) file names. You can also navigate to the directory where the file is located and select the file from the list of the directory contents. Exporting to compressed Maestro, PDB, and SD files is supported.
If you want to export entries to files without using the Export dialog box, enter the entryexport command in the Command Input Area. Note that options such as file format type also need to be included in the command.
The Export dialog box includes the standard file selection tools that usually appear in File Selectors. Options for selecting the structures to be exported and how they are exported are displaye by default. You can hide them by clicking Options. The options are described below.
The default selection for Files of type is By extension, which means that if you type a file name with its extension, Maestro determines the file type from the extension, and warns if it fails to find a valid type. Otherwise you can choose a particular file type, and the extension is added if a valid extension for the chosen file type is not given.
Append structures to the file rather than overwriting. This option is only available for Maestro, MacroModel and SD file formats. For PDB and Mol2 files, this option is disabled and files are always overwritten. For Maestro, MacroModel, and SD formats, when Append is selected, the structures project are appended to the selected file. Otherwise, the file is overwritten with the structures selected for export.
Use the version 1 format when writing Maestro files. This is the format used for Maestro files in Suite 2012 and earlier releases. The version 2 format saves space by removing whitespace and redundant property data. This option is included for backward compatibility.
This section contains options for exporting structures to PDB files.
When writing a PDB file, include SEQRES, HELIX, SHEET, TURN, and SSBOND records.
When writing a PDB file, store information on the bond order by writing duplicate CONECT records for multiple bonds. If this option is not selected, only one CONECT record is written for any bond, regardless of its order, and so information on the bond order is not stored in the PDB file.
Reorder the atom list so that it is written out in ascending order of residue number. This action ensures that all the atoms from a given residue are in a contiguous block in the PDB file. The option is useful when 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.
This section contains options for exporting MDL SD files.
Use the V3000 format when writing SD files. This is 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.
Write the property names in the SD file as they appear in the Project Table (the display name). The default is to write out the internal name, which has prefixes that indicate the type and origin of the property 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 and 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 using SD files to transfer data between Maestro and other applications and want to maintain consistent naming. If you want to rename properties before export, you can do so in the Rename Property panel.
Specify the source of the structures to be exported. The choices are:
Workspace (all atoms)—export the entire contents of the Workspace. This option is selected by default if no entries are selected in the Project Table. Each entry in the Workspace is exported as a separate structure.
Workspace (displayed atoms only)—export only the atoms that are displayed in the Workspace. The displayed atoms are exported as a single structure.
Selected entries—export the entries that are selected in the Project Table.
Specify the properties that are to be exported by choosing from this option menu.
All—export all properties in the Project Table.
Shown—export the properties that are shown in the Project Table. You can change the properties that are displayed in the Show Property dialog box.
Selected—select the properties to export. When chosen, the Select button is made available so that you can select the properties.
Properties are exported in the order that they appear in the Project Table. You can change the order of the properties in the Reorder Properties dialog box before you export them.
Click this button to select the properties to export. Opens a standard property selection dialog box, so you can choose the properties. The number of properties selected is reported to the right of this button. The property selection is stored both as a project preference and a user preference; it is initially set to the shown properties.
Only available when you choose Selected from the Properties to be exported option menu.
Choose whether to export all entries to the same file, export each entry to a different file, or export each entry group to a different file. The default is to export all entries to the same file. The choice you make determines whether the File names are option menu is available, and what items are presented on it.
Choose a naming scheme for the file names when you export to multiple files, as chosen from the Files option menu.
The complete file name is composed of the base name plus an extension. The extension is determined from the format selected in the Export dialog box: Maestro, PDB, etc.. You can change the default extensions in the General - Files tab of the Preferences panel.
Base names are created using the choice made from the File Names Are option menu. There are five options for creating a base name if you chose Export each entry to a different file:
_). There are four options for creating a base name if you chose Export each entry group to a different file:
Special characters and spaces are replaced with underscores (_)
when using the name or title as part of the file name.
The file name specified in the File name text box is used as the file name portion in the first three cases for each choice, with the extension stripped off if it exists.
In the last two cases, the file name is not used. If you want to navigate to a directory with either of these options chosen, you must double-click on the directory: you cannot click on a directory and press ENTER in this case.
If you use the entry name, entry title, or group title, you must ensure that they are unique. Otherwise, when a duplicate name or title is found, you will have to choose between overwriting the first file with that name, or skipping the entry with the duplicate name or title. For these two options, the File name option menu is not available, but you can choose the file format from the Files of type option menu.
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