Export Dialog Box

Export (save) entries from the current project to a file or a number of files, in Maestro, PDB, Mol2, SD, protein or small molecule CIF, Desmond (CMS), SMILES, GAMESS, MOPAC, XYZ, Gaussian, or Phase hypothesis format, or to a range of other formats supported by Babel. You can create new structure files or append to an existing structure file.

To open this panel, choose File → Export Structures in the main window or in the Project Table panel.

  • Using
  • Features
  • Additional Resources

Using the Export Dialog Box

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.maegz) and relative (e.g. file1.maegz) 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 both compressed and uncompressed Maestro, PDB, Desmond, and SD files is supported; the default format is compressed Maestro format, with extension .maegz. Exporting to a Phase hypothesis file (.phypo) is only supported for a single Phase hypothesis per file. You can export multiple hypotheses to individual files or to a single Maestro file.

On Windows, the settings for exporting are shown in a separate dialog that opens after specifying the location and file name. On macOS and Linux, the file selection and settings dialogs are combined.

If you want to export entries to files without using the Export dialog box, you can use the entryexport command in the Command Input Area. Note that options such as file format type also need to be included in the command.

Export Dialog Box Features

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 displayed by default. You can hide them by clicking Options. The options are described below. On Windows, you can choose to show the native file selector separately from the options—see File chooser dialogs (Windows only) options.

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. If you use the .cif extension, Maestro determines whether the structure is a small molecule or a protein and exports in the appropriate CIF format. 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. The default is .maegz.

Structure source to be exported option menu

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.
Properties to be exported option menu

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.

Select button

Click this button to select the properties to export. Opens a Multiple Property Selector, 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.

Files option menu

Choose whether to export all entries to the same file, export each entry separately, or export each entry group separately. For the last choice, the ungrouped entries are treated as a single group. 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. The files that the entries or groups are exported to depend on the file naming choice, which could result in the same file name for several entries or groups.

Append option

Append structures to the file rather than overwriting. This option is only available for Maestro and SD file formats. For PDB and Mol2 files, this option is disabled and files are always overwritten. For Maestro 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.

File names are option menu

Choose a naming scheme for the file names when you export to multiple files, as chosen from the Files option menu. The files the entries are exported to depend on this choice, which could result in the same file name for different entries or groups.

The file extension is determined from the format selected from the Files of type option menu. You can change the default extensions in the General - Files tab of the Preferences panel.

There are three options for creating a file name if you chose Export each entry individually:

  • Just entry titles, e.g. title1, title2, ... .
  • Base name + entry title, e.g. abc_entry1, abc_entry2, ...
  • Base name + automatic number, e.g. abc_1, abc_2, ...

Special characters and spaces in the entry titles are replaced with underscores (_).

For exporting entry groups to individual files, there are also three options:

  • Just group titles, e.g. title1, title2, ... .
  • Base name + group title, e.g. abc_title1, abc_title2, ...
  • Base name + automatic number, e.g. abc_1, abc_2, ...

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 base name portion of the file name.

If you use the entry title or group title in the file name, you should ensure that they are unique. If they are not unique, they are made unique by appending _n where n is a number, generated in the same way as if you chose to add an automatic number.

Thus, if you have two entries named bob, and you choose Export each entry individually and Just entry titles for saving and naming the files, and export them in .mae format, you will get two files, bob.mae and bob_1.mae.

If you select Append and export entries or groups individually, Maestro creates the file name and checks whether the file exists first; if it does it appends to that file. If not, it creates a new file. So if you exported the two entries named bob again, they would both be appended to bob.mae.

PDB option section

This section contains options for exporting structures to PDB files.

Reorder by residue number option

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.

CMS option section

This section contains options for exporting CMS files that are stored within the project. The structures that are exported must have originated from CMS files. The options for the files and properties to export are restricted to ensure that each structure is exported with all its properties to a single file. The structures that are exported are the original, imported CMS structures from the entries that are being exported, and do not include any changes made to the structures after import. This feature is useful for Materials Science applications that update CMS files and store them in the project (see for example Manipulate Cell Panel).

Include trajectory option

Export the trajectory when the structure is exported, if it has one. The trajectory is copied from the path to the trajectory stored in the original CMS file, and is written to the same directory as the CMS file. The trajectory must exist at the location specified by the path (indicated by the presence of the T button in the Entry List).

SD options section

This section contains options for exporting MDL SD files.

Use V3000 format option

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.

Use display names option

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 an 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 Change Property Dialog Box.

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