Edit Job Dialog Box

This dialog box allows you to edit the entire input file or the geometry (the structure). You can use it to change settings and add settings that are not available from the GUI. The structures can be displayed in the Workspace, and updated while you are editing.

To open this dialog box, click the arrow next to the Settings button in any of the Jaguar panels and choose Edit.

Using
Features
Additional Resources

Using the Edit Job Dialog Box

You can edit the entire input file, by selecting Input file, or just the geometries (the structures) in the zmat, zmat2, and zmat3 sections, by selecting Structure.

To edit the text, you can type in new text, cut, copy, and paste within the editing area, using the tools on the Edit menu, or copy and paste within the editing area or from another application, by highlighting the text and inserting it with the middle mouse button. The paste buffer is persistent: you can cut or copy, close the dialog box, reopen it, and paste the text in.

If you want to copy settings from a completed calculation that was incorporated into your project, you can click on the link to the input file (or restart file) in the Project Table, and choose View. The file opens in a text viewer, in which you can select and copy text. You can then paste it into the editing area of this dialog box. You might need to display all properties (use the Property Tree) to see the file name property, as it is hidden by default.

If you choose Structure, the Structure menu is displayed on the menu bar. This menu enables you to convert between Cartesian and Z-matrix representations of the geometry, view and assign standard atom labels, and standardize the Z-matrix representation for transition state searches and IRC scans. If you convert from Z-matrix to Cartesian format, any variables or other information is lost. Converting to Z-matrix format adds variables, which are assigned values in a zvar section.

To view changes made to the geometry in the Workspace, click Preview. The structure in the Workspace is updated to reflect the current state of the geometry.

If you delete the entire geometry, the structure is removed from the Workspace. If you add zmat2 and zmat3 sections (for example, by cutting and pasting) for a transition state search or an IRC scan, these geometries appear in the Reactant, Product, or Transition State tabs when you select Structure. If you try to add these sections for a single-structure task, a warning is displayed.

When you are editing the input for a single-structure task, you must not have more than one entry displayed in the Workspace. If you don't have a structure for input, you can add it in this dialog box, but you cannot view it in the Workspace as the structure whose coordinates you added is not part of a project entry.

Note: If you add any @, *, or # symbols in this dialog box to specify counterpoise atoms, atoms for Hessian refinement, or constraints, these symbols are removed when you click OK. To keep these symbols in the input file, choose Write from the File menu, then run the Jaguar job from the command line or click the Tasks button and browse to Jaguar → Run Input Files. If you read the input file back into Maestro, the symbols are removed from the input. The exception is that constraints that you add by picking in the Workspace are kept.

File Menu

This menu contains two items: Write and Revert.

Write

Opens a file selector so you can write the input file in its current state.

When you write a file, any @, *, or # symbols that you added by hand to specify counterpoise atoms, atoms for Hessian refinement, or constraints, are written to the file. These symbols are removed when you click OK to close the Edit Job dialog box.

Revert

Returns the input file to the state it was in when you opened the dialog box.

Edit Menu

Provides the standard Cut, Copy, and Paste items. You can also use the usual keystrokes (Ctrl+X, Ctrl+C, Ctrl+V) to copy and paste text.

Structure Menu

This menu provides tools for conversion between Z-matrix and Cartesian format, for standardizing Z-matrix format for the structures in a transition state search or IRC scan, and for viewing and assigning atom labels. This menu is only available when you select Structure from the Edit options.

Convert to Z-matrix
Convert to Cartesian
View Atom Labels

Convert to Z-matrix: Converts the geometry to Z-matrix format.
Convert to Cartesian: Converts the geometry to Cartesian format.
View Atom Labels: View the atom labels in the Workspace.

Edit Options

These options determine whether you can edit the entire input file (Input file) or just the geometry (Structure). If you choose Structure, the Structure menu is displayed on the menu bar, and for transition state searches and IRC scans, the structures are displayed in tabs.

Editing Text Area

Editable text area. You can type text in this area, and you can cut, copy and paste text using the Edit menu. You can paste text into this area using the middle mouse button. If you edit structures for transition state searches and IRC scans, the editing text area for the coordinates or the Z-matrix are displayed in tabs, Reactant, Product, and Transition State. Each tab has an Include structure in workspace option, so that you can control which structure or structures are displayed.

Preview Button

Displays the structure in its current state in the Workspace.