The Atom List Editor

The Atom List Editor window is displayed when you select the Tools=>Atom List menu item or click on the Atom List button. This tool presents the coordinates and other parameters for the molecule in the active View window in an editable spreadsheet format. The window’s default configuration is illustrated below.

ed_aed.tif
The Atom List Editor

The columns that are present in the table are controlled by the buttons in the toolbar. Columns corresponding to highlighted buttons are visible. Only buttons relevant to the current molecular structure are active. Individual columns may be displayed/hidden using the items on the Columns menu. You can also go directly to a specific atom (by number) using the Go To control in the toolbar.

You can select all items within a column by double clicking on the column header. You can sort all selected rows based on the current column using the Rows=>Sort Selected submenu.

The default configuration of this window displays the molecule’s Z-matrix and Cartesian coordinates. Different data can be selected for display using the toolbar buttons.

Icon View/Specify
Z-matrix coordinates
Cartesian coordinates
Optimization status
Fractional coordinates for PBC
ONIOM layer assignment and parameters
Molecular Mechanics atom type and charge
PDB file residue and chain data (read-only)
Isotope mass

Clicking one of the lettered display icons will show or hide all columns in that group. You can also control the display of every individual column by selecting or deselecting it in the Columns menu or in the submenu attached to the relevant icon via the small triangle to its right.

The following figure illustrates the columns that may be present in this window for each icon.

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Additional Atom List Editor Columns

Beginning at the top and moving down and from left to right, these columns are controlled by the Show ONIOM Columns button, the Show MM Type Columns button, the Show Fractional Coordinates Columns button, the Show PDB Columns button, the Show Mass Columns button, and the Show Optimization Flag Columns button. Note that shaded columns are read-only.

Any of the molecular parameters can be edited in this spreadsheet-like window. Atoms’ parameters (or data) may be selected in the table by clicking on, clicking and dragging, or Ctrl and clicking on their Row cell in the leftmost column. Select all atoms in the Atom List Editor by double-clicking any of the named column headers; click again to deselect all.

You can add additional atoms by scrolling to the bottom of the window, selecting an element in the Symbol column, and then clicking the Add button. This inserts a new row into the list filled with default values.

Atom Highlighting and Display

In general, atoms in View windows can be selected or unselected. Selected atoms are colored yellow (see below). Within the Atom List Editor, atoms can also be highlighted. In this case, they are colored light blue.


Atom Selection, Highlighting and Hiding
The View on the left has 6 selected atoms, 2 highlighted atoms, and 4 hidden atoms (an invisible methyl group bonded to the
seemingly bare ring carbon). The latter two properties are indicated in the corresponding columns of the
Atom List Editor.

The dot in the Highlight column controls the highlighting of the the corresponding atom in the molecule’s View window. If an atom is both selected and highlighted, it appears as light blue.

The items on each of the popup menus in the Display column control whether each atom is visible in the View window. They have the following meanings when applied to a single atom:

When multiple rows in the atom list are selected, then turning highlighting on or off or changing the Display menu selection for any atom with the selection will affect all of the corresponding atoms.

Defining Isotopologues

The I button controls the display of isotopologue definitions. You can add one or more isotopologue columns to the table using this button. You can specify which one to use for frequency analysis using the vibrational results features. The isotopes specified for Isotopologue 0 are used for input files created with the molecule.

If you select one or more rows of the table and them click in an isotopologue field, a popup menu containing the valid isotopes for that element will appear. For example, the menu for carbon contains: 12, 13 14 and Default. When you make a selection from one of these menus, your choice will be applied to all selected rows containing the same element. There is no way to reset all atoms to their defaults in a single operation.

Atom List Editor Menus

The various menu items in the Atom List Editor window are described below. The File menu includes items related to saving and printing the data in the table:

The Edit menu items allow you to modify the contents of the molecule specification:

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Assigning MM Charges with the Atom List Editor

This dialog is used to automatically assign charges to atoms for use in Molecular Mechanics calculations. The Target menu specifies which atoms should be assigned charges: all atoms, all selected atoms, or all atoms currently lacking an MM charge. The Action menu specifies which charge scheme should be used. Amber94 charges are always available. The other options in the list are available when they have been previously computed for the structure in a Gaussian calculation.

The View menu controls atom highlighting within view windows while the Atom List Editor is in use. Each item in the first section is a toggle, and a check mark next to it within the menu indicates that it is enabled:

The remaining items on the View menu have the following effects:

The Rows menu controls whether some or all atoms within the molecule are visible in the table and also provides some shortcuts for selecting groups of atoms:

The Columns menu allows you to specify which columns appear in the table on an individual column basis. The first few items in the menu correspond to the default columns in the table, which are independent of the various column display buttons. You can select which columns appear for the Z-Matrix Coordinates and Connectivity, Cartesian Coordinates, Optimization Flags, Isotope Mass, Fractional Coordinates, ONIOM Data, MM Types, and PDB Data buttons via the corresponding submenus. The Cartesian Coordinates item has the same function as the corresponding button—although, individual coordinates cannot be selected separately.