The Atom List Editor
The Atom List Editor window is displayed when you select the menu item or click on the 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.
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
menu. You can also go directly to a specific atom (by number) using the 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
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 |
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Z-matrix coordinates |
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Cartesian coordinates |
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Optimization status |
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Fractional coordinates for PBC |
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ONIOM layer assignment and parameters |
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Molecular Mechanics atom type and charge |
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PDB file residue and chain data (read-only) |
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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
The following figure illustrates the columns that may be present in this window for each icon.
Additional Atom List Editor Columns
Beginning at the top and moving down and from left to right, these columns are controlled by the
button, the button, the button, the button, the button, and the 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 Atom List Editor by double-clicking any of the named column headers; click again to deselect all.
cell in the leftmost column. Select all atoms in theYou can add additional atoms by scrolling to the bottom of the window, selecting an element in the
column, and then clicking the button. This inserts a new row into the list filled with default values.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 View window. If an atom is both selected and highlighted, it appears as light blue.
column controls the highlighting of the the corresponding atom in the molecule’sThe items on each of the popup menus in the View window. They have the following meanings when applied to a single atom:
column control whether each atom is visible in theWhen multiple rows in the atom list are selected, then turning highlighting on or off or changing the all of the corresponding atoms.
menu selection for any atom with the selection will affectThe
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:
, and . 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.The various menu items in the Atom List Editor window are described below. The menu includes items related to saving and printing the data in the table:
The
menu items allow you to modify the contents of the molecule specification:
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
menu specifies which atoms should be assigned charges: all atoms, all selected atoms, or all atoms currently lacking an MM charge. The 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 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:
menu controls atom highlighting within view windows while theThe remaining items on the
menu have the following effects:The
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
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 , , , , , , , and buttons via the corresponding submenus. The item has the same function as the corresponding button—although, individual coordinates cannot be selected separately.