Atom Selection Dialog Box

The Atom Selection dialog box (ASD) allows you to select atoms based on various properties. It allows for rapid specification of atoms and supports construction of complicated groupings.

You can define selection criteria by entering a text-based Atom Specification Language (ASL) expression directly, or by choosing options in the dialog box.

The Atom Selection dialog box is organized into categories: atom, residue, molecule, chain, entry, substructure notation, and set. Each category contains a list of properties and values available for selection. A selection is defined by choosing a property and values for that property. The selection can then be added, removed, or intersected with other selections. The results are displayed in an ASL expression in the ASL text box. Each new step modifies the ASL expression and updates the markers in the Workspace, allowing you to preview the selection before proceeding with the task.

Additional features include specifying atoms by proximity and creating named sets.

Note: You cannot select atoms in locked project entries, you must unlock them first.

To open this panel, you can:

  • click on the Selection toolbar

  • click in the picking tools of a panel, then click Select

  • choose Select → Define

  • Using
  • Features
  • Additional Resources

Using the Atom Selection Dialog Box

To select an atom group defined by a category:

  1. Open the tab for the desired category.

  2. Select a property from the list on the left.

    The center portion of the tab is updated to provide the appropriate tools for selecting a value for the property. Depending on the property type, you then enter the desired value, select an option, choose from a list, or pick atoms in the Workspace.

    After you have made your choice, the selected atoms are marked in the Workspace with purple markers, if Show Markers is selected. If the choice was made by typing into a text box, you must click Update Markers to see the purple markers for the selection.

  3. Then you can either:

    • Click Add to include the atoms in the selection.
    • Click Subtract to exclude the atoms from the selection (select everything except these atoms).

    The markers change to light blue, the ASL expression for this atom group is displayed in the ASL text box below, and the number of matching atoms is displayed in the status line near the bottom of the panel. This is the current selection.

For example, place a molecule in the Workspace. In the ASD, open the Atom tab, select Atom Number In Entry from the list, type in 1-10 in the Atom Number In Entry text box, click Update Markers, then click Add and click OK.

You can also augment or limit the selection by further criteria:

  1. Define another atom group by selecting a property (from another category, if you wish) and choosing the values of that property.

  2. Then you can do any of the following:

    • Click Add to add these new atoms to the selection.
    • Click Subtract to subtract these new atoms from the selection.
    • Click Intersect to make the selection consist of the atoms that are in both the current selection (blue) and the new atom group (purple). This is the intersection of the two sets.

For example, in the Atom tab, select Element from the property list, select C from the Element list, then click Intersect. Only the carbon atoms that were in the original list are in the new list.

By repeating this process, you can build up a complex ASL expression that selects just the atoms you want. The order in which you make the various selections of groups of atoms to add is important: the ASL expression is built up sequentially.

Below are some examples of atom selections. Before starting an example, click Clear to clear the current ASL expression.

To select all carbon atoms in the backbone of a protein:

  1. In the Atom tab, select Element from the list of properties.
  2. Select C from the list of elements.
  3. Click Add to add the atom group to the ASL expression.
  4. Select Backbone/Side Chain from the list of properties.
  5. Select the Backbone option.
  6. Click Intersect to restrict the current ASL expression to be applied only to protein backbone atoms.

To select all side chains within 5.0 Å of a ligand in the active site of a ligand/receptor complex:

  1. In the Entry tab, select the entry name for the ligand from the list of entries.
  2. Click Add to make this entry name the current ASL expression.
  3. Click Proximity to open the Proximity dialog box.
  4. Enter 5.0 in the text box, select Residues in the Fill section, select Exclude source, then click OK.
  5. In the Residue tab, select the Backbone/Side Chain property.
  6. Select the Sidechain option.
  7. Click Intersect to restrict the current ASL expression to include only atoms in the protein side chain.

To select a range of residues but exclude proline residues:

  1. In the Residue tab, select Sequence from the property list.
  2. Select the appropriate chain from the list of chains in the top scrolling list.
  3. Select a range of residues in that chain from the lower scrolling list.
  4. Click Add to make this residue range the current ASL expression.
  5. Select the Residue Type property.
  6. Select PRO from the list of residue types.
  7. Click Subtract to exclude proline residues from the current ASL expression.

Atom Selection Dialog Box Features

The Atom Selection dialog box contains seven category tabs: Atom, Reside, Molecule, Chain, Entry, Substructure, and Set. Each tab consists of three sections. The left section contains a list of properties for that category. When you select a property, a set of tools is displayed in the center section. On the right are buttons for combining the new selection with the current selection. These tools become available when you have selected a property value.

Category Tabs

Each tab represents a category of properties by which you can select atoms.

Atom: Choose individual atoms that have the selected property and value.

Residue: Choose all atoms in residues that have the selected property and value.

Molecule: Choose all atoms in molecules that have the selected property and value.

Chain: Choose all atoms in chains that have the selected property and value.

Entry: Choose all atoms in entries that have the selected property and value.

Substructure: Choose all atoms in the selected substructure (SMARTS pattern).

Set: Choose all atoms in the selected set.

Property Value Selection Tools

There are three kinds of property value selection tools.

  • Lists: For properties whose values are a name, such as Element, you can select one or more members from a list. Multiple members can be selected from the list using the standard conventions for multiple selection, using the Shift and Ctrl (Cmd) keys when you click.

  • Text boxes: For properties that have numerical values, such as atom number or partial charge, you can enter the value in the text box. For text (string) properties such as SMARTS patterns, you can enter the text in the text box. Below the text box are examples of the syntax for the selection and the range of possible values. When this kind of selection tool is available, the Update Markers button also becomes active. When you click this button, the text is parsed and the corresponding atoms are marked.

    Warning: If you press Enter after typing the values, the default action, Add, is performed. You can undo this action with the Undo button.

  • Options: For properties that are defined by some kind of classification, such as hydrogen atoms that are polar or non-polar, you can select them by clicking the appropriate option.

Note: Only the values available in the displayed structure are listed.

Combining Tools

Each tab has three buttons on the right that can be used to combine the new atom group with the current selection.

  • Add: adds the new atom group to the current selection, using a logical OR operation on the ASL expression. The resulting selection includes all atoms that are in either the new atom group or the current selection. This is the default action, which is performed if you press ENTER.

  • Subtract: subtracts the new atom group from the current selection, using a logical AND NOT operation on the ASL expression. The resulting selection includes all atoms that are in the current selection but not in the new atom group. (If this is the first operation, the default current selection is "all".)

  • Intersect: takes only the common members of the new atom group and the current selection, using a logical AND operation on the ASL expression. The resulting selection includes only the atoms that are in both the new atom group and the current selection.

In addition to these three buttons, the Invert button at the bottom of the panel inverts the entire current selection, using a logical NOT operation. All atoms that were selected are unselected, and all atoms that were unselected are selected.

Markers

If Show Markers is selected, markers for both the new atom group and the current selection are displayed in the Workspace. Markers for the new atom group are purple and are offset from the atoms slightly. Markers for the current selection are light blue. If you are selecting a range of property values by entering them in a text box, click Update Markers to see the markers for the new atom group.

Proximity

The Proximity button opens the Proximity Dialog Box, in which you can select atoms based on their distance from the atoms defined by the current selection (the source atoms). You can specify the distance in angstroms or in terms of the number of bonds. If the boundary for inclusion intersects a molecule or a residue, you can choose to include the entire molecule or residue using the Fill buttons. You can either include or exclude the source atoms in the selection. The Update Markers button updates the markers for the proximity selection so that you can view the selection in the Workspace before accepting it.

If you want to ensure that molecules and residues are filled, but no residue or molecule crosses the boundary, you cannot use the Proximity dialog box directly. You need to select the opposite of what you want, then invert the selection.

For example, to select all residues that lie strictly outside a 10 Å boundary of the current selection:

  1. Click Proximity to open the Proximity dialog box.
  2. Under Proximity, select Within, enter 10 in the text box, and select Angstroms.
  3. Under Fill, select Residues.
  4. Deselect Exclude source to include the source atoms.
  5. Click OK to select these atoms. The selection now includes all atoms within the boundary and all atoms that are part of residues that cross the boundary.
  6. Click Invert to select all atoms in complete residues that are strictly beyond the chosen boundary.

Create Set

The Create Set button opens a dialog box that enables you to name and store the existing ASL expression for use as a set definition. The sets created in this manner are the same as sets created with the Sets panel, and can be selected in the Set tab. These sets are automatically saved with the project and are restored when the project is opened again.

Editing Tools

Several editing tools make it easier to create your own ASL expressions:

  • ASL text box—You can type ASL expressions directly into the ASL text box. The hand-edited expressions are considered part of the last operation performed with the mouse and can be undone and redone as part of that operation, but cannot be undone or redone separately.

  • All—Selects all atoms in the Workspace.

  • Undo—Undoes the last action. You can undo multiple operations with repeated clicks on the Undo button.

  • Redo—Redoes the last action.

  • Clear—Clears the ASL text box.

  • Invert—Inverts the expression in the ASL text box, so that those atoms are NOT selected.

  • Previous—Replaces the existing expression with the atom selection defined the last time the Atom Selection dialog box was used.

  • Selection—Replaces the current expression with an expression for the Workspace selection.

  • Atom Num—Converts the expression to list each atom explicitly by atom number.

  • Res Num—Converts the expression to list each residue explicitly by residue number.

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