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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 ASD 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.
To open the Atom Selection dialog box, you can:
Click the common objects button in any picking tools section in any panel and choose Select.
Choose Select from the Select button on the Edit toolbar.
Choose Edit → Select Atoms → Select.
To select an atom group defined by a category:
Open the tab for the desired category.
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.)
Then you can either:
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:
Define another atom group by selecting a property (from another category, if you wish) and choosing the values of that property.
Then you can do any of the following:
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.
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.
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 or Maestro substructure).
Set: Choose all atoms in the selected set.
There are three kinds of property value selection tools.
Note: Only the values available in the displayed structure are listed.
Each tab has three buttons on the right that can be used to combine the new atom group with 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.
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.
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:
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.
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: Recalls the last expression 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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