Create Custom Set Dialog Box

Using the Create Custom Set Dialog Box

A custom set specifies an atom selection, and is built up in steps. Each step consists of one or more criteria for selection of atoms, which are connected by conditions. The step is added to the previous steps as a set of atoms to be added to or removed from the atom selection. The set is expressed in Atom Specification Language, or ASL.

To create a simple custom set:

1. Type a name in the Set Name text box.
2. Select an atom set from the list on the left.
3. Select any options for this set from the center pane.
4. Click Save Set.

To create a set with a condition:

1. Type a name in the Set Name text box.
2. Select an atom set from the list on the left.
3. Select any options for this set from the center pane.
4. Select Add condition.
5. Click Next.
6. Select an atom set from the list on the left.
7. Select any options for this set from the center pane.
8. (Optional) Click ONLY IF to change it to BUT NOT if this is the desired condition.
9. Click Step.
10. Click Save Set.

To create a set with two steps:

1. Type a name in the Set Name text box.
2. Select an atom set from the list on the left.
3. Select any options for this set from the center pane.
4. Click Step.
5. Select an atom set from the list on the left.
6. Select any options for this set from the center pane.
7. (Optional) Click Also Select to change it to Deselect if this is the desired condition.
8. Click Step.
9. Click Save Set.

 

Create Custom Set Dialog Box Features

• Set name text box
• Atom set list
• Options section
• Step actions section
  • Add condition option
  • Step or condition toggle
  • Action button
• Atom selection query text area
• More button menu
• Select button

Set name text box

Enter the name of the set in this text box. The default is SetN, where N is the next unused index.

Atom set list

List of choices for atom sets to include in the custom set. When you choose an item from the list, the Options section displays options relevant to the item, and the number of atoms that match is displayed below the options. The choices are given below, with notes on their definition or use.

• Current Selection, Current Displayed Atoms—these are defined by the atoms that are selected/displayed at the time when + Step or Save Set is clicked (whichever comes first), not by the selection/display when this dialog box was opened or when the custom set is used. You can change the selection or the display while this dialog box is open, which allows you to use these two atom sets multiple times.
• All Atoms—all atoms in whatever structure it is applied to. (ASL expression all)
• Ligands—ligand-sized molecules. The criteria for defining a ligand can be set in the Preferences Panel, in the Ligand Detection Preferences, and there are no options in this dialog box. (ASL expression ligand)
• Binding Sites—these are defined by the criteria specified with the options.
• Proteins, Nucleic Acids, Hydrogens, Secondary Structures—can be restricted to subsets by the options.
• Waters, Solvents, Ions, Metal Atoms, Heavy Atoms—these are defined in the same way as for Quick Select selection, and have no options.
• Entry IDs, Chain Names—these are selected by the options.

Options section

This section displays options for the atom set that is selected in the list, if there are any. These options can be used to define or restrict the atom set, define how the atoms are specified in the atom set, or provide information about the atom set. The number of atoms in the atom set that are matched in the Workspace is displayed below the options. The options are described below for the atom sets that have them.

Current Selection, Current Displayed Atoms

The options give you the choice of how to represent the selected atoms, in terms of residue, molecule, atom numbers and chain names. You can change the atom selection or the displayed atoms in the Workspace while this dialog box is open.

Binding Sites

Distance options

The binding site is primarily defined by a cutoff distance on the atoms in the protein from any ligand atom. These options give three preset distances and a text box to specify a different distance.

Expand to full residues option

Expand the cutoff to include entire residues, so if a residue has any atom within the cutoff distance, the entire residue is included in the binding site. This option is selected by default.

Exclude solvents option

Exclude any solvent molecules from the binding site definition. Solvent molecules are small molecules other than water that are considered as part of the solvent (ASL expression solvent). This option is not selected by default.

Exclude ligands option

Exclude ligand molecules from the binding site definition. This option is selected by default.

Proteins

The options can be used to restrict the protein atoms to side chain, backbone, or C-alpha atoms.

Nucleic Acids

The nucleic acids can be restricted to DNA or RNA, and the atoms to side chain or backbone atoms.

Hydrogens

The hydrogens can be restricted to polar or nonpolar, and for each of these to particular structure types (protein, ligand, solvent, all).

Secondary Structures

The options can be used to restrict atoms in secondary structures to those in helices, strands, or loops.

Entry IDs, Chain Names

For each of these objects, the atom set is defined by entering the particular instances in a text box, as a comma-separated list. The Load from Workspace button appends the instances that are represented in the Workspace to the text box.

Step actions section

Perform actions on the current step, and specify conditions that connect steps.

Add condition option

Select this option to add a condition to the current step, i.e. a new atom set connected to the current step contents by a condition. The text on the action button changes to Next, and you can then click this button to add the atom set for the condition. This option is disabled until you have selected an atom set, at which point you can add a condition to the step.

Operation button

This button is for switching between alternative operations for connecting a step to the previous step or a condition to the current step, or for adding a global condition. It changes according to context.

When adding a condition to the current step and you have selected an atom set, the alternatives are:

• ONLY IF—atoms that are already defined for the current step only if they are also in the current atom set (logical AND)
• BUT NOT— atoms that are already defined for the current step if they are not in the current atom set (logical AND NOT)

When adding a step, the alternatives are the same as those used for picking atoms:

• Also Select—add the atoms defined by the step to the selection defined by the atom selection query (logical OR).
• Deselect— remove the atoms defined by the step from the selection defined by the atom selection query (logical AND NOT).

When adding a global condition and you have selected an atom set, the alternatives are:

• AND—atoms that are already defined in the atom selection query if they are also in the current step
• AND NOT—atoms that are already defined in the atom selection query if they are not in the current step

Action button

This button changes according to context, and can have the following actions:

• Step—Add the current step to the query, connected by the operation specified on the operation button. The ASL expression for the step is added to the Atom selection query text area, with either an OR (Also Select) or AND NOT (Deselect).

• Add—Add a global condition to the query. The query is surrounded by parentheses, and the current step is added, connected by the operation specified on the operation button. The message "Adding global condition" is shown at the top of the step actions section, along with an X button to cancel the addition. You can add conditions to the current atom set, just as for a regular step, before adding the step to the atom selection query.

• Next—Proceed to define the atom set for a local (within-step) condition. Clicking this button adds the ASL for the current atom set to the Atom selection query text area, clears the selection in the atom set list, and disables a number of features, to indicate that the specification of the condition is not complete. The message "Adding condition" is shown at the top of the step actions section, along with an X button to cancel the addition.

Atom selection query text area

Displays the ASL expression (query) for the current state of the atom set. Once there is an expression in this area, the Select and Save Set buttons apply to the content of this area. The number of atoms in the Workspace that match the query are shown in the Status bar, next to the Select button.

More button menu

This button menu shows operations that can be applied to the atom selection query.

• Invert Query—invert the entire query, so that it deselects rather than selects, or vice versa. (Adds a global NOT.)
• Add Global Condition—Add a condition at the top level of the query. The current query is placed in parentheses, and you can define a new step with local conditions to add to the query.
• Select by Proximity—select atoms based on their distance from the atoms defined by the current query. Opens the Select by Proximity dialog box .
• Convert to Atom Numbers—convert the query to list each atom explicitly by atom number; the list replaces the query.
• Convert to Residue Numbers—convert the query to list each residue explicitly by residue number; the list replaces the query.
• Undo—undo the last change to the atom selection query.
• Redo—redo the last change that was undone.
• Clear All—clear the entire query.

Select button

Select the atoms in the Workspace that are currently defined by the expression in the Atom selection query text area. If there is no expression in the Atom selection query text area, the atoms defined by the selection in the atom set list (qualified by any options) are selected.