Save Selection as Custom Set Dialog Box

Save Selection as Custom Set Dialog Box Features

• Set name text box
• Save as list
• Define by options
  • Options for specific atoms
  • Options for full residues
  • Options for objects in tree
• View ASL link
• Hide ASL link
• Matches text

Set name text box

Specify the name of the atom set in this text box.

Save as list

Choose the object type that is used to define the atoms in the set. This object type is used to construct the ASL expression for the set. The Define by options depend on the choice you make from the list.

Define by options

Select options for how the objects are referenced in the set. The options depend on the object type you selected from the Save as list.

Options for specific atoms

These options are available when you choose to define the set in terms of specific atoms.

• Atom numbers in Workspace—the set matches atoms that have the same Workspace-level atom numbers as the current selection. The atom numbers of the Workspace atoms change when atoms are added to or removed from the Workspace (whether by build operations or by entry inclusion and exclusion), so this option is useful when the Workspace contents is fixed, or when the identities of the atoms don't change when inclusion changes, such as when switching conformers or trajectory frames.
• Atom numbers within entry—the set matches atoms that have the same entry-level atom numbers. These atom numbers do not change when the Workspace contents changes. If there is more than one entry in the Workspace, the atom numbers could match more than one entry. The atoms can be constrained to match the atom number and the entry ID so that they only match once: this is done with the Constrain by entry option.
• Constrain by entry—Atoms in the set must match the entry-level atom numbers and the entry ID. This ensures that the ASL expression only matches This option is available if you select Atom numbers within entry. The option is useful for reproducing an atom selection for a particular set of entries.

Options for full residues

These options are available when you choose to define the set in terms of entire residues.

• Residue numbers only— the set matches atoms that have the residue numbers found in the current selection. The residues do not have to be fully selected to be included in the set. No account is taken of insertion codes, so the set includes residues with different insertion codes but the same residue number.
• Residue names & numbers—the set matches atoms that have the same residue number and name as those in the current selection. No account is taken of insertion codes.
• Constrain by entry & chain—the set matches atoms that have the same residue number, residue name, entry ID and chain name as those in the current selection.

Options for objects in tree

These options are available when you choose to define the set in terms of objects in the Structure Hierarchy tree.

• Highest selected level in tree—the set is defined by the object at the highest level in the tree, e.g. 'solvent' rather than 'water' or individual water molecules.
• Lowest selected level—the set is defined by the object at the lowest level in the tree, e.g.individual water molecules rather than 'water' or 'solvent'.
• Constrain by—the set must match the entry ID or chain name, or both (depending on which check boxes you check), as well as the selected objects.

View ASL link

Hide ASL link

Show or hide the ASL expression that is constructed from the selection by applying the options you selected. The ASL expression is shown in a noneditable text box below this link. You can select text in the ASL expression, which you can copy and paste.

Matches text

This text reports the number of atoms and residues in the Workspace that are matched by the set definition. The number may differ from the number of atoms or residues in the selection, if the ASL expression does not define the atoms uniquely.