Selection

A selection is a set of items (atoms, bonds, residues, models) chosen by the user that:

• is highlighted in the graphics window with green outlines (default, see set selection)
• marks the items for subsequent operations:
  • with the Actions menu
  • can be specified as sel in commands, for example: style sel stick
  • can be listed with info selection
  • can be named with menu: Select... Define Selector or command name frozen for later use in commands and Basic Actions
  • certain of their attributes can be inspected and potentially modified using the Selection Inspector
  • indicates scope of action of Toolbar icons:
    • Molecule Display: 
    • Nucleotides: 
    • Map: 
    • Graphics: 
  • indicates scope of action of certain mouse modes:  (rotate/translate selected modes)
• can be created:
  • with the Select menu: by chain ID, residue name, element, type of structure, sequence, zone, attribute value, etc.
  • with the select command
  • by clicking with the mouse in the graphics window (...and doubleclicking for a selection context menu), by default:
    • Ctrl-click to start selection (replace)
    • Shift-Ctrl-click to add/subtract (toggle)
    This button assignment can be changed with mousemode .
    
  • by clicking links in the Chain information and Non-standard residues tables shown in the Log when a structure is opened (for example, see the Protein-Ligand Binding Sites tutorial)
  • by dragging a box around residues in an associated sequence
  • with various other commands and tools
• can be broadened with the up arrow key, the Select menu, or the command select up, and subsequently narrowed with the down arrow key, the Select menu, or select down, within the selection cascades:
  • bond ↔ bond and its endpoint atoms
  • atom ↔ residue ↔ protein secondary structure element (helix, strand, or coil) ↔ connected set of atoms (except not crossing chain ID boundaries) ↔ all atoms with same chain ID ↔ whole model ↔ model hierarchy
  • pseudobond ↔ pseudobond model ↔ model hierarchy
• can be inverted with the right/left arrow keys or the Select menu

Selecting a standard (atom-associated) molecular surface automatically also selects the atoms used to define it. If the whole surface model is selected, all of the atoms used to define that surface are selected, even atoms that are completely buried. Typically all of the atoms in a biopolymer chain are used to define a surface, but other sets of atoms can be specified with the surface command. If a surface patch is selected with the mouse, only the atom(s) directly contributing to that patch are selected. Conversely, selecting an atom selects its surface patch(es).

Nonmolecular surfaces can be selected as a whole. Selectable objects such as atoms and bonds under or behind a volume surface can be selected with the mouse if the surface is transparent (not completely opaque) or shown as mesh. If the mouseclick is on a surface region that does not overlie another selectable object, however, the surface model will be selected.

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Arrow-Key Shortcuts

When the mouse focus is in the graphics window, arrow-key shortcuts adjust the selection:

• up arrow – broaden the selection
• down arrow – narrow the selection
• right arrow or left arrow – invert the selection within selected models
• Shift-right arrow or Shift-left arrow – invert the selection within all models

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Selection Context Menus

Doubleclick-selecting an item in the main window (see mousemode) shows a context menu, typically including options to hide or delete the selected atoms, bonds, and/or pseudobonds. (Hidden selected atoms can be reshown using the icon, and all types of hidden items shown with the show command.)

• If exactly two atoms are selected, the selection context menu will include a Distance option to add a distance monitor between them.
• If a bond is selected, the selection context menu will include an option to Adjust Torsion (activate the torsion and show the Adjust Torsions interface for setting it interactively).
• If the selection contains part of a single amino acid, the context menu will include a choice to Mutate Residue with the Rotamers tool.

See also: context menus, Distances

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Selection vs. Direct Specification in Commands

Command-line target specification strings, including logical operations (and/or/not) and zones, can be given directly in commands, bypassing selection. However, target specification may include sel to indicate the current selection, and selections are useful in other contexts, such as defining the scope of action when an icon is clicked.