Picking Tools

Picking tools are a set of panel tools that are used to select atoms in the Workspace for a particular operation. The operation depends on the panel in which the picking tools appear, and is named in the title of the picking tools section of the panel (the picking tools box.) Picking tools are also referred to as picking controls. There are two styles of picking tools, which differ in the kinds of buttons available. All the buttons are described below.

There are two types of picking operations:

  • Transient Picking: The operation specified for the picking action is performed immediately.

  • Persistent Picking: Each pick adds the picked atoms to the definition shown in the ASL text box. The operation specified by the panel is issued when a particular button in the panel is clicked.

  • Features
  • Additional Resources

Picking Tools Features

Title

The title is a text line located on the top left of the picking tools border (for example, Apply Current Color, Atoms For Surface Generation, or Define buffered atoms). The title briefly states what action will be taken with selected atoms.

ASL text box

This text box displays the ASL expression for the atoms that are picked. It can be used to enter an ASL expression. It may have its own label. See Atom Specification Language for more information on ASL expressions.

Clear button

Click this button to clear the entire selection, so that no atoms are selected. The button is displayed inside the ASL text box when there is an ASL expression present. In some panels, the clear button is a separate button with an X on it.

Save button

Click to save the current ASL. A New ASL dialog opens with a text box, which is automatically populated with the content in the ASL text box. Saved ASLs can be accessed using the Atoms selections button from any panel with these picking tools.

All button

Click to select all atoms in the Workspace.

Atom selections button

This button displays a list of common objects that you can add to the selection, by choosing the list item, and buttons for defining an atom selection and using the previous definition of an atom selection.

This button is present in some panels but not others. The objects on the list are:

  • Saved ASLs—Select an ASL which has been previously saved using the Save button. Hover to open a menu of saved ASLs. Only available if an ASL has been saved.

  • Workspace Selection—Use the atoms that are already selected in the Workspace.

  • Displayed Atoms—Add the atoms that are displayed in the Workspace to the selection.

  • Protein—Add all protein residues to the selection.

  • Protein Backbone—Add atoms from protein backbones to the selection.

  • Protein Side Chains—Add atoms from protein side chains to the selection

  • Protein Near Ligand—Add residues to the selection from proteins that are within 5 Å of the ligand (as defined in the Ligand Detection tab of the Preferences panel).

  • Ligands—Add atoms to the selection from ligand-sized molecules (as defined in the Ligand Detection tab of the Preferences panel).

  • Nucleic Acids—Add atoms from all nucleic acids (DNA, RNA) to the selection.

  • Waters—Add atoms from all water molecules to the selection.

  • Ions—Add atoms from charged molecules that have less than 10 non-hydrogen atoms to the selection.

  • Metal Atoms—Add all metal atoms (all elements to the left of B, Si, Ge, Sb, Po in the periodic table) to the selection.

  • Heavy Atoms—Add all non-hydrogen atoms to the selection.

  • Hydrogens-All—Add all hydrogen atoms to the selection.

  • Hydrogens-Nonpolar—Add hydrogen atoms that are attached to carbon atoms to the selection.

  • Hydrogens-Nonpolar Ligand—Add to the selection hydrogen atoms that are attached to carbon atoms in the ligand (as defined in the Ligand Detection tab of the Preferences panel).

  • Hydrogens-Polar—Add hydrogen atoms that are attached to atoms other than carbon to the selection.

  • Membrane—Add atoms that are part of membrane molecules (POP, POPE, POPC, DPPC, DMPC) to the selection.

The two buttons apply an atom selection defined by an ASL expression:

Selection, Load Selection, Use Workspace Selection, or Get from Workspace Selection button

Use the atoms that are selected in the Workspace for the ASL expression. Available in some panels, not in others.

Previous button

Use the atom selection that was last used in the Atom Selection Dialog Box. Available in some panels, not in others.

Select button

Open the Atom Selection Dialog Box to make an atom selection. Available in some panels, not in others.

Dihedral button

Click to open the Dihedral Selection Dialog Box, in which you can select protein dihedral angles by name.

Pick option and menu

Select Pick to activate picking. You can then select objects by clicking on atoms, bonds, or ribbons in the Workspace. The Pick option is automatically selected when you choose an item from the Pick option menu.

The Pick option menu (if present) is used to determine the type of structural object that is selected when you click on an atom, bond, or ribbon. For example, if you choose Molecule from the Pick option menu, and click on an atom in the Workspace, all the atoms in that molecule are selected for the current operation. Depending on the action to be performed, the Pick option menu contains one or more of the following items:

  • Atoms
  • Bonds
  • Residues
  • Chains
  • Molecules
  • Entries

If the option menu is not present, the type of structure to pick is determined by the parent panel.

Markers or Show markersoption

Select to display or undisplay markers (colored dots for atoms and lines for bonds) that highlight the atoms that are currently selected.

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