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Picking Controls |
Picking controls are a set of controls that are used to select atoms in the Workspace for a particular operation. The operation depends on the panel in which the picking controls appear, and is named in the Title of the picking controls section of the panel (the picking controls box.) Picking controls are also referred to as picking tools.
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.
The title is a text line located on the top left of the picking controls 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.
This text box displays the ASL expression for the atoms that are picked. It can be used to enter an ASL expression.
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.
Click to select all atoms in the Workspace.
This button displays a list of common atom groups 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.
The atom groups on the list are:
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 Settings dialog box).
Ligands—Add atoms to the selection from ligand-sized molecules (as defined in the Ligand Detection Settings dialog box).
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 Settings dialog box).
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:
Select—Open the Atom Selection dialog box to make an atom selection.
Previous ASL—Use the atom selection that was last used in the Atom Selection dialog box.
Click to open the Dihedral Selection dialog box, in which you can select protein dihedral angles by name.
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 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:
You can set a preference to show the index of the object type in the status bar when the pointer is over an atom. The preference is under Feedback – Workspace in the Preferences panel.
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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