10.1 General Description of the Expression Dialogs

The Expression dialog was designed to be an all-purpose selection tool. It is presented in SYBYL under several different titles: Atom Expression, Bond Expression, Substructure Expression, Sequence Expression, Molecule Expression. Which dialog is displayed depends on the type of selection that is required by the present activity. Although the various Expression dialogs are very similar to each other in layout, there are a few differences. In the dialog description below, these differences are noted.

Atoms, Bonds, Monomers	Indicates the selection mode, the type of object on which to base the expression formula. For example, if Atoms is chosen, clicking an atom highlights just that atom and the formula will contain the atom ID. If Monomers is chosen, clicking an atom highlights the entire monomer to which the selected atom belongs and the formula will contain the residue number. (Note: The Substructure Expression, and Sequence Expression dialogs only have the Monomer option available, and the Molecule Expression dialog does not have this pull-down menu.)
Selected	Displays the number of objects that are selected in the currently active molecule area. This field is noneditable.
Highlight	Turn on to highlight the selected objects in the SYBYL window. (The check box is on by default.)
Union	The Boolean operator to use when combining two groups of selected objects. Union--Add subsequent selections. The remaining highlighted objects are in either of the two groups of selected objects. Difference--Subtract subsequent selections. The remaining highlighted objects are those found in the first group of selected objects, but not the second. Intersection--Find the common objects between current selection and subsequent selections. The remaining highlighted objects are those found in both groups of selected objects. (Note: This pull-down menu is not available in the Molecule Expression dialog.)
Sets	Displays the Sets dialog for choosing defined sets to include in the selection. Chirality or a radius can also be defined in this dialog. The option menu selection determines the options that are available in the Sets dialog. (Note: This button is not available in the Molecule Expression dialog.)
Atom Types, Bond Types, Monomer Types	Displays the Atom Types, Bond Types*, Monomer Types dialog, respectively, for selecting by available type. Notes: For the Atom Types dialog, turning on a check box for a chemical element highlights all atom types involving this element in the list. When bonds are being selected based on atom types, all bonds connected to specified atoms are highlighted. The Types button is not available in the Molecule Expression dialog.
Substructures	Displays the Substructures dialog for selecting by residue, water, or other defined substructure. (Note: This button is not available in the Molecule Expression dialog.)
All	Selects all objects in the area specified in the Molecules field.
Clear	Unselects all objects.
Undo	Undoes the last action. Useful when experimenting with selections.
Invert	Inverts the current selection.
Rectangle Pick	Invokes the rectangle tool. Using the left mouse button, click, hold, and drag the cursor until a rectangle is drawn around the desired objects. Release the mouse button to select all objects whose coordinates are within the rectangle and within the Z-clip volume. Only available when in Full Screen Mode and Viewing Mode set to Mono.
Molecules	Lists molecule area and name of all displayed molecules. Click a molecule area in the list to highlight it and make it the active one. (Note: The number of items visible in the list can be extended using TAILOR SET DIALOG NUM_MOL_VISIBLE.)
Expression	Displays the current formula/expression to use for selecting objects. If this field is edited directly, you must press Apply to update the highlighted atoms in the display area. For additional information about the formulas that you can use to select objects, see Objects and Expressions.
Apply	Selects the objects as defined by the formula shown in the Expression field.
Create Set	Defines a new set containing the selected atoms specified in the Expression field. Specify a name for the set. This new set is added to the list of predefined sets in the Sets dialog. (Note: The new set is temporary unless you save the molecule. Otherwise, it is lost once the molecule is deleted from the display)

*Definitions for bond types are:

1--Single	ar--Aromatic
2--Double	du--Dummy
3--Triple	un--Unknown (cannot determine from parameter tables)
am--Amide	nc--Non-chemical

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