View Compound Workbench Toolbox

Introduction to the Toolbox

Summary of Toolbox Button Functions

QuickTools

To change a property such as bond type, first select the bond and then click on the Toolbox button corresponding to the new property. To create new objects having a particular property, make certain you have nothing selected in the workspace before you click on a component in the Periodic Table. Then click on the Toolbox button for the property you want. For example, to create double-bonded oxygen atoms, select O from the Periodic Table, click on the Double Bond tool button, and left-click in the workspace to place the atoms or bonds.

Select the NEXT PAGE button below for additional details about the Toolbox buttons.

Measure. Calculates interatomic or interfeature distances and angles for selected objects.

Tether.Specifies mapping correspondences for use by the Compare/Fit command.

Set Stereochemistry. Brings up a menu of buttons to specify the type of stereochemistry for a selected stereocenter as described below.

For additional information, see "Inverting Bridgehead Stereochemistry."

Toggle R-S. Switches stereocenters between R and S configurations. Selecting the entire molecule and then selecting this tool produces an enantiomer, since all the chiral centers are inverted.

Set R Chirality. Specifies R chirality for the selected stereocenter.

Set S Chirality. Specifies S chirality for the selected stereocenter. For additional information, see "Inverting Bridgehead Stereochemistry."

Toggle Known-Unknown. Switches the stereochemistry of the selected stereocenter between known and unknown. The (R)? or (S)? label indicates which stereoisomer is being displayed and that-although displayed as chiral- the stereochemistry is actually unspecified. For more information on unknown stereochemistry, see "Unknown Stereochemistry."

Set Relative Stereochemistry. Specifies that the relationship between two or more selected stereocenters is relative to one another. (Currently Catalyst supports only one set of relative stereocenters per molecule.) For more details, see "Relative Stereochemistry."

Toggle Axial-Equatorial. Switches carbon bonds in a ring between axial and equatorial positions.

Toggle Cis-Trans. Switches the selected exocyclic double bond between cis and trans configurations.

Set Bond Type. Specifies the bond type for the selected bond. If nothing is selected, specifies the type of bond to be drawn.

For information on aligning double bonds in the 2D workspace, see "Changing the Orientation of Double Bonds in the 2D Workspace."

Erase. Removes the selected objects from the 2D and 3D workspaces.

Fit to Window. Resizes and centers all of the objects in the selected workspace so that they are visible in the window.

Tile Objects. Spreads out objects in the selected 2D or 3D workspace so that they do not overlap and can be seen individually.

Select 2D/3D Workspace. Selects the 2D or 3D workspace for using the Fit to Window and Tile Objects tools, or for editing.

Set Bond Style. Specifies the display style for the selected bonds. If nothing is selected, these tools reset the display style for bonds to be drawn.

If two atoms are selected, they are bonded with the currently selected bond type, and the bond is displayed in the default simple line style.

If possible, the stereochemistry of the attached atoms is reset to reflect the bond style selected. The wiggly line style causes the stereochemistry of the attached atoms to be set to unknown.

For the wedge styles, if previously displayed as a wedge, the direction of the wedge is reversed.

Changing the alignment of double bonds in the 2D workspace. To select one of the 2D alignments for double bonds (shown in the illustration below), select the double bond in the workspace. Then left-click on the Double Bond button to cycle through the three different placements of the lines representing the double bond. You can also cycle through the alignments by selecting the double bond and then pressing the equal (=) key once to display each of the alternatives.

Measure Tool

Measure. Calculates interatomic, bond, or interfeature distances and angles for selected objects and displays their values in the History Window. The measurements reported depend upon how many objects you select, and in what order you select them (if there are more than two). The relative workspace coordinates (x, y, z) for each selected object also are given in each measurement.

You can measure distances between atoms, angles between bonds, torsion (dihedral) angles around a bond, and out-of-plane angles. If you select more than four objects, the Measure tool reports values for the last four selected objects only. Specify measurement units for distance and angles by selecting Global Preferences from the Preferences menu and making your selections in the Global Preferences dialog box.

Distance. If two connected atoms A and B (or the bond that connects them) are selected, the distance between them is reported as A-B = n angstroms, meaning that the length of their bond is n angstroms. If the two atoms are not directly connected by a bond, the measurement is given as A:B = n angstroms.

For example, if you select atoms O3 and C1 in the isoleucyl conformer at the left and use the Measure tool, the distance is reported as

O3-C1 = 1.223001 angstroms

If you select O3 and C4, which do not share a bond, the distance is reported as

O3:C4 = 2.377455 angstroms

Angle. If you select atoms A, B, C in order and then select the Measure tool, the History Window displays the values of the interatomic distances C-B and B-A as well as the angle formed by the vectors C-B and B-A. The second atom selected is considered the vertex of the angle measured. The angle's value is also displayed in the Status Area.

Thus, if you select atoms C4, C1, and O3 in order and then select the Measure tool, the following measurements are reported in the History Window:

C4-C1 = 1.516994 angstroms

C1-O3 = 1.223001 angstroms

C4-C1-O3 = 120.000 degrees


Note: The atoms you select for use with the Measure tool do not have to be contiguous.

Quick method for measuring valence angles. A quick way to calculate interatomic distances and a valence angle is to select the two contiguous bonds which form the angle, and then select the Measure tool. For instance, in the previous example you can select the C1-O3 bond and the C4-C1 bond instead of atoms C4, C1, and O3. The History Window reports the respective values for the interatomic distances and the valence angle. The value of the valence angle also appears in the Status Area.

Dihedral angles. If you select four atoms in A, B, C, D order, the History Window reports the values of the interatomic distances A-B, B-C, and C-D; the angles A-B-C and B-C-D; and the angle between planes A-B-C and B-C-D. The dihedral angle between A-B-C and C-D-E also appears in the Status Area.

Thus, in the example, if you select atoms N6, C4, C1, and O3 in order and then select the Measure tool, the following measurements are reported:

N6-C4 = 1.467002 angstroms
C4-C1 = 1.516994 angstroms
C1-O3 = 1.223001 angstroms
N6-C4-C1 = 109.500 degrees
C4-C1-O3 = 120.000 degrees
N6-C4-C1-O3 = 60.000 degrees

In the previous example, the last three readings represent the angles formed by the atoms selected. The illustrations that follow describe the angles in order, using rotated versions of the molecule to show the angles more clearly.

Angle 1. The angle formed by bonds C4-C1 and C1-O3.

C4-C1-O3 = 120.000 degrees

Angle 2. The angle formed by bonds N6-C4 and C4-C1.

N6-C4-C1 = 109.500 degrees