View Hypothesis Workbench

To Add Angle Constraints

You can specify the range of possible values for an angle by adding an angle constraint. You can specify angle constraints for the angle between three atoms or functions, whether they are connected or not. You can also specify constraints for torsion angles and the angle between a vector and a plane.

Details on how to add angle constraints are given below. For information on how to add torsion angle constraints, see "How to Add Torsion Angle Constraints."

To Add Angle Constraints

With the hypothesis features in the View Hypothesis workspace, select the three atoms or functions, or a vector and a plane, needed to define the constraint angle.
If you are using atoms or features, remember to select them in an order such that the second one is the vertex. For example, selecting a node A, then B, then C will give the angle between the line from A to B and the line from B to C, whereas selecting in order B-C-A will give the angle between the line from B to C and the line from C to A, as illustrated in the following diagram.
From the Toolbox select the Set Constraint Tolerance tool,

or from the Constraints menu select the Define Constraint
command, and then select the Angle option from the popup menu.
The constraint is added and the Constraint Tolerance dialog box appears, showing the default range for the angle.
Enter a new constraint name, if you want to change the default.
Modify the minimum and maximum values for the angle, if desired.
Press the OK button.
The changes are applied and the dialog box disappears.
Note: The Cancel button dismisses the dialog box, but does not remove the constraint.
The angle constraint just defined is indicated by an angle marker.

For more information select one of the following:

To Add Torsion Constraints

Torsion Angle Constraints

You can add torsion angle constraints by selecting two vectors, or any set of four atoms or features, A, B, C, D, where the constraint specifies the minimum and maximum angles between the ABC and BCD planes. If atom A is a substituent of B, B is connected to C, and D is a substituent of C, this defines the torsional angle between the AB and CD bonds, as illustrated in the following diagram.

To Add Torsion Constraints:

In the View Hypothesis workspace, select the four atoms/ functions or two vectors required to define the torsion angle.
Remember to select the atoms in the order that defines the desired angle, as shown in the example below.
Select the Set Constraint Tolerance tool in the Toolbox, or select the Define Constraint command and then the Torsion option on the popup menu.
The torsion constraint is added and the Constraint Tolerance dialog box appears, showing the default range for the torsion angle.
If desired, enter a new constraint name, and modify the default minimum and maximum values for the torsion angle. Note that angles are measured clockwise around torsion axis B-C as viewed from and starting at the initial line A-B. Torsion angles measured in a counterclockwise direction have a negative sign.
Press the OK button to apply the changes and dismiss the dialog box.
The defined constraint is indicated by a yellow torsion angle marker.
Rotate the hypothesis, if necessary, so that you can clearly see the marked torsion angle.

For more information select one of the following:

To Add Excluded Volumes

Excluded Volume Constraints

You can add an excluded volume constraint to a hypothesis (or to a template molecule) to specify one or more spherical spaces in a hypothesis that must not contain any atoms or bonds. For example, you might want to represent a region of a molecule that cannot contain any topology because it might impinge sterically on a receptor.

During a database search, a hypothesis with an excluded volume matches only molecules that have no atoms or bonds within the defined excluded volume. When doing a Compare/Fit operation, no fit of two objects is acceptable if an excluded volume is penetrated.

Currently, hypotheses generated in the Generate Hypothesis workbench do not contain excluded volumes. However, in the View Hypothesis workbench you can manually add excluded volumes to either a generated hypothesis or a constructed hypothesis that has location constraints.

If you add an excluded volume to a hypothesis, it automatically becomes part of the hypothesis. If you add an excluded volume to a template molecule, as a step in creating a hypothesis, it is temporarily a separate hypothesis that is not attached to the molecule on which it is located. This is a similar procedure to showing and then adding hypothesis functions using a template molecule.

At least three location constraints must be included in a hypothesis with an excluded volume, to fix its coordinates relative to other features.

For an example, see "Examples of Excluded Volumes."

For the procedure, see To Add Excluded Volumes."

To Add Excluded Volumes

In the View Hypothesis workspace, select the atoms that define the boundary of the exclusion volume. The centroid of the selected atoms will be the default center of the displayed excluded volume sphere.
From the Constraints menu, select the Add Excluded Volume command.
A black Mesh style excluded volume sphere is displayed, and the Excluded Volume Tolerance dialog box appears. In the example, the excluded volume is displayed in Transparent Style
.
The default radius is 1.5 angstroms. In the example, this size fits inside the selected atoms. If the selected atoms are closer together than 1.5 angstroms, the excluded volume will overlap them.
Change the name of the excluded volume in the Name field, if desired.
Enter the desired radius for the excluded volume in the Excluded Volume Size field.
Change the X, Y, Z values, if desired. The X, Y, Z fields specify the coordinates of the center of the excluded volume in the hypothesis' coordinate system. You might want to change these coordinates if you have acquired precise data about the exact location of the excluded volume, such as from X-ray crystallography.
Select the OK button to apply the changes and dismiss the dialog box.
Add at least three location constraints to the hypothesis by selecting an atom or feature and selecting the Define Constraint command on the Constraints menu, and then Location on the popup menu. The location constraints will be most meaningful if added to atoms or features that define the boundary of the excluded volume.
Save the hypothesis using the Save To Lab As command.

For more information, select one of the following:

Examples of Excluded Volumes

Defining Geometric Objects

Geometric objects centroid, vector, hydrogen bond donor, hydrogen bond acceptor, and best-fit plane can be used to define constraints in a hypothesis, although they do not represent constraints by themselves. You can add them to a hypothesis to define the geometric characteristic of your target molecule. For example, you can define the centroid of a ring and refer to it with a distance constraint or use it as the center of an excluded volume. Or you can define a best-fit plane for some topological feature and use it to define a constraint involving a distance or angle. Or you can define a hydrogen bond acceptor vector and then use its projected point to define some aspect of a receptor.

Pick the type of constraint you want information about:

To Add a Centroid

A centroid marks the center of geometry of a selected set of atoms or features with a small blue sphere.

In the View Hypothesis workbench, select the atoms or features whose center of geometry is to be defined, such as all atoms in the example fragment below.
From the Constraints menu, choose the Define Geometric Object command, then select Centroid from the popup menu.
< A small blue sphere appears, indicating the centroid of the selected atoms.

The location of the centroid can be used to define a distance constraint from the group of atoms to which it refers, for example.

To Add a Vector

A vector geometric object is an axis with a head and a tail, and hence a direction. To add a vector to a hypothesis:

In the View Hypothesis workbench, identify two atoms or features that can be used to define the head and tail of the vector.
Select the atom/feature to represent the location of the tail of the vector.
Extend select (with middle mouse button) the atom at the location of the head.
From the Constraints menu, choose the Define Geometric Object command, then select the Vector option from the popup menu.
A blue arrow appears, pointing from the atom or function you selected first to the atom or function you selected second.

To Add a Hydrogen Bond Donor Vector

There are three ways to create a hydrogen bond donor feature in the View Hypothesis workbench:

By adding a hydrogen bond donor function to a template molecule using the Show Function Mapping command. See "Using a Template Molecule to Place Functions."
By adding a hydrogen bond donor function as a free-standing hypothesis from the Feature Dictionary. See "Using the Feature Dictionary."
By adding a hydrogen bond donor geometric object to an atom specification that has an attached hydrogen (hypothesis fragment), as described below.

To Add a Hydrogen Bond Donor Vector

You can add a hydrogen bond donor geometric object to any atom specification in a hypothesis that has a hydrogen count of one or more:

In the View Hypothesis workbench, select the target atom in the hypothesis.
From the Constraints menu, choose the Define Geometric Object command, then select Hydrogen Bond Donor option from the popup menu.

A green and white cone is attached to the selected atom specification, with the open end of the cone in the direction of one attached hydrogen. The target acceptor is represented as a small blue sphere at the open end of the cone, where the electrons of the hydrogen bond acceptor are located.

To Add a Hydrogen Bond Acceptor Vector

Hydrogen Bond Acceptor Vector

There are three ways to create a hydrogen bond acceptor feature in the View Hypothesis workbench:

By adding a hydrogen bond acceptor function to a template molecule using the Show Function Mapping command. See "Using a Template Molecule to Place Functions."
By adding a hydrogen bond acceptor function as a free-standing hypothesis from the Feature Dictionary. See "Using the Feature Dictionary."
By adding a hydrogen bond acceptor geometric object to an atom specification that has a lone pair count of one or more (hypothesis fragment), as described in the following section.

Adding a Hydrogen Bond Acceptor Vector

You can add a hydrogen bond acceptor vector to any atom specification in a hypothesis that has a lone pair count of one or more:

In the View Hypothesis workbench, select the target atom in the hypothesis.
From the Constraints menu, select the Define Geometric Object command, then select Hydrogen Bond Donor option from the popup menu.
A green and white cone is attached to the selected atom specification, with the open end of the cone expanding out in the direction of the target hydrogen donor. The target donor is represented as a small blue sphere at the open end of the cone.

To Add Best-Fit Plane

Best-Fit Plane

You can add a best-fit plane to a hypothesis to represent a complicated structure such as a ring system. An RMS (root mean squared) fit of the selected points in a hypothesis is computed to find the best-fit plane. A vector normal to the best fit plane, through the centroid of the selected points, also is computed and displayed.

In a hypothesis select three or more atom specifications or features for which you want to display the best-fit plane.
From the Constraints menu, choose the Define Geometric Object command, then select the Best Fit Plane option from the popup menu.
A square blue grid appears, centered between the selected atom specifications or functions, as shown below. The vector in the center of the grid represents the normal to the plane.
You can select the plane, the normal vector, or the head of the vector separately to use in constructing a constraint that refers to the features that were used to define the objects.

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Last updated April 17, 1996 at 12:28pm PDT.