Cerius2 Modeling Environment

7       Geometry Analysis

The Visualizer's analysis and evaluation tools enable you to closely examine the three-dimensional structure of the models you are studying.

This section explains

This section contains information on:

Measuring models

Calculating close contacts

Model surfaces

Vector properties

Related information

Some other Cerius² application modules also contain various types of functionality for analyzing model geometry or calculating other types of surfaces. Information on using these tools is found in the specific documentation for the relevant application modules.

Table 5. Finding information about geometry analysis of models

If you want to know about:	Read:
Measuring distances, angles, torsions, and inversions of models.	Measuring models.
Examining and changing the model's geometry.	Editing the structure.
Refining the model's conformation.	Refining the conformation.
Close contacts between nonbonded atoms.	Calculating close contacts.
Solvent-accessible surfaces for models of a molecule, surface, or crystal.	Model surfaces.
van der Waals surfaces for models.	Model surfaces, Atom and bond display styles.
Displaying surfaces.	Surfaces--style and transparency.

You should already know...

The basics of starting Cerius² and using its interface are demonstrated in Introducing Cerius2 and described in The Cerius2 Interface.

You need to know how to build (Basic building) and/or load (Loading model structure files) models and should know how to select atoms in model(s) (Selecting atoms and groups of atoms).

If your session contains several models, you should know how to specify the current model (Specifying the current model) or select atoms in more than one model simultaneously (Selecting atoms in several models).

Measuring models

You can measure distances, angles, planes, torsions, and inversions for the atoms in a model and display these measurements in the model window or the text window.

Finding information

This section includes information on measuring:

Distances

Angles

Planes

Torsions

Inversions

Accessing the tools

Access the Measurements control panel by selecting the Geometry/Measurements... menu item in the main control panel's menu bar.

Display of measurements

The calculated measurements are represented in the model window by lines and labels. These are automatically updated whenever the model is modified, enabling you to monitor the effects of manipulations as you perform them.

You can display all measurements in the text window by clicking the List measurements action button.

Removing displayed measurements

To remove all measurements from the display, click the Delete measurements action button. To temporarily hide the calculated measurements (without deleting them), check the Hide measurements check box.

You can selectively delete measurements by selecting the appropriate measurement tool (see below) and then re-selecting the atoms that were picked to calculate those measurements.

Example

A tutorial example of using the Measurements control panel is found under Measuring components of the model's geometry.

Additional information

Please see the on-screen help for details on the functioning of each control in the Measurements control panel.

Distances

To measure the distances between atoms, you use the Distance tool.

You can use it in two different ways:

• Select the Distance tool and then pick atom pairs whose distances you want to measure. These atoms need not be bonded to each other. The distance(s) in angstroms are indicated in the model window.

or:

• Select any number of atoms and then double-click the Distance tool. The lengths (in angstroms) of each bond existing between selected atoms are indicated in the model window.

Related information

Information on examining and changing bond lengths is contained under Examining and changing bond lengths.

Angles

To measure the angle involving any three atoms, you use the Angle tool.

You can use it in two different ways:

• Select the Angle tool and then pick atom triplets whose angles you want to measure. These atoms need not be bonded to one another. The angle(s) in degrees are indicated in the model window.

or:

• Select any number of atoms and then double-click the Angle tool. The angles (in degrees) of each existing valence angle connecting three consecutively bonded, selected atoms are indicated in the model window.

Related information

Information on examining and changing angles is contained under Examining and changing angles.

Planes

To measure the angle between any two planes, you use the Plane tool.

You can:

• Select the Plane tool. Pick three atoms that define the first plane and then three that define the second plane.

or:

• Select three atoms that define the first plane and then three that define the second plane. Then double-click the Plane tool.

Torsions

To measure the torsion angle involving any four atoms, you use the Torsion tool.

You can use it in two different ways:

• Select the Torsion tool and then pick sets of four atoms whose dihedral angles you want to measure. These atoms need not be bonded to each other. The angle(s) in degrees are indicated in the model window.

or:

• Select any number of atoms and then double-click the Torsion tool. The angles (in degrees) of each existing torsion among four consecutively bonded, selected atoms are indicated in the model window.

Related information

Information on examining and changing torsions is contained in Examining and changing torsions.

Inversions

To measure the inversion or out-of-plane angle involving any four atoms, you use the Inversion tool. These atoms need not be bonded to each other. The vertex atom is the first one picked.

First set the definition according to which the inversion is calculated with the Inversion popup.

Then you can:

• Select the Inversion tool and then pick four atoms whose inversion (out-of-plane angle) you want to measure.

or:

• Select the desired four atoms and then double-click the Inversion tool. These atoms need not be bonded to each other.

Calculating close contacts

Accessing the tools

Access the Close Contacts control panel by selecting the Geometry/Close Contacts... menu item in the main control panel's menu bar. You use this control panel to calculate and display close contacts between all or selected atoms in one or more models.

Contact criteria

Two criteria are available for determining whether atoms are too close together:

• If the distance between the atomic centers is less than a specified cutoff distance. Choose DISTANCE and enter the Cut-off in angstroms.

• If the distance between the atom centers is less than (r₁ + r₂), where is a specified ratio and r₁ and r₂ are the van der Waals radii of the two atoms. Choose VDW RADIUS and enter the VDW Ratio (). A 1 means that close contacts are indicated whenever van der Waals spheres are just touching each other.

You may want to exclude certain atom pairs from the close contact calculation. You can exclude BONDED atoms or atoms in the same GROUP, FRAGMENT, or MODEL.

When excluding bonded atoms, you can specify a distance (in terms of number of bonds) within which atoms should be excluded. For example, a bond separation of 1 means to exclude only directly bonded atoms from the search. Choose BONDED and enter the Separation, in number of bonds.

For example (figure below), if the bond separation is 1, the distances between directly bonded atoms (1-2 and 2-3) are ignored. If the bond separation is 2, the distance between atoms 1 and 3 is also ignored:

Groups (Defining and selecting groups) are defined with the Groups control panel, which is accessed by clicking the Define Groups... pushbutton on the Close Contacts control panel or by selecting Edit/Groups from the menu bar.

A fragment includes all members of a bonded set of atoms. You would, for example, set the exclusion to FRAGMENT if you were examining the fit of a small molecule to a receptor or surface in the same model and wanted to ignore any close contacts within a fragment. However, if the small molecule and receptor were present as different models, you would set the exclusion to MODEL.

Calculating close contacts

Set the selection criteria and then click the CALCULATE close-contacts action button to calculate and display close contacts.

Display of close contacts

Once calculated, close contacts are continuously updated when fragments are moved, rotated, cleaned (Refining the conformation), etc. This enables you, for example, to position a fragment inside a larger structure while monitoring close contacts between the two or to monitor close contacts during minimization.

Additional information

Please see the on-screen help for details on the functioning of each control in the Close Contacts control panel.

Model surfaces

What is a Connolly surface?

You can use the Connolly surface utility to calculate and display a van der Waals or a Connolly surface for all or part of a model:

• A Connolly surface is the van der Waals surface of the model that is accessible to a solvent molecule having a nonzero radius. The surface is generated by rolling a spherical probe of a specified radius over the van der Waals surface of the model (Figure 2).

• A van der Waals surface is generated when the probe radius is zero.

Where the probe contacts only one atom of the model, the Connolly surface is equivalent to the van der Waals surface of the model. Where the probe contacts two or three atoms simultaneously, the Connolly surface is equivalent to the van der Waals surface of the probe (Figure 2). The resulting surface represents the solvent-accessible surface of the molecule (assuming that a molecule of solvent is a sphere with the same radius as the probe).

Accessing the tools

Access the Connolly Surfaces control panel by selecting the Geometry/Connolly Surfaces... menu item in the main control panel's menu bar. You use this control panel to calculate and display Connolly surfaces involving all or selected atoms in your model. You can:

• Calculate a surface for the entire model. Set both Atoms to be surfaced and Atoms in calculation to ALL.

• Calculate a surface that surrounds only selected atoms. Set both Atoms to be surfaced and Atoms in calculation to SELECTED.

• Calculate a partial surface. Set Atoms to be surfaced to SELECTED and Atoms in calculation to ALL.

Set the Calculation Preferences controls in the Connolly Surfaces control panel as desired, then click the CALCULATE pushbutton to calculate and display a Connolly surface.

Displaying Connolly surfaces

Once you have calculated (and displayed) a surface for all or selected atoms in a model, you can toggle the display of that surface by using the Hide check box.

Tip

A Connolly surface is not part of the fragment itself. So if you delete all or part of the fragment, the surface remains unchanged until you recalculate or delete it.

Before a new surface is calculated and displayed, the existing surface is deleted. If you want to view two different Connolly surfaces on a model, copy the model to a second model space (Copying whole models from one model space to another), generate the second surface for the copy, change its color, and then display both models together using the overlay display mode (Controlling model visibility and the display mode).

Saving and loading Connolly surfaces

Connolly surfaces can be saved and loaded using the Save Surface... and Load Surface... pushbuttons, respectively, on the Connolly Surfaces control panel. The file format is compatible with equivalent files generated in POLYGRAF and has a default extension of .dot. Note that the file saves only the position and color of the dots that make up the surface; the atomic positions are not saved in this file.

For operating the file selector control in the Load Connolly Surface and Save Connolly Surface control panels, please see Finding model file(s).

Additional information

Please see the on-screen help for details on the functioning of each control in the Connolly Surfaces, Load Connolly Surface, and Save Connolly Surface control panels.

Vector properties

Calculating vector properties

Vector attributes are output by other Cerius² modules, such as the quantum chemistry modules, which are licensed and documented separately.

Accessing the tools

Access the Vector Properties control panel by selecting the Geometry/Vector Properties... menu item in the main control panel's menu bar. You use this control panel to display vector properties on all or selected atoms in your model.

Displaying vector properties

You can use the Vector Properties control panel to show, remove, or hide available vector properties. If you want to edit the style or size of the displayed vectors, click the Preferences... pushbutton to access the Vector Preferences control panel.

Additional information

Please see the on-screen help for details on the functioning of each control in the Vector Properties and Vector Preferences control panels.