QSAR Visualization Settings Panel

This panel provides controls for the visualization of the Phase QSAR model in the Workspace.

To open this panel, click QSAR Visualization in the Atom-Based QSAR Panel

  • Using
  • Features
  • Additional Resources

Using the QSAR Visualization Settings Panel

This panel allows you to view the QSAR model in 3 dimensions, and to examine the spatial distribution of contributions to the model. The cubes of the model are colored by the sign of the coefficient: blue for positive coefficients and red for negative coefficients. Positive coefficients indicate an increase in activity, negative coefficients a decrease. You can use the visualization of the coefficients to identify characteristics of ligand structures that tend to increase or to decrease activity.

To view the cubes that are occupied by the displayed ligands instead of the entire model, select Workspace ligands in the View volume occupied by section.

To view the effect of a particular kind of atom, select Selected atom class in the View effects from section, and choose the atom class from the option menu.

To filter out cubes that have small coefficients, and therefore do not affect the activity much, you can use the sliders for the positive and negative coefficients in the Regression Coefficient Visualization section.

QSAR Visualization Settings Panel Features

View Effects From Controls

These controls allow you to choose whether to view the effects from all classes of atoms, or selected classes of atoms, and whether to combine effects from multiple classes or view them separately.

View effects from list

Lists the atom or feature classes for which visualizations can be displayed. Visualization is done for the classes that are selected in this list. You can select multiple rows with shift-click and control-click.

Combine effects option

When this option is selected, the effects from the selected classes are combined before visualization. When it is deselected, the effects from each class are visualized separately.

View Volume Occupied By Options

These options allow you to choose whether to view the volume occupied by the QSAR model or by the ligands that are included in the Workspace.

Workspace ligands option

Display the cubes of the QSAR model grid that are occupied by the ligands that are in the Workspace.

QSAR Model option

Display all the cubes that are occupied in the QSAR model.

Regression Coefficient Visualization Section

This section provides controls for the choice of QSAR model and the display of its coefficients.

Number of PLS factors option menu

Select the number of PLS factors from this menu to determine which QSAR model is displayed.

Effect option menu

Select the effect for which the transparency, threshold, and color settings are to be made. The Combined choice applies when you select the Combine effects option.

Cube transparency slider

Adjust the transparency of the cubes for the selected effect from 0% (opaque) to 100% (transparent).

Positive coefficient threshold slider and color controls

The slider adjusts the threshold for the display of positive regression coefficients for the selected effect. Cubes that have coefficients that are smaller in magnitude than the threshold are not displayed. The slider covers the entire range of positive coefficients; at the maximum, the coefficients that have the maximum magnitude are still displayed.

The color of the cubes for the selected effect can be selected from the Color option menu.

Negative coefficient threshold slider

Adjust the threshold for the display of negative regression coefficients for the selected effect. Cubes that have coefficients that are smaller in magnitude than the threshold are not displayed. The slider covers the entire range of negative coefficients; at the maximum, the coefficients that have the maximum magnitude are still displayed.

The color of the cubes for the selected effect can be selected from the Color option menu.

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