Field-Based QSAR Visualization Settings Panel

Field-Based QSAR Visualization Settings Panel Features

 

• View contours from list
• View field intensity from list
• Contour style options
• Number of PLS factors option menu
• Field option menu
• Contour values sliders
• Contour colors option menus
• Field intensity sliders

View contours from list

Select one or more fields from this list to view their contours in the Workspace. These are the surfaces drawn at a particular value of the field.

View field intensity from list

Select a field from this list to view the field intensities at each grid point in the Workspace.

Contour style options

Choose the display style for the contour surfaces, from Solid, Mesh, or Dot. The default is Solid, but the choice you make is stored as the new default.

Number of PLS factors option menu

Choose the QSAR model that is displayed by its number of PLS factors.

Field option menu

Choose a field to set the contour cutoffs.

Contour value sliders

Use the sliders to set the value of the field fraction at which the surface is contoured, i.e. the isovalue for the surface. Negative and positive values of the fields can be controlled independently. The value is the coefficient of the field value in the PLS model (Coeff) multiplied by the standard deviation in the field values at any given grid point evaluated over the training set (StdDev).

Contour color option menus

Set the color for the positive and negative surfaces of the contours. The default colors are given in the table below.

Table 1. Default colors for field contours

Field Type	Positive	Negative
Force Field Steric	Green	Yellow
Force Field Electrostatic	Blue	Red
Gaussian Steric	Green	Yellow
Gaussian Electrostatic	Blue	Red
Gaussian Hydrophobic	Yellow	White
Gaussian Hbond Acceptor	Red	Magenta
Gaussian Hbond Donor	Purple	Cyan
Gaussian Aromatic Ring	Orange	Gray

A positive region for a Gaussian field means that it is favorable for the field property, and a negative value means that it is unfavorable. For electrostatic fields, a positive region is favorable for positive charges, and a negative region is favorable for negative charges.

Field intensity sliders

Set the cutoff values of the field at which the color is the brightest (maximum saturation). Fields with greater absolute values than the cutoff are displayed at the maximum brightness. Negative and positive values can be controlled independently. The colors used are red for negative values and blue for positive values. The sliders affect the field that is selected in the View field intensity from list.