Surface Display Options Dialog Box

This dialog box allows you to set options for surfaces that control the transparency, surface style, and color scheme. Some of these controls are available from the surfaces shortcut menu.

To open this dialog box, click the Display Options button in the Surface Manager Panel, or right-click on a surface in the Workspace and choose Display Options.

  • Features
  • Additional Resources

Surface Display Options Dialog Box Features

Name text box

Specify a name for the surface. The name is shown in the Surface Name column of the Surface Manager Panel.

Style options

Choose between Solid, Mesh, and Dot. Only Solid is affected by the value of Transparency. Mesh and Dot are always drawn fully opaque; when they are selected, the transparency controls are not available.

Transparency text boxes and link button

Set the default transparency of the front surface and the back surface in the text boxes. You can link the two so that they are synchronized, by clicking the link button to the right of the boxes.

These controls affect how transparent or opaque the surface is. Transparency only affects surfaces drawn in Solid style. Other styles are always drawn fully opaque. The transparency defined here sets the maximum transparency when angle-dependent transparency is in use (see under Viewing settings in the Preferences Panel).

Color scheme option menu

Choose the type of color scheme from this option menu. For each type, controls for the settings relevant to that type are displayed below this option menu.

Constant color settings

In the Constant color scheme, a single color is applied to the whole surface, or a different single color is applied to each surface of paired surfaces.

Color button

Click this button to open a color selector and choose the color for the surface (or the positive surface for paired surfaces). The color chosen is displayed on the button.

Negative button

Present for paired surfaces, which have a surface for positive values and a surface for negative values. Click this button to open a color selector and choose the color for the negative surface. The color chosen is displayed on the button.

Electrostatic potential settings

In this scheme, the surface is colored by value of the electrostatic potential at the surface, evaluated from the partial charges of the atoms that were used to generate the surface. This coloring scheme requires partial charges, which can be generated from a MacroModel or Jaguar calculation, or from the default force field by choosing Edit → Assign → Partial Charges.

Color ramp option menu

Choose from several color ramps for the range of values in the electrostatic potential.

Min and Max text boxes

Set the minimum and maximum value of the electrostatic potential that is represented by the color range in the ramp. Values outside this range are mapped to the color at the corresponding end of the ramp.

Reset button

Reset the values in the Min and Maxtext boxes to the minimum and maximum value of the electrostatic potential.

Other property settings

In this scheme, the surface is colored according to the values of a chosen property.

Property option menu

Choose the property to color the surface by. Coloring is based on the nearest atom to that part of the surface, using the nearest atom's property value. Most of the color schemes are described in the Coloring Atoms topic. The Atom Color and CA Atom Color schemes simply color the surface according to the color of the nearest atom or the nearest alpha carbon atom (CA, CA1, or CH3 in ACE residue).

The Partial Charge coloring scheme requires a calculation on the entry that generates partial charges, such as a MacroModel calculation or a Jaguar calculation. You can also generate partial charges using the default force field by choosing Edit → Assign → Partial Charges. If partial charges are not available, the surface appears completely white.

Mapped from volume settings

In this scheme, the surface is colored by the values of a selected volume. For example, you can color a van der Waals surface with the values of the electrostatic potential generated by Jaguar. The units of the electrostatic potential are shown in the Comments column of the surface table in the Surface Manager Panel.

Volume option menu

Select the volume that defines the property values to map onto the surface. The volumes listed are those in the Surface Manager Panel. If the volume you want isn't present, you can import it, and the menu is updated.

Color ramp option menu

Choose a ramp to use from the available color ramps. The menu lists the ramps in the installation and any custom ramps.

Min and Max text boxes

Set the minimum and maximum value of the volume data that is represented by the color range in the ramp. Values outside this range are mapped to the color at the corresponding end of the ramp.

Reset button

Reset the values in the Min and Maxtext boxes to the minimum and maximum value of the volume data.

Show legend in Workspace option

Display a legend for the color ramp in the Workspace, which consists of a horizontal bar representing the entire range of volume data values, and colored according to the values of the color ramp. The values set in the Min and Max text boxes are marked as vertical bars with the values above. The surface name for the volume is displayed below the legend bar. The legend (with units) is displayed and hidden with the corresponding surface.

Limit option

Control how much of the surface is displayed, by limiting the surface display to the portion that is within a given distance from the atoms that are selected in the Workspace.

Display surface within X Å of selected atoms text box

Set the distance from the atoms that are selected in the Workspace for which the surface is displayed.

Update from Selection button

When the atom selection in the Workspace changes, click this button to update the surface display for the new selection.

Isovalue slider and text box

Change the value of the volume data for which the surface is computed, either using the slider or entering the value in the text box. This changes the extent of the surface: larger values usually mean smaller surfaces. The isovalue is applied to the selected surfaces. The isovalue can also be changed from the Surface Manager Panel.

Related Topics