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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 the Surface Display Options dialog box, you can:
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.
Drag the slider to change the transparency of the front or back of the surface, or enter the transparency in the text box.
Select this option (the default) to apply the same transparency to both front and back of the surface. When selected, dragging one slider or entering a value in one of the text boxes changes the value for the other side of the surface. Deselect this option to adjust the transparency of the front and back of the surface independently.
The Surface Table shortcut menu offers several presets for transparency: 0%, 25%, 50%, and 75%, which set the transparency of both front and back of the surface, and Front Face 100%, which makes the front face transparent and the back face opaque.
Choose between Solid, Mesh, and Dot. Only Solid is affected by the value of Transparency. Mesh and Dot are always drawn fully opaque.
The surface is colored according to the values of the chosen property. 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 Color Schemes 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, an Impact calculation, or a Jaguar calculation. You can also generate partial charges by choosing Assign Partial Charges from the Tools menu. If partial charges are not available, the surface appears completely white.
The Electrostatic Potential coloring scheme also requires partial charges. In this scheme, the surface is colored by the value of the electrostatic potential at the surface evaluted from the partial charges of the atoms that were used to generate the surface. If you choose this scheme, you can choose a color ramp from the Color ramp option menu. By default, the range of colors is determined by the range of property values. You can set minimum and maximum property values for the ends of the color ramp in the Minimum and Maximum text boxes. The colors for property values outside the minimum and maximum are set to the colors at the appropriate end of the ramp.
This option provides two option menus and a button:
This option allows you to color the selected surface by the values of the volume selected from the list. For example, you can color a van der Waals surface with the values of the electrostatic potential generated by Jaguar. The features available for controlling the color are as follows:
To enhance the perception of depth, select Darken colors by cavity depth. This option changes the color shade according to how far the surface is from a smooth surface that encloses ("fills in") the cavity.
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