VIDA User Manual

Previous: 5.10 Grid Visualization Up: 5. 3D Display Next: 5.12 Custom Views

---

• 5.11.1 Display Styles
• 5.11.2 Color
  • 5.11.2.1 Atom Color
  • 5.11.2.2 Concavity
  • 5.11.2.3 Curvature
  • 5.11.2.4 Distance
  • 5.11.2.5 Electrostatics
  • 5.11.2.6 Grid
  • 5.11.2.7 Hydrogen Bond Potential
  • 5.11.2.8 Hydrophobicity
  • 5.11.2.9 Surface Potential
• 5.11.3 Selection

 
5.11 Surface Visualization

Surfaces are infinitely thin three dimensional connected regions that represent objects such as molecular or accessible surfaces of molecules. Surfaces can be selected (or scribed), cropped, colored, and made transparent in part or in whole.

 
5.11.1 Display Styles

Surfaces can be visualized in one of three display styles: Solid, Mesh, and Points. These individual style can be seen in Figure 5.19.

Figure 5.19: Surface rendering examples showing (a) solid rendering, (b) mesh rendering, and (c) point rendering.

[Solid] [Mesh] [Points]

 
5.11.2 Color

There are a number of surface specific coloring schemes in addition to the standard single color scheme. The following schemes are discussed below: atom color, concavity, curvature, distance, electrostatics, grid, hydrogen bond potential, hydrophobicity, and surface potential.

Figure 5.20: Various different surface coloring schemes

[Single color] [Color by Atom] [Color by Concavity] [Color by Curvature] [Color by Distance] [Color by Electrostatics] [Color by Hydrogen Bond Potential] [Color by Hydrophobicity]

 
5.11.2.1 Atom Color

The atom color scheme colors each vertex on the surface using the color of the nearest atom to that vertex in the molecule that the surface was created from (see Figure 5.20(b)). This scheme will not work if the surface was not created from a molecule and also if that molecule is not currently present.

 
5.11.2.2 Concavity

The concavity scheme colors each vertex on the surface according to how concave the surface is at that vertex using a red-to-white gradient where red indicates a region of high concavity (see Figure 5.20(c)).

 
5.11.2.3 Curvature

The curvature scheme colors each vertex on the surface according to the curvature of the surface at that vertex using a grey-to-green gradient where green indicates a region of high curvature (see Figure 5.20(d)).

 
5.11.2.4 Distance

The distance scheme colors each vertex by its distance from either the selected set of atoms or the visible set of atoms (if none are selected at the time of coloring). Each band of color represents a distance of one Angstrom from the selected set. The color banding is continuously repeated as the distance increases, but the colors fade to white with each repetition to show the distance effect (see Figure 5.20(e)).

 
5.11.2.5 Electrostatics

The electrostatics scheme colors each vertex on the surface according to the electrostatic potential at that vertex using a red-to-blue gradient from -7.0 to +10.0 (see Figure 5.20(f)). This range can be changed if desired in the application preferences in the Surfaces section.

The electrostatic potential at the surface is calculated using OpenEye's Zap toolkit (for more information, please see the Zap toolkit documentation). By default, VIDA will use the molecule's input partial charges in the calculation (if any were specified). However, if no partial charges were specified, VIDA will assign partial charges using either MMFF94 (the default) or AM1-BCC [3,4]. The choice of charge model can be specified in the application preferences. If a molecule has greater than 50 heavy atoms, MMFF94 will always be used in place of AM1-BCC regardless of the set preferences.

Proteins have an alternative charging option based on residue information. The charge model can be seen in the table below. This model is used by default (if no partial charges were specified), but it can be disabled in the application preferences.

 
5.11.2.6 Grid

The grid scheme colors each vertex on the surface according to the grid potential at that vertex using a red-to-blue gradient from the minimum grid value to the maximum grid value. The grid potential is determined by mapping the specified grid onto the surface.

 
5.11.2.7 Hydrogen Bond Potential

The hydrogen bond potential scheme colors each vertex according to the hydrogen bond class of the nearest atom to that vertex in the molecule that the surface was created from (see Figure 5.20(g)). This scheme will not work if the surface was not created from a molecule and also if that molecule is not currently present.

 
5.11.2.8 Hydrophobicity

The hydrophobicity scheme colors each vertex according to a specified hydrophobic color scale based on residue information associated with a given vertex. This scheme will not work if the surface was not created from a protein and also if that protein is not currently present.

There are four different scales available: Charifson, Eisenberg, Kyte-Dolittle, and White Octanol. The Charifson scale applies defined colors based on residue information. The other three scales each return a specific hydrophobicity value which is then used to return a color based on a brown-to-blue gradient between -2.5 and +2.5 for Eisenberg, -4.5 and 4.5 for Kyte-Dolittle, and -4.0 and 4.0 for White Octanol.

 
5.11.2.9 Surface Potential

The surface potential scheme colors each vertex according to the potential value at that vertex using a red-to-blue gradient from the surface potential minimum to the surface potential maximum. This scheme is different than the electrostatic scheme in that the coloring is based on the stored potential values as opposed to calculated potential values. Typically, surfaces generated within VIDA will not have any stored potential values. However, surfaces created externally using OpenEye's Spicoli toolkit for example can store values in the potential field and as such can be colored accordingly.

5.11.3 Selection

Vertices can be selected simplying by clicking on the desired location. A line of vertices can be selected by selecting one vertex and then by holding down the Shift key when selecting another. This starting selection can be grown (and shrunk) using the Selection pane in the Style Control (see Section 5.1.1). Double-clicking on the surface will select the entire surface.

---

				VIDA User Manual

Previous: 5.10 Grid Visualization Up: 5. 3D Display Next: 5.12 Custom Views

---

Documentation released on 23 May 2007.