Surface Color (Electrostatic Surface Coloring)

Surface Color can color surfaces according to volume data (any type, including electrostatic potential) or by geometry (distance from a point, axis, or plane). Surface Color acts on:

• molecular surfaces (MSMS models)
• surface models from Volume Viewer, Multiscale Models, and Intersurf
• GRASP surfaces
• caps on such surfaces created by Surface Capping

Thanks to Steve Ludtke for developing the original version of this tool, Isosurface Colorizer (distributed with the EMAN package). This new implementation uses C++ code to accelerate the color calculations.

There are several ways to start Surface Color, a tool in the Volume Data category. It is also available as Electrostatic Surface Coloring in the Surface/Binding Analysis category.

The surface of interest should first be displayed in Chimera. How to display the surface depends on the type; for example, Actions... Surface... show is one way of displaying a molecular surface, while a GRASP surface is displayed by opening a GRASP surface file. The surface can then be chosen from the menu next to Color surface. If the surface has a cap (created with Surface Capping) the cap will be treated as part of the surface for coloring purposes. The option to Only color sliced surface face allows coloring of only the cap and not the remainder of the surface.

To color by volume data (electrostatic potential or any other type):

Click Open map data... to browse to and open the volume data file. If the data file has already been opened, however, it can be chosen from the pulldown list that also includes the distance options. The transformed coordinates of the chosen surface and the volume data (but see below) are used to map data values to surface vertices. The value for each vertex is found by trilinear interpolation from the eight corners of the enclosing volume grid cell. Vertices outside the bounds of the volume data will be colored according to the color well marked Color outside volume. Non-orthogonal data are handled correctly.

• Radius - distance from a point. The point is defined by the Origin coordinates.
• Cylinder radius - distance from an axis. The axis is defined by any point on the axis and a direction. The point is defined by the Origin coordinates. The three values in the Axis field specify direction. For example, (1 0 0), (0 1 0), and (0 0 1) specify directions along the X, Y, and Z axes, respectively. Any three values can be entered, however (the axis need not be parallel to the X, Y, or Z axis).
• Height - topographic height (distance from a plane) The plane is defined by any point on the plane and a vector normal to the plane. The point is defined by the Origin coordinates. The vector is defined by the values in the Axis field, as described above.

For any of the distance options, Origin coordinates can be entered directly, or Center can be used to set the origin to the center of the bounding box of the chosen surface. The Origin and Axis are specified in the untransformed coordinate system of the chosen surface, not the viewing coordinate system.

• The number of Colors can be 2, 3, 5, 10, 15, or 20. Each color can be adjusted by clicking its color well, and the data value associated with the color can be edited. If a value is blank, the corresponding color will not be used. At least two values must be specified.
• Clicking a Pattern setting populates the color wells with a set of colors:
  • Rainbow - standard rainbow colors, starting with red and ending with blue
  • Gray - grayscale, starting with black and ending with white
  • Red-Blue - going from red to blue with white in the middle (traditionally used to show electrostatic potential)
• Set full range colormap values sets the data values to range linearly from the minimum to the maximum surface data value.

The color mapping is defined by the specified color/value pairs, or thresholds. The data value for each surface vertex is compared to the thresholds. Vertices with values lower than any threshold are assigned the color of the lowest-value threshold, while vertices with values higher than any threshold are assigned the color of the highest-value threshold. The colors of the remaining vertices are obtained by linear interpolation between the nearest lower and higher thresholds. Finally, each surface triangle is colored by linearly interpolating its vertex colors. Colors are defined by red, green, blue and opacity/transparency components.

Clicking Uncolor reverts the coloring scheme of the chosen surface to:

• for molecular surfaces, the model-level color of the corresponding molecule model (see coloring hierarchy)
• for other surface models, the surface color in single-color mode

Close dismisses the Surface Color dialog. Help brings up this manual page in a browser window.

Molecular surface capping after coloring. If a molecular surface (MSMS model) is colored and later capped with Surface Capping, the cap will not be colored automatically. It is necessary to click Color again to color the cap, after which the cap color will update automatically.

Volume data must be displayed before it can be transformed separately. There is no volume model until the data is displayed with Volume Viewer. When there is no volume model, the transformation of the volume data is assumed to be the same as that of the chosen surface. To use a different transformation for data mapping, the volume data must be displayed and the volume model moved while the surface model is held fixed (or vice versa).