Surface Color (Electrostatic Surface Coloring)

Surface Color colors surfaces by volume data such as electrostatic potential or by distance from a point, axis, or plane. It does not calculate electrostatic potential; any of several separate programs can be used to generate the potential and write it to a file that can then be opened in Chimera.

Surface Color acts on molecular surfaces and surfaces of class Surface_Model (see list; includes GRASP surfaces and those from Volume Viewer, Multiscale Models, and Icosahedron Surface) and any caps on such surfaces. Surface Color information is included in saved sessions.

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 (including from the Volume Viewer Tools menu). It is also available as Electrostatic Surface Coloring in the Surface/Binding Analysis category. In addition, simply opening an electrostatic potential file will automatically start Electrostatic Surface Coloring.

The surface of interest should first be displayed in Chimera, then chosen from the menu next to Color surface. How to display a surface depends on its type. For example, a molecular surface can be displayed with Actions... Surface... show or the command surface, whereas a GRASP surface is displayed by opening a GRASP surface file. Any surface cap will be treated as part of the surface for coloring purposes. Only color sliced surface face allows coloring only the cap and not the remainder of a surface.

To color by electrostatic potential or other volume data:

Click Open map data... to browse to and open the volume data file (if not already open). Each open volume data set and its gradient norm will be listed in the same pulldown menu as the distance options. Choosing a data set allows coloring by the data values directly, while choosing its gradient norm allows coloring by how steeply the values change in space. (Details...) Vertices outside the bounds of the volume data will be colored according to the color well marked Color outside volume.

• 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.

When first started as Surface Color, the tool initally contains five colors in rainbow order; started as Electrostatic Surface Coloring, it contains transparent red, white, and blue.

• 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
• Set full range colormap values sets the data values to range linearly from the minimum to the maximum surface data value.

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.

Data value interpolation. The transformed coordinates of the chosen surface and the volume data (but see below) are used to map data values to surface vertices.

• For coloring by volume data values directly, the value for each surface vertex is found by trilinear interpolation from the eight corners of the enclosing volume grid cell.
• For coloring by volume data gradient norm, the gradient at each volume grid point is computed by taking the difference in volume data values between the next and preceding grid points along each axis and dividing by twice the grid spacing. The gradient at a surface vertex is found by trilinear interpolation from the eight corners of the enclosing volume grid cell. The norm of the interpolated gradient (the length of the gradient vector) is used for assigning colors.

Color mapping. 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.

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).

Molecular surface capping after coloring. If a molecular surface 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.