Tool: Surface Color

Surface Color colors surfaces by:

• volume data (map) value or gradient norm
• electrostatic potential (ESP), a type of volume data for which values offset from the surface are used
• distance from a point, axis, or plane

... corresponding to color command coloring by map value and by distance. See also: Render by Attribute, Color Key, coulombic, mlp, making images, ChimeraX videos: coloring by electrostatic potential, coloring a map by local resolution

The Surface Color dialog can be opened from the Depiction or Volume Data section of the Tools menu and manipulated like other panels (more...).

The surface to color should be chosen from the list of available surface models, and the type of coloring designated. Coloring by distance:

• radius – distance from a point (the origin); clicking Center sets the origin to the center of the surface model
• cylinder radius – distance from a line defined by the origin coordinates and an axis vector
• height – distance from a plane defined by the origin coordinates and an axis vector perpendicular to the plane

Coloring by a specified map:

• electrostatic potential
• volume data value
• volume data gradient norm

A series of color wells is shown, with fields below them to enter the corresponding values. Choosing to color by electrostatic potential fills in the values (if they were blank) to span the range -10 to +10. If no values are filled in, the entire range of values (as defined by the surface points and the data) will be spread across the colors when Color is clicked. The number of color/value pairs can be changed in the options. The colors can be changed individually by clicking a color well and using the system color editor, or collectively by choosing a palette in the options.

Clicking Color colors the surface according to the current settings, whereas Uncolor returns the surface to its previous single-color setting (which is not necessarily how it was colored immediately before Color was clicked, but see also undo). Clicking Key starts the Color Key tool and draws a color key to match the current Surface Color settings. Help shows this page in the Help Viewer.

[back to top: Surface Color]

Clicking Options shows/hides additional options:

• Colors – number of color/value pairs (default 3)
• Palette – choices of coloring palette (default red-white-blue )
• Clicking Reverse puts the color/value pairs in the opposite order.
• Clicking Set fills in the values to span the full range and performs the coloring, same as clicking Color.
  
  
• Surface offset (electrostatic coloring only) – how far out from each surface vertex, along its normal, to evaluate the data (default 1.4 Å). The rationale for looking outward is to show the values that any atoms binding to the outside of the surface would “see” at their centers. A molecular surface in ChimeraX is the solvent-excluded surface where the surface of a spherical probe can lie. The default probe radius is 1.4 Å, so an offset of 1.4 Å approximates the solvent-accessible surface, about as close as the probe center can get to the molecule. **However, an offset of 0.0 may be preferred for coloring the cap of a clipped surface, and a zero or negative offset for coloring the surface of one structure by the potential from another.**
  
  
• Color outside volume (map coloring only) – what color to use for surface points outside of the map boundaries (default )
  
  
• Only color clipped surface face – whether to color only the cap of a clipped surface
• Report value at mouse position – whether mouseover should report the data value for that surface vertex in the status line