Scolor colors surface models and their caps. It is the command-line implementation of Surface Color and Color Zone. See also: color, rangecolor, rainbow, transparency, coulombic, apbs, sop, volume, msc
scolor #0 geometry cylindricalThe surf-model argument can be a specific model number or range of model numbers preceded by #, or simply # to indicate all applicable surfaces. The method can be:
scolor #0 geom radial cmap 100,gray:150,blue:200,purple
scolor #0 volume #1 cmap -10,red:0,white:10,blue
scolor #1 zone @ca range 5
Simply use the specified color, where color_name can be any color name that specifies a single color. The general options do not apply to this method.• scolor surf-model zone atom-spec [ range cutoff ] [ autoUpdate true | false ]
Color surface patches to match the specified atoms or markers. The range option indicates a cutoff (default 2.0) in physical distance units, typically Å. The autoUpdate option indicates whether to update the coloring of a surface automatically when its shape changes. The ~scolor command discontinues coloring by zone. See also: Color Zone• scolor surf-model volume volume-model [ perPixel true | false ] [ colorOutsideVolume color_name ] [ offset d | start,end,N ] general-options
Color by volume data such as electron density or electrostatic potential, where volume-model is the model number (preceded by #) of the volume data set. The perPixel option indicates whether to determine color separately for each surface pixel instead of interpolating across surface triangles (see details). Per-pixel coloring tends to give smoother color gradations. Values at surface vertices are determined by interpolation except when per-pixel coloring is used (see details). The colorOutsideVolume option specifies how to color for surface vertices that fall outside the volume data grid. The color_name can be any color name that specifies a single color; the default is #800080008000 (a dark gray). The offset option specifies how far out from each surface vertex, along its normal, to evaluate the data (default 0.0):• scolor surf-model gradient volume-model [ colorOutsideVolume color_name ] [ offset d | start,end,N ] general-options
- d - a single offset distance
- start,end,N (three values separated by commas only) - starting distance, ending distance, and how many offsets to evaluate within that range, respectively. For example, offset 1.5,3.0,3 specifies offsets of 1.5, 2.25, and 3.0. Values from multiple offsets are averaged per surface vertex. Specifying multiple offsets turns off any per-pixel coloring.
Color by volume data gradient norm, where volume-model is the model number (preceded by #) of the volume data set. Gradients (how steeply the values change in space) at surface vertices are determined by interpolation (see details). The colorOutsideVolume and offset options are as described above for volume.• scolor surf-model geometry radial [ center center ] [ coordinateSystem N ] general-options
Color by distance from a point. The point can be specified with center, where center can be:• scolor surf-model geometry cylindrical [ center center ] [ axis axis ] [ coordinateSystem N ] general-options
Color by distance from an axis. The axis is defined by any point on the axis and a direction. The point can be specified with center and the direction with axis, where axis can be:• scolor surf-model geometry height [ center center ] [ axis axis ] [ coordinateSystem N ] general-options
The default is the Z-axis in the coordinate system of the surface. The coordinateSystem option indicates that specifications of center and/or axis should be interpreted in the coordinate system of a reference model. N is the reference model number preceded by #. The default coordinate system is that of the surface being colored.
- x - X-axis
- y - Y-axis
- z - Z-axis
- x,y,z (three values separated by commas only) - an arbitrary vector
- an atom-spec of exactly two atoms (not necessarily bonded or in the same model) or one bond. A bond can only be specified by selecting it and using the word selected, sel, or picked; any atoms also selected at the time will be ignored.
Color by distance from a plane, or topographic height. The plane is defined by any point on the plane and a vector normal to the plane. The point can be specified with center and the vector with axis. The coordinateSystem option indicates that specifications of center and/or axis should be interpreted in the coordinate system of a reference model. N is the reference model number preceded by #. The default coordinate system is that of the surface being colored.
cmap palette | value1,color1:value2,color2:...
Use the specified color mapping, which can be either a pre-defined palette (colors listed in ascending value order):
or a series of value,color pairs (no spaces) separated by colons only. A color can be any color name that specifies a single color.
- redblue (default) - red, white, blue
- rainbow - red, yellow, green, cyan, blue
- cyanmaroon - #0f1bc7adcf5b (a dark cyan), white, #9eb820005eb8 (a dark maroon)
- gray - black, white
reverseColors true | false
Whether to reverse the order of the colors in the palette.
cmapRange full | low,high
What data values should map to the extremes of the palette: the default full, meaning the minimum and maximum values found (at surface vertices), or specified low and high values separated by a comma only. Values less than low will map to the same color as low, and values greater than high will map to the same color as high. When multiple surfaces are colored in a single command, the full range is determined separately for each surface.
capOnly true | false
Whether to color only surface caps and not the rest of a surface.
autoUpdate true | false
Whether to update the coloring of a surface automatically when its shape changes. For example, the shape of a surface cap changes as clipping is adjusted, and a molecular surface changes shape when it is recomputed with a different probe radius. This updating only accounts for changes in the shape of a surface, not changes in its position or orientation relative to other models.