Input file for the below example
Yowza! Now our picture contains all the information from 1.0 sigma to
the maximum (5.7503 in this case) within the given contoured region.
Where do you think the heavy metal sites are located (and do their
occupancies or relative thermal order look the same?)?
// density is scaled from 1.000000 to 12.154083 box{ <0,0,0>, <1,1,1> texture{ pigment {rgbt 1} finish {ambient rgb <0,0,0>}} interior{ media{ intervals 100 samples 1,20 emission <0.5,0.5,0.5> absorption <0,0,0> scattering { 1,<0,0,0> } confidence 0.999 variance 1/500 density { density_file df3 "edmap.1.df3" interpolate 1 density_map { [0 rgb 0] [1.0 rgb 10] } color_map { [0.0 rgb <0,0,0>] [0.001 FOO_5] [0.5 FOO_6] [1.0 FOO_7] } } } } no_shadow hollow scale <1.00, 1.00, 1.00> translate <0.00, 0.00, 0.00> matrix <1.00, 0.00, 0.00, 0.00, 1.00, 0.00, 0.00, 0.00, 1.00, 0.00, 0.00, 0.00> }Forget most of the mumbo jumbo except for the density_map and color_map definitions (if you want the details for all the variables, see the povray user guide). The density_map declaration specifies a value (the df3 unsigned shorts are converted to values between 0.0 to 1.0 in terms of floats) and how density values should be interpolated. In the above definition, the map is simply rendered with increasing (relative) brightness from 0 to 10. The color map can be used to actually modify the color blend through that density_map. Given the definition above, at density_level 0 no color is displayed. This is ramped to FOO_5 (blue in our previous definitions) at a density level of 0.001, and then to FOO_6 (red in this case) at maximum sigma. Feel free to play with these values (or insert new ones) to obtain interesting effects. By taking the second example and modifying the color map to:
color_map { [0.0 rgb <0,0,0>] [0.001 FOO_5] [0.2 FOO_6] [0.4 FOO_7] }The following is the result:
set maptype 2; set mapramp from black to red; set mergemap 1; contour 2fofc at 1.0 covering require in residue 1012, loc A and not $backb; set mapramp from black to green; set mergemap 3; contour fofc at 2.0 covering require in residue 1012, loc A and not $backb;