Chimera Commands Index

msc multiscale-surf-id atom-spec distance

~msc multiscale-surf-id

Msc colors surfaces from Multiscale Models to match nearby atoms. It acts similarly to Color Zone, except that msc will infer symmetry-related atom positions for which coordinates have not been loaded.

The multiscale-surf-id is the ID number (shown in the Model Panel) of the surface model created by Multiscale Models. Surface vertices within the cutoff distance of an atom in atom-spec or of any of its inferred copies will be assigned the same color as the atom. When multiple atoms are within the cutoff, a vertex will be colored to match the closest one. Each surface triangle is colored by linearly interpolating its vertex colors. Colors are defined by red, green, blue and opacity/transparency components.

For example, atoms could be colored by B-factor using rangecolor or Render by Attribute. All of the chain surfaces in Multiscale Models could then be colored to match, using a command something like:

msc #1 #0 5.0
By contrast, Color Zone would only color surfaces near the chain copies with loaded coordinates.

The command ~msc restores the colors assigned in the Multiscale Models dialog. Note that changing surface parameters in Multiscale Models will also revert the coloring.

See also: color, rangecolor, rainbow, scolor, sop colorCopy, mcopy, Render by Attribute, Color Zone