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Tool: Color Zone

Color Zone colors volume data (map) surfaces to match nearby atoms or markers. A map that has been colored by zone can then be split into separate maps for the different zones. Coloring by zone is also implemented as the command color zone (with more options than shown in this tool), and splitting as volume splitbyzone. For coloring by segmentation region, see segmentation. See also: Volume Viewer, Surface Zone, Segment Map, Map icon , ChimeraX video: coloring each protein in an EM map

Color Zone can be started from the Volume Data section of the Tools menu. The tool window can be moved, resized, etc.

The surface to color should be chosen from the list of available map models, and the atoms to use specified as selected atoms (the current selection) or chosen from the list of available atomic models. All atoms of a chosen model will be used, including ligand, solvent, etc., even if they are not displayed. To use only the biopolymer portion of a model, either the remaining atoms should be deleted, or only those atoms selected and designated as selected atoms instead.

Clicking Color colors vertices in the chosen surface that are within the specified Coloring radius of any of the atoms. When multiple atoms are within the cutoff distance, a vertex will be colored to match the closest one. Vertices not within the cutoff of any atom are assigned the default surface color (single-color mode). Each surface triangle is colored by linearly interpolating its vertex colors. Colors are defined by red, green, blue and opacity/transparency components.

The Coloring radius can be adjusted by moving the slider or by typing in a new value. The slider is logarithmic to cover a wide range of values. If the set of atoms is changed, or if an atom is recolored or repositioned relative to the surface, Color must be clicked again to update the surface coloring.

Clicking Uncolor returns the surface to its default color (single-color mode).

Split Map splits the corresponding map into separate data sets for the zones. A data set is created for each distinct color and for the “uncolored” data (in the zone remaining when the color zones are subtracted from the original volume). Values outside the respective zones are set to zero. The new data sets are named by appending numbers (0, 1, 2, ...) to the name of the original map. The number 0 is associated with the uncolored region, whereas the other numbers correspond to the distinct colors in an unpredictable order. The original map is hidden but not modified.

Clicking Help shows this page in the Help Viewer.

UCSF Resource for Biocomputing, Visualization, and Informatics / September 2021