[Chimera-users] Coloring molmap surfaces
goddard at sonic.net
Fri Feb 24 11:04:46 PST 2012
> Greetings Tom
> How can color the molmap surface of certain atoms/residues.
> Many Thanks, Vijay
Use the Color Zone dialog to color a molmap surface to match nearby
atom colors (menu Tools / Volume Data / Color Zone). You select the
atoms you want to use for color (e.g. menu Select / Select All) choose a
distance range from those atoms to color in the Color Zone dialog and
press the Color button.
In Chimera 1.6 (release candidate available on the web) or daily
builds there is a command version of color zone. For example
scolor #0 zone @ca range 5
says to color molmap surface #0 to match C-alpha atom colors within a
distance of 5 Angstroms.
To avoid jagged edges in the coloring you should use the molmap
gridSpacing option to specify a grid size about 1/5 to 1/10 the map
resolution. The default value is 1/3 of map resolution making a fairly
coarse surface mesh. Colors are only assigned to the mesh vertices, so
a fine mesh is needed for smooth boundaries between different color regions.
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