[Chimera-users] Coloring molmap surfaces

Tom Goddard 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
Hi 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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