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. Tom