Hi M. Dutta, I'm not clear whether you want to color a density map of a virus, or a PDB model. If you want to color the density map there is a new tool called "Color Zone" (menu Tools / Volume Data / Color Zone) that lets you color patches of surfaces near selected atoms or markers. If you have an atomic model docked to the map, you can color the atoms, select them, then use Color Zone to color the surface within some specified distance of the atoms. If you don't have a docked model, you can place markers on the density map using the Volume Path Tracer tool (menu Tools / Volume Data / Volume Path Tracer). The markers behave just like atoms -- they can be colored and have their colors painted onto nearby surface patches. This Color Zone tool is only in Chimera version 1.2154 (the latest snapshot release) which is only available on Linux and Mac right now. I could provide you the Color Zone tool separately to work with the Windows Chimera version 1.2143 if needed. Documentation for Color Zone is available by pressing the Help button on the Color Zone dialog. We don't have online documentation for it yet. Tom