Hi Mario, I wrote some Python code you can add to your copy of Chimera to color helices and strands in ribbon display mode. Make a directory called ColorSecondary and put files ChimeraExtension.py and __init__.py in it as given below. Then either move this directory into the chimera "share" directory (chimera/share on Windows and Linux, and Chimera.app/Contents/Resources/share on Mac) or use Chimera menu entry Favorites/Preferences, Catogory tools and add the directory containing ColorSecondary to the list of directories where Chimera looks for extensions. If you do the latter, press the Save button on the Preferences dialog so it remembers this new search directory the next time you run Chimera. Now Chimera will show an menu entry Extensions/Utilities/Color secondary structure. If nothing is selected it sets ribbon colors for all open molecules, or if some residues are selected just those are colored. This is the standard behaviour of entries in the Actions menu. It is a bit tedious to use this cascaded menu entry so I added an accelerator "c2" that does the coloring. Accelerators are not enabled by default. You use Tools/Keyboard/Accelerators on to enable them. To have them always enabled on start-up you use Favorites/Preferences, category Tools to indicate they should always be turned on at start-up. A couple other accelerators for showing a ribbon: rr = show round ribbon, ha = hide atoms. Accelerators are described in more detail in the Chimera manual. Tom =================== ColorSecondary/ChimeraExtension.py follows: import chimera.extension # ----------------------------------------------------------------------------- # class Color_Secondary_EMO(chimera.extension.EMO): def name(self): return 'Color secondary structure' def description(self): return 'Color helices and sheets in ribbon representation' def categories(self): return ['Utilities'] def icon(self): return def activate(self): self.module().color_secondary_structure() return None # ----------------------------------------------------------------------------- # def color_accel(): 'Color ribbons with helices red, sheets cyan, and the rest white' import ColorSecondary ColorSecondary.color_secondary_structure() import Accelerators Accelerators.add_accelerator('c2', 'Color secondary structure', color_accel) # ----------------------------------------------------------------------------- # chimera.extension.manager.registerExtension(Color_Secondary_EMO(__file__)) =================== ColorSecondary/__init__.py follows # ----------------------------------------------------------------------------- # def color_secondary_structure(): import chimera helix_color = chimera.Color_lookup('red') sheet_color = chimera.Color_lookup('cyan') turn_color = chimera.Color_lookup('white') default_color = chimera.Color_lookup('white') rlist = chosen_residues() for r in rlist: if r.isHelix: color = helix_color elif r.isSheet: color = sheet_color elif r.isTurn: color = turn_color else: color = default_color r.ribbonColor = color # ----------------------------------------------------------------------------- # Use the same selection criteria that the Action menu uses. # def chosen_residues(): from chimera import actions, selection residues = actions.instances(adjustToLevel = selection.SelSubgraph)[0] return residues