Hi Huy, Chimera does not have a command to get rid of surface components with small enclosed volume. I've attached a script that will do that. You display your surfaces then open this Python script with File / Open.... The volume limit is set in the script near the bottom and you'll have to edit that. If you change the contour level all the small blobs will return and you have to rerun (ie reopen) the script. Tom # ----------------------------------------------------------------------------- # Hide connected components of a surface with small enclosed volume. # # Tested with Chimera version 1.2500. Will not work with 1.2470 or earlier. # def hide_small_blobs(p, volume): varray, tarray = p.geometry from numpy import ones, intc mask = ones((len(varray),), intc) from _surface import connected_pieces cplist = connected_pieces(tarray) hid = 0 for vi, ti in cplist: ta = tarray.take(ti, axis = 0) from MeasureVolume import enclosed_volume vol, holes = enclosed_volume(varray, ta) if not vol is None and vol < volume: mask.put(vi, 0) hid += 1 p.setTriangleMaskFromVertexMask(mask) print ('Hid %d of %d connected surface components having volume < %.5g' % (hid, len(cplist), volume)) # ----------------------------------------------------------------------------- # Return all surface pieces if none are selected. # def selected_surface_pieces(): import Surface plist = Surface.selected_surface_pieces() if len(plist) > 0: return plist from chimera import openModels from _surface import SurfaceModel plist = [] for m in openModels.list(modelTypes = [SurfaceModel]): plist.extend(m.surfacePieces) return plist # ----------------------------------------------------------------------------- # volume = 100.0 for p in selected_surface_pieces(): hide_small_blobs(p, volume)