marshmallows.py

from pymol import cmd

count = 0

def marshmallows_one(sel, col, name, resl=1):
   global count
   count += 1
   cmd.delete('map%i' % count)
   cmd.delete('surf%i' % count)
   cmd.do("remove hydro")
   cmd.do("bg_color white")
   #cmd.do("hide everything")
   cmd.do("set surface_quality, 1")
   cmd.do("alter all, b=50")
   cmd.do("alter all, q=1")

   cmd.do("set gaussian_resolution,10")
   cmd.do("map_new map%i, gaussian, %i, (%s and name CA), 10" % (count, resl, sel))
   cmd.do("isosurface %s, map%i" % (name, count))

   cmd.do("color %s, %s" % (col, name))
   cmd.do("set antialias, 2")
   cmd.do("set ray_trace_gain, 0.4")
   cmd.do("set ray_shadows, 0")
   cmd.do("set specular, 0")
   cmd.do("show surface, %s" % name)

def marshmallows(sel):
   cmd.delete("surf*")
   cmd.delete("map*")
   COLs = ("green", "cyan", "magenta", "yellow", "pink")
   COLs = COLs + COLs + COLs
   cmd.do("remove hydro")
   cmd.do("bg_color white")
   cmd.do("hide everything")
   cmd.do("set surface_quality, 1")
   cmd.do("alter all, b=50")
   cmd.do("alter all, q=1")
   cmd.do("set gaussian_resolution,10")

   for i, c in enumerate(cmd.get_chains(sel)):
      cmd.do("map_new map%s, gaussian, 1, (%s and chain %s), 10" % (c, sel, c))
      cmd.do("isosurface surf%s, map%s" % (c, c))
      cmd.do("color %s, surf%s" % (COLs[i % 2], c))

   cmd.do("set antialias, 2")
   cmd.do("set ray_trace_gain, 0.4")
   cmd.do("set ray_shadows, 0")
   cmd.do("set specular, 0")
   cmd.do("show surface, surf*")