mmagnus / rna-tools

cmd.extend('rg', rg)

def rr(rainbow=False):

  """

  rhiju's favorite coloring of RNA

  with 2' OH as spheres,

  bases as filled rings, and backbone as cartoon

  ribbons, rainbow colored from 5' to 3'. No hydrogens,

  change: don't color the backbone

  """

  # cmd.bg_color( "white" )

  # cmd.hide('everything' ) # don't hide

  cmd.show('sticks','not elem H')

  #cmd.color( 'red','resn rG+G+DG')

  #cmd.color( 'forest','resn rC+C+DC')

  #cmd.color( 'orange','resn rA+A+DA')

  #cmd.color( 'blue','resn rU+U+DT+BRU')

  #cmd.set( 'cartoon_ring_color',  'red','resn rG+G+DG')

  #cmd.set( 'cartoon_ring_color',  'forest','resn rC+C+DC')

  #cmd.set( 'cartoon_ring_color',  'orange','resn rA+A+DA')

  #cmd.set( 'cartoon_ring_color',  'blue','resn rU+U+DT+BRU')

  #cmd.set( 'cartoon_ring_color',  'red','resn RG+G+DG+RG3+RG5')

  #cmd.set( 'cartoon_ring_color',  'forest','resn rC+C+DC+RC+RC3+RC5')

  #cmd.set( 'cartoon_ring_color',  'orange','resn rA+A+DA+RA+RA3+RA5')

  #cmd.set( 'cartoon_ring_color',  'blue','resn rU+U+DT+BRU+RU+RU3+RU5')

  cmd.select('bases','name c2+c4+c5+c6+c8+n1+n2+n3+n4+n6+n7+n9+o2+o4+o6+n1p')

  cmd.select('backbone_', 'name o1p+o2p+o3p+p+c1*+c2*+c3*+c5*+o2*+o3*+o4*+o5*')

  cmd.select('sugar', 'name c1*+c2*+c3*+c4*+o2*+o4*')

  AllObj=cmd.get_names("all")

  cmd.color( 'red','resn RG+G+RG3+RG5 and name N1+C6+O6+C5+C4+N7+C8+N9+N3+C2+N1+N2')

  cmd.color( 'forest','resn rC+C+RC+RC3+RC5 and name N1+C2+O2+N3+C4+N4+C5+C6')

  cmd.color( 'orange','resn rA+A+RA+RA3+RA5 and name N1+C6+N6+C5+N7+C8+N9+C4+N3+C2')

  cmd.color( 'blue','resn rU+U+RU+RU3+RU5 and name N3+C4+O4+C5+C6+N1+C2+O2')

  cmd.select( 'backbone_', " (name o1p+o2p+o3p+p+op1+op2+'c1*'+'c2*'+'c3*'+'c5*'+'o2*'+'o3*'+'o4*'+'o5*'+'c1*'+'c2*'+'c3*'+'c4*'+'o2*'+'o4*'+c1'+c2'+c3'+c5'+o2'+o3'+o4'+o5'+c1'+c2'+c3'+c4'+o2'+o4') and (not name c1+c2+c3+c4+c5+o2+o3+o4+o5) ")

  for x in AllObj:

    cmd.show( "cartoon", x )

    #cmd.spectrum( "count", "rainbow", x+" and backbone" )

    #cmd.color( 'white', 'backbone' )

  cmd.cartoon("tube", "backbone" )

  cmd.set( "cartoon_ring_mode", 3 )

  cmd.set( "cartoon_ring_transparency", 0.0 )

  #CMD.set( "cartoon_tube_radius", 0.8)

  cmd.hide( "sticks", "backbone" )

  cmd.alter( "name o2*","vdw=0.5" )

  cmd.show( "spheres", "name o2'+'o2*' and not name o2" )

  cmd.show( "sticks", "name 'o2*'+'c2*'" )

  cmd.alter( "resn mg", "vdw=1.0")

  cmd.alter( "resn hoh", "vdw=0.5")

  cmd.show( "spheres", "resn mg+sr+co+zn")

  # clean up

  cmd.delete('backbone_')

  cmd.delete('bases')

  cmd.delete('sugar')

def render_rna():

  rr()

def rg(rainbow=False):

  """

  rhiju's favorite coloring of RNA

  with 2' OH as spheres,

  bases as filled rings, and backbone as cartoon

  ribbons, rainbow colored from 5' to 3'. No hydrogens,

  change: don't color the backbone

  """

  # cmd.bg_color( "white" )

  # cmd.hide('everything' ) # don't hide

  cmd.show('sticks','not elem H')

  #cmd.color( 'red','resn rG+G+DG')

  #cmd.color( 'forest','resn rC+C+DC')

  #cmd.color( 'orange','resn rA+A+DA')

  #cmd.color( 'blue','resn rU+U+DT+BRU')

  #cmd.set( 'cartoon_ring_color',  'red','resn rG+G+DG')

  #cmd.set( 'cartoon_ring_color',  'forest','resn rC+C+DC')

  #cmd.set( 'cartoon_ring_color',  'orange','resn rA+A+DA')

  #cmd.set( 'cartoon_ring_color',  'blue','resn rU+U+DT+BRU')

  #cmd.set( 'cartoon_ring_color',  'red','resn RG+G+DG+RG3+RG5')

  #cmd.set( 'cartoon_ring_color',  'forest','resn rC+C+DC+RC+RC3+RC5')

  #cmd.set( 'cartoon_ring_color',  'orange','resn rA+A+DA+RA+RA3+RA5')

  #cmd.set( 'cartoon_ring_color',  'blue','resn rU+U+DT+BRU+RU+RU3+RU5')

  cmd.select('bases','name c2+c4+c5+c6+c8+n1+n2+n3+n4+n6+n7+n9+o2+o4+o6+n1p')

  cmd.select('backbone_', 'name o1p+o2p+o3p+p+c1*+c2*+c3*+c5*+o2*+o3*+o4*+o5*')

  cmd.select('sugar', 'name c1*+c2*+c3*+c4*+o2*+o4*')

  AllObj=cmd.get_names("all")

  cmd.color( 'gray','resn RG+G+RG3+RG5 and name N1+C6+O6+C5+C4+N7+C8+N9+N3+C2+N1+N2')

  cmd.color( 'gray','resn rC+C+RC+RC3+RC5 and name N1+C2+O2+N3+C4+N4+C5+C6')

  cmd.color( 'gray','resn rA+A+RA+RA3+RA5 and name N1+C6+N6+C5+N7+C8+N9+C4+N3+C2')

  cmd.color( 'gray','resn rU+U+RU+RU3+RU5 and name N3+C4+O4+C5+C6+N1+C2+O2')

  cmd.color('gray', "name c1*+c2*+c3*+c4*+o2*+o4*+C1'+C2'+C3'+C4'+O2'+O4'")

  cmd.select( 'backbone_', " (name o1p+o2p+o3p+p+op1+op2+'c1*'+'c2*'+'c3*'+'c5*'+'o2*'+'o3*'+'o4*'+'o5*'+'c1*'+'c2*'+'c3*'+'c4*'+'o2*'+'o4*'+c1'+c2'+c3'+c5'+o2'+o3'+o4'+o5'+c1'+c2'+c3'+c4'+o2'+o4') and (not name c1+c2+c3+c4+c5+o2+o3+o4+o5) ")

  for x in AllObj:

    cmd.show( "cartoon", x )

    #cmd.spectrum( "count", "rainbow", x+" and backbone" )

    #cmd.color( 'white', 'backbone' )

  cmd.cartoon("tube", "backbone" )

  cmd.set( "cartoon_ring_mode", 3 )

  cmd.set( "cartoon_ring_transparency", 0.0 )

  #CMD.set( "cartoon_tube_radius", 0.8)

  cmd.hide( "sticks", "backbone" )

  cmd.alter( "name o2*","vdw=0.5" )

  cmd.show( "spheres", "name o2'+'o2*' and not name o2" )

  cmd.show( "sticks", "name 'o2*'+'c2*'" )

  cmd.alter( "resn mg", "vdw=1.0")

  cmd.alter( "resn hoh", "vdw=0.5")

  cmd.show( "spheres", "resn mg+sr+co+zn")

  # clean up

  cmd.delete('backbone_')

  cmd.delete('bases')

  cmd.delete('sugar')

cmd.extend('rg', rg)