Create high quality ball-and-stick molecular images with Pymol

pymol_style.py

# BallnStick creates a ball and stick representation of an object 
# Add_VDW creates a copy of an object with full-sized, transparent spheres
# Bondi VDW values added below to override default Pymol settings

from pymol import cmd

# Bondi VDW values 
cmd.alter("elem Ac", "vdw=2.00")
cmd.alter("elem Al", "vdw=2.00")
cmd.alter("elem Am", "vdw=2.00")
cmd.alter("elem Sb", "vdw=2.00")
cmd.alter("elem Ar", "vdw=1.88")
cmd.alter("elem As", "vdw=1.85")
cmd.alter("elem At", "vdw=2.00")
cmd.alter("elem Ba", "vdw=2.00")
cmd.alter("elem Bk", "vdw=2.00")
cmd.alter("elem Be", "vdw=2.00")
cmd.alter("elem Bi", "vdw=2.00")
cmd.alter("elem Bh", "vdw=2.00")
cmd.alter("elem B ", "vdw=2.00")
cmd.alter("elem Br", "vdw=1.85")
cmd.alter("elem Cd", "vdw=1.58")
cmd.alter("elem Cs", "vdw=2.00")
cmd.alter("elem Ca", "vdw=2.00")
cmd.alter("elem Cf", "vdw=2.00")
cmd.alter("elem C ", "vdw=1.70")
cmd.alter("elem Ce", "vdw=2.00")
cmd.alter("elem Cl", "vdw=1.75")
cmd.alter("elem Cr", "vdw=2.00")
cmd.alter("elem Co", "vdw=2.00")
cmd.alter("elem Cu", "vdw=1.40")
cmd.alter("elem Cm", "vdw=2.00")
cmd.alter("elem Ds", "vdw=2.00")
cmd.alter("elem Db", "vdw=2.00")
cmd.alter("elem Dy", "vdw=2.00")
cmd.alter("elem Es", "vdw=2.00")
cmd.alter("elem Er", "vdw=2.00")
cmd.alter("elem Eu", "vdw=2.00")
cmd.alter("elem Fm", "vdw=2.00")
cmd.alter("elem F ", "vdw=1.47")
cmd.alter("elem Fr", "vdw=2.00")
cmd.alter("elem Gd", "vdw=2.00")
cmd.alter("elem Ga", "vdw=1.87")
cmd.alter("elem Ge", "vdw=2.00")
cmd.alter("elem Au", "vdw=1.66")
cmd.alter("elem Hf", "vdw=2.00")
cmd.alter("elem Hs", "vdw=2.00")
cmd.alter("elem He", "vdw=1.40")
cmd.alter("elem Ho", "vdw=2.00")
cmd.alter("elem In", "vdw=1.93")
cmd.alter("elem I ", "vdw=1.98")
cmd.alter("elem Ir", "vdw=2.00")
cmd.alter("elem Fe", "vdw=2.00")
cmd.alter("elem Kr", "vdw=2.02")
cmd.alter("elem La", "vdw=2.00")
cmd.alter("elem Lr", "vdw=2.00")
cmd.alter("elem Pb", "vdw=2.02")
cmd.alter("elem Li", "vdw=1.82")
cmd.alter("elem Lu", "vdw=2.00")
cmd.alter("elem Mg", "vdw=1.73")
cmd.alter("elem Mn", "vdw=2.00")
cmd.alter("elem Mt", "vdw=2.00")
cmd.alter("elem Md", "vdw=2.00")
cmd.alter("elem Hg", "vdw=1.55")
cmd.alter("elem Mo", "vdw=2.00")
cmd.alter("elem Nd", "vdw=2.00")
cmd.alter("elem Ne", "vdw=1.54")
cmd.alter("elem Np", "vdw=2.00")
cmd.alter("elem Ni", "vdw=1.63")
cmd.alter("elem Nb", "vdw=2.00")
cmd.alter("elem N ", "vdw=1.55")
cmd.alter("elem No", "vdw=2.00")
cmd.alter("elem Os", "vdw=2.00")
cmd.alter("elem O ", "vdw=1.52")
cmd.alter("elem Pd", "vdw=1.63")
cmd.alter("elem P ", "vdw=1.80")
cmd.alter("elem Pt", "vdw=1.72")
cmd.alter("elem Pu", "vdw=2.00")
cmd.alter("elem Po", "vdw=2.00")
cmd.alter("elem K ", "vdw=2.75")
cmd.alter("elem Pr", "vdw=2.00")
cmd.alter("elem Pm", "vdw=2.00")
cmd.alter("elem Pa", "vdw=2.00")
cmd.alter("elem Ra", "vdw=2.00")
cmd.alter("elem Rn", "vdw=2.00")
cmd.alter("elem Re", "vdw=2.00")
cmd.alter("elem Rh", "vdw=2.00")
cmd.alter("elem Rb", "vdw=2.00")
cmd.alter("elem Ru", "vdw=2.00")
cmd.alter("elem Rf", "vdw=2.00")
cmd.alter("elem Sm", "vdw=2.00")
cmd.alter("elem Sc", "vdw=2.00")
cmd.alter("elem Sg", "vdw=2.00")
cmd.alter("elem Se", "vdw=1.90")
cmd.alter("elem Si", "vdw=2.10")
cmd.alter("elem Ag", "vdw=1.72")
cmd.alter("elem Na", "vdw=2.27")
cmd.alter("elem Sr", "vdw=2.00")
cmd.alter("elem S ", "vdw=1.80")
cmd.alter("elem Ta", "vdw=2.00")
cmd.alter("elem Tc", "vdw=2.00")
cmd.alter("elem Te", "vdw=2.06")
cmd.alter("elem Tb", "vdw=2.00")
cmd.alter("elem Tl", "vdw=1.96")
cmd.alter("elem Th", "vdw=2.00")
cmd.alter("elem Tm", "vdw=2.00")
cmd.alter("elem Sn", "vdw=2.17")
cmd.alter("elem Ti", "vdw=2.00")
cmd.alter("elem W ", "vdw=2.00")
cmd.alter("elem U ", "vdw=1.86")
cmd.alter("elem V ", "vdw=2.00")
cmd.alter("elem Xe", "vdw=2.16")
cmd.alter("elem Yb", "vdw=2.00")
cmd.alter("elem Y ", "vdw=2.00")
cmd.alter("elem Zn", "vdw=1.39")
cmd.alter("elem Zr", "vdw=2.00")
cmd.rebuild()

# workspace settings
cmd.bg_color("white")
cmd.set("ray_opaque_background", "off")
cmd.set("orthoscopic", 0)
cmd.set("transparency", 0.5)
cmd.set("dash_gap", 0)
cmd.set("ray_trace_mode", 1)
cmd.set("ray_texture", 2)
cmd.set("antialias", 3)
cmd.set("ambient", 0.5)
cmd.set("spec_count", 5)
cmd.set("shininess", 50)
cmd.set("specular", 1)
cmd.set("reflect", .1)
cmd.space("cmyk")

# defines BallnStick settings
def BallnStick( arg1 ):
    cmd.show("sticks", arg1)
    cmd.show("spheres", arg1)
    cmd.color("gray85","elem C and "+arg1)
    cmd.color("gray98","elem H and "+arg1)
    cmd.color("slate","elem N and "+arg1)
    cmd.set("stick_radius",0.07, arg1)
    cmd.set("sphere_scale",0.18, arg1)
    cmd.set("sphere_scale",0.13, arg1+" and elem H")
    cmd.set("dash_gap",0.01, arg1)
    cmd.set("dash_radius",0.07, arg1)
    cmd.set("stick_color","black", arg1)
    cmd.set("dash_gap",0.01)
    cmd.set("dash_radius",0.035)
    cmd.hide("nonbonded", arg1)
    cmd.hide("lines", arg1)
    cmd.zoom(arg1)
    cmd.hide("labels")

# defines VDW Sphere settings
def Add_VDW( arg1 ):
    cmd.copy(arg1+"_vdw", arg1)
    cmd.set("sphere_scale",1.0, arg1+"_vdw and elem H")
    cmd.rebuild()
    cmd.set("sphere_scale", 1, arg1+"_vdw")
    cmd.hide("nonbonded", arg1+"_vdw")
    cmd.hide("lines", arg1+"_vdw")
    cmd.hide("sticks", arg1+"_vdw")
    cmd.set("sphere_transparency", 0.7, arg1+"_vdw")

cmd.extend( "BallnStick", BallnStick );
cmd.extend( "Add_VDW", Add_VDW );

Use Pymol to prepare publication quality images of small molecules:

In Pymol execute the script: 'run pymol_style.py'

To display an object (e.g. asp) in ball-and-stick format: BallnStick asp or BallnStick all

To display van der Waals surface: Add_VDW asp