Create high quality PyMOL visualizations

pymol_style.py

# Originally created by: Rob Paton
# https://gist.github.com/bobbypaton/1cdc4784f3fc8374467bae5eb410edef
# Modified by: Kate Fieseler

# 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
from pymol import util

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

for element, vdw in bondi_vdw.items():
    cmd.alter(f"elem {element}", f"vdw={vdw:.2f}")

cmd.rebuild()

# GitHub: matteoferla color palette
color_palette = {
    'turquoise': [0.18823529411764706, 0.8352941176470589, 0.7843137254901961],
    'coral': [1.0, 0.4980392156862745, 0.3137254901960784],
    'teal': [0.0, 0.5019607843137255, 0.5019607843137255],
    'sage': [0.6980392156862745, 0.6745098039215687, 0.5333333333333333],
    'lavender': [0.9019607843137255, 0.9019607843137255, 0.9803921568627451],
    'mustard': [1.0, 0.8588235294117647, 0.34509803921568627],
    'aquamarine': [0.4980392156862745, 1.0, 0.8313725490196079],
    'feijoa': [0.6470588235294118, 0.8431372549019608, 0.5215686274509804],
    'rose': [1.0, 0.0, 0.4980392156862745],
    'paleturquoise': [0.6862745098039216, 0.9333333333333333, 0.9333333333333333],
    'lightcoral': [0.9411764705882353, 0.5019607843137255, 0.5019607843137255],
    'lightpurple': [0.8117647058823529, 0.6235294117647059, 1.0],
    'lightblue': [0.5294117647058824, 0.807843137254902, 0.9803921568627451],
    'lightgreen': [0.5647058823529412, 0.9333333333333333, 0.5647058823529412],
    'lightyellow': [1.0, 1.0, 0.8784313725490196],
    'lightorange': [1.0, 0.6274509803921569, 0.47843137254901963],
    'lightpink': [1.0, 0.7137254901960784, 0.7568627450980392],
    'robinsegg': [0.0, 0.8, 0.8],
    'cerulean': [0.0, 0.4823529411764706, 0.6549019607843137],
    'periwinkle': [0.8, 0.8, 1.0]
}

for color_name, rgb in color_palette.items():
    cmd.set_color(color_name, rgb)

# Custom color palette
custom_colors = {
    'canary': [251/255, 248/255, 204/255],
    'orangecream': [253/255, 228/255, 207/255],
    'peach': [255/255, 207/255, 210/255],
    'lightpurple': [241/255, 192/255, 232/255],
    'purple': [207/255, 186/255, 240/255],
    'purpleblue': [163/255, 196/255, 243/255],
    'blue': [144/255, 219/255, 244/255],
    'lightblue': [142/255, 236/255, 245/255],
    'marine': [152/255, 245/255, 225/255],
    'green': [185/255, 251/255, 192/255]
}

for color_name, rgb in custom_colors.items():
    cmd.set_color(color_name, rgb)

# Defines BallnStick settings
def BallnStick(arg1):
    cmd.show("sticks", arg1)
    cmd.show("spheres", arg1)
    cmd.color("gray85", f"elem C and {arg1}")
    cmd.color("gray98", f"elem H and {arg1}")
    cmd.color("slate", f"elem N and {arg1}")
    cmd.set("stick_radius", 0.07, arg1)
    cmd.set("sphere_scale", 0.18, arg1)
    cmd.set("sphere_scale", 0.13, f"{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")

def BallnStickThick(arg1, color):
    cmd.show("licorice", arg1)
    cmd.show("spheres", arg1)
    cmd.unset("stick_color", arg1)
    util.cnc(arg1)
    cmd.color(color, f"elem C and {arg1}")
    cmd.color("slate", f"elem N and {arg1}")
    cmd.set("stick_radius", 0.17, arg1)
    cmd.set("sphere_scale", 0.18, arg1)
    cmd.set("dash_radius", 0.07, arg1)
    cmd.set("dash_gap", 0.05)
    cmd.set("dash_radius", 0.035)
    cmd.hide("nonbonded", arg1)
    cmd.hide("everything", f"{arg1} and elem H")
    cmd.zoom(arg1)

# Defines VDW Sphere settings
def Add_VDW(arg1):
    vdw_object = f"{arg1}_vdw"
    cmd.copy(vdw_object, arg1)
    cmd.set("sphere_scale", 1.0, f"{vdw_object} and elem H")
    cmd.rebuild()
    cmd.set("sphere_scale", 1, vdw_object)
    cmd.hide("nonbonded", vdw_object)
    cmd.hide("lines", vdw_object)
    cmd.hide("sticks", vdw_object)
    cmd.set("sphere_transparency", 0.7, vdw_object)

# Defines protein settings for binding site
def prettyProteinBindingSite(chain, binding_residues=None, ligand_resn=None):
    """
    Example:
        PyMOL> prettyProteinBindingSite chainB, binding, LIG
    """
    cmd.show("cartoon", chain)
    cmd.color("gray80", chain)

    if binding_residues:
        cmd.show("sticks", binding_residues)
        # hide nonpolar hydrogens on residues
        cmd.hide("everything", f"(hydro and {binding_residues} and (elem H and not (neighbor elem N+O)))")

    if ligand_resn:
        # Exclude the ligand based on its residue name
        cmd.color("gray80", f"elem C and {chain} and not resn {ligand_resn}")
    else:
        # If no ligand provided, color normally
        cmd.color("gray80", f"elem C and {chain}")
    
    cmd.hide("sticks", "backbone")

def setPretty():
    # 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("antialias", 3)
    cmd.set("ambient", 0.5)
    cmd.set("spec_count", 5)
    cmd.set("shininess", 50)
    cmd.set("specular", 1)
    cmd.set("reflect", 0.1)
    cmd.space("cmyk")

# Extend PyMOL commands
cmd.extend("prettyProteinBindingSite", prettyProteinBindingSite)
cmd.extend("setPretty", setPretty)
cmd.extend("BallnStick", BallnStick)
cmd.extend("BallnStickThick", BallnStickThick)
cmd.extend("Add_VDW", Add_VDW)

Default PyMOL:

With setPretty:

Transparency:

set cartoon_transparency, 0.0

set cartoon_transparency, 0.6

BallnStick Representations

BallnStick ligand Directly from Rob Paton's pymol_style.py !

BallnStickThick ligand, marine

BallnStickThick ligand, purpleblue

BallnStickThick ligand, orangecream

Lighting settings (in Plugin)

Rubber with ambient value increased

X-Ray with reflect = 1 and light_count = 1

Surface transparency
show surface, chainB
set transparency, 0.4

set transparency, 0.2

# https://pymolwiki.org/index.php/FocalBlur and get script!
run ~/pymol_focal_blur.py
FocalBlur

FocalBlur samples=20, aperture=2.0

FocalBlur samples=20, aperture=4.0