PyMOL POV-Ray ambient occlusion rendering

make_pov.py

# make_pov.py
#
# Original script written by Robert Campbell
# Modified by Tsjerk A. Wassenaar and Patrice Peterson

from os.path import splitext
from pymol import cmd

def make_pov(file, name="PymolObject", clip=False):
        f1, f2 = file, splitext(file)[0] + '.inc'

        # We don't use the original header but construct our own
        _, data = cmd.get_povray()
        with open(f1,'w') as povfile:
            # #version directive is mandatory since 3.7
            # Default settings are imported from an inlcude file
            povfile.write("""#version 3.7;
#include \"pymoldefaultsettings.inc\"
""")

            # Get PyMOL view
            povview = cmd.get_view()
    #           r11, r12, r13 - 3x3 Rotation matrix (model space to camera space)
    #           r21, r22, r23
    #           r31, r32, r33
    #           c1,  c2,  c3  - Vector from camera position to origin of rotation (camera space)
    #           o1,  o2,  o3  - Origin of rotation (model space)
    #           s1,  s2,  or  - Slab near and far, FOV flag

            # Light source
            # TODO:
            # - Lighting position and size
            povfile.write("""
// Weak highlight within the sky sphere
light_source {
    500
    // Light intensity depends on color brightness
    rgb .5
    // Cylindrical and spot lights can be area lights as well
    area_light 100*x, 100*y, 100, 100
    // Automatically adapt number of light sources
    adaptive 1
    // Add random positional noise to light source positions
    jitter
    // Use circular area light
    circular
    // Always normalize the light area with regard to the ray
    orient
}

// invisible pseudo-sky sphere
sphere {
    0, 1
    pigment {
        color rgb 1
    }
    finish {
        emission .5
    }
    // make sure the sphere is big enough to cover the entire scene
    scale 1000
    hollow
    // make sphere invisible for direct rays
    no_image
}
""")

            # Camera
            viewport_x, viewport_y = cmd.get_viewport()
            x_ratio = float(viewport_x)/viewport_y
            if povview[17] < 0:
                camtype = "perspective"
            else:
                camtype = "orthographic"
            povfile.write("""
camera {
    %s
    location <0.0, 0.0, 0.0>
    // original aspect ratio: w:h = %s:1
    // Account for left-right mirroring
    right -x*image_width/image_height
    up y
    angle %s
    look_at <0.0, 0.0, -1.0>
}
""" % (camtype, x_ratio, abs(povview[17])))

            # Finally, the molecule data itself
            if clip:
                    objtype = "difference"
                    objclip = ""
                    if clip in ["near","both"]:
                            objclip = objclip + "plane { z, -%f }" % povview[15]
                    if clip in ["far","both"]:
                            objclip = objclip + "plane { z, -%f }" % povview[16]
            else:
                    objtype = "object"
                    objclip = ""
            povfile.write("""
#declare %s = union { #include "%s" }
%s { %s %s }
""" % (name, f2, objtype, name, objclip ) )

        with open(f2,'w') as povfile:
            povfile.write(data)


cmd.extend('make_pov',make_pov)

pymoldefaultsettings.inc

// PyMOL default settings file
// automatically included by the make_pov script
global_settings {
    assumed_gamma 2.2
    adc_bailout 1/255
    charset utf8
    // 1 unit in coordinate system = 1 cm
    // To calculate SSLT for different materials
    mm_per_unit 10
    // Only with +q9 or higher
    subsurface {
        // Number of sample rays for diffuse (first value) and single
        // (second value) scattering
        // Lower values -> better performance
        samples 50, 50
        // Use subsurface scattering on radiosity photons
        radiosity on
    }

    radiosity {
        gray_threshold 0.0
        brightness 1
        // not smaller than 0.0039
        adc_bailout 0.005
        // not lower than 2 for isosurfaces, not bigger than 3
        recursion_limit 3
        // lowers error bound during pretrace, removes blotches (default 0.5)
        low_error_factor 0.5
        // Fraction of screen to follow bounced rays (default 0.015)
        // Too small → rendering gets slow; too high → no natural darkening
        // of crevices as rays get reused
        minimum_reuse 0.015
        maximum_reuse 0.2
        // Min and maxsize of block in mosaic preview during pretrace
        // default 0.08
        pretrace_start 0.08
        // not smaller than 0.02 (default 0.04)
        pretrace_end 0.04
        count 150
        // Max number of radiosity values to be blended together (default
        // 4, max 20)
        // Smaller than 4 → patchiness
        nearest_count 10
        // lower error bound → more artifacts (requires higher count), but
        // also higher quality
        error_bound 0.4
    }
}

// default texture
#default {
    finish {
        diffuse 0.6
        specular 0.7
        roughness 0.12
    }
}