PyMol Orbital Visualization

Notes for a Houk Group style molecular orbital visualization in PyMol

---

Gaussian .fchk to .cube

for i in {27,28,29};do cubegen 0 MO=$i {Name}.fchk {Name}-$i.cub -2 h;done

---

In PyMol

Build Isosurface

isosurface {desired-isosurface-name}-n, {filename.cube}, -0.02
isosurface {desired-isosurface-name}-p, {filename.cube}, +0.02

Transparency

set transparency, 0.2

From 0 to 1

Color Surface

Let’s go Houkie style

set surface_color, density, *n
set surface_color, forest, *p

Other Visualization Settings for structures

From Cooper

set valence, 0
hide everything
show sticks
show spheres
show labels
show dashes
set stick_radius, .07
set sphere_scale, .18
set sphere_scale, .13, elem H
set bg_rgb=[1, 1, 1]
set stick_quality, 50
set sphere_quality, 4
color gray85, elem C
color red, elem O
color slate, elem N
color gray98, elem H
set stick_color, black
set ray_trace_mode, 1
set ray_texture, 2
set antialias, 3
set ambient, 0.5
set spec_count, 5
set shininess, 50
set specular, 1
set reflect, .1
set dash_color, black
set dash_gap, .2
set dash_length, .1
set dash_round_ends, 0.1
set dash_radius, .05
set ray_trace_gain, 10
set stick_h_scale, 1
set ray_shadow, off
set label_size, 60
set label_distance_digits, 2
set orthoscopic, on

Combining Transparent Objects in Ray Trace

Use Setting->Transparency->Multi-layer
ref