How to Make Publication-Quality Figures in PyMOL: Ray Tracing, Resolution and Journal Requirements

Ray tracing — why it matters and how to use it

The default PyMOL display uses OpenGL rendering — fast, interactive, but not publication quality. Ray tracing is a physically accurate lighting simulation that traces individual light rays through the scene, producing smooth surfaces, realistic shadows, and proper depth cues. The difference between a standard screenshot and a ray-traced image at the same resolution is dramatic.

# Basic ray trace at viewer resolution
ray

# Ray trace at specific pixel dimensions
ray 1200, 900

# Ray trace and export in one command
png figure1a.png, width=1200, height=900, dpi=300, ray=1

# Ray trace mode (1 = production quality, 0 = fast preview)
set ray_trace_mode, 1    # standard photorealistic
set ray_trace_mode, 3    # outline mode (black outlines, good for diagrams)

Resolution and DPI — getting the numbers right

Most journal figure rejections due to image quality come from two mistakes: submitting screenshots instead of ray-traced renders, and not understanding that pixel count × DPI determines physical print size. The PyMOL ray command takes pixel dimensions — you need to calculate the right pixel count for your target print size.

Background color — white, black, or transparent

# White background — do this before every publication figure
bg_color white
set ray_opaque_background, 1    # ensures background is white, not transparent

# Transparent background (for Illustrator compositing)
bg_color white
set ray_opaque_background, 0
ray
png figure_transparent.png      # transparent PNG — no background

# Presentation / dark theme (not for journals)
bg_color black

Lighting and shadows

PyMOL’s default lighting is acceptable for interactive use but looks flat in publication figures. Four settings control the majority of the lighting character:

# Publication-standard lighting
set ambient,     0.40
set specular,    0.25
set light_count, 4
set ray_shadow,  1

# For a softer, more diffuse look (good for surfaces)
set ambient,     0.50
set specular,    0.15
set light_count, 6

# For dramatic depth (talks, covers)
set ambient,     0.25
set specular,    0.40
set light_count, 2
set ray_shadow,  1

Cartoon settings for publication

# Rounded helices (publication standard — enable first)
set cartoon_fancy_helices,   1

# Smooth loops between secondary structure elements
set cartoon_smooth_loops,    1

# Tube radius for coil/loop regions
set cartoon_tube_radius,     0.4   # default 0.5 — thinner looks cleaner

# Anti-aliasing for smoother edges
set antialias,               2     # range 1–4; 2 is best quality/speed balance

# Higher surface quality if surface is in the figure
set surface_quality,         2     # default 0; use 1 or 2 for publication

Saving as PNG and TIFF

# PNG export — most common, works for all journals
ray 1200, 900
png figure1a.png, dpi=300

# Combine ray + export in one command (cleaner scripts)
png figure1a.png, width=1200, height=900, dpi=300, ray=1

# TIFF export — required by some journals (Nature, Cell)
# PyMOL doesn't export TIFF natively — export PNG first,
# then convert with ImageMagick (free, command line):
# convert figure1a.png -compress LZW figure1a.tif

# Check DPI of the exported file (ImageMagick)
# identify -verbose figure1a.png | grep Resolution

The master figure script

Save every publication figure as a reusable .pml script. This makes it trivial to regenerate a figure after reviewer requests, adjust colors for revision, or create a panel set with consistent settings. Here is a complete template:

# ── Load and prepare ──────────────────────────────
fetch 4XYZ
as cartoon
hide everything, resn HOH

# ── Color scheme ──────────────────────────────────
util.cbc                         # color by chain
color slate, chain A             # override specific chains
color salmon, chain B
show sticks, resi 273 and chain A  # active site residue
color red, resi 273 and chain A

# ── Cartoon quality ───────────────────────────────
set cartoon_fancy_helices, 1
set cartoon_smooth_loops, 1
set cartoon_tube_radius, 0.4

# ── Background ────────────────────────────────────
bg_color white
set ray_opaque_background, 1

# ── Lighting ──────────────────────────────────────
set ambient, 0.40
set specular, 0.25
set light_count, 4
set ray_shadow, 1
set antialias, 2

# ── View (paste get_view output here) ─────────────
set_view (\
    0.92, -0.21,  0.32,\
   -0.18,  0.45,  0.87,\
   -0.35, -0.87,  0.35,\
    0.00,  0.00, -85.0,\
   12.50,  8.30, 10.20,\
   65.00, 105.0, -20.0)

# ── Render and export ─────────────────────────────
png figure1a.png, width=1200, height=900, dpi=300, ray=1

Journal requirements

Pre-submission checklist

• White background set — bg_color white and set ray_opaque_background, 1
• Fancy helices enabled — set cartoon_fancy_helices, 1
• Smooth loops enabled — set cartoon_smooth_loops, 1
• Lighting adjusted — ambient 0.35–0.45, specular 0.2–0.35, light_count 4
• Anti-aliasing set — set antialias, 2
• Ray traced at correct pixel dimensions for target figure size and DPI
• DPI specified in png export — png filename.png, dpi=300
• Format matches journal requirements (PNG, TIFF, or EPS as needed)
• Session saved as .pse for later revisions
• .pml script saved — figure can be regenerated from scratch