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Use when creating publication-quality molecular figures with proper styling, ray tracing, and export settings through PyMOL.
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Based on SOC occupation classification
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| name | publication-figures |
| description | Use when creating publication-quality molecular figures with proper styling, ray tracing, and export settings through PyMOL. |
| version | 0.1.0 |
Settings and workflows for creating journal-quality molecular visualizations.
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cmd.*code via:~/.pymol-agent-bridge/bin/pymol-agent-bridge exec "..."(or heredoc for multi-line). See @pymol-fundamentals for details.
cmd.bg_color("white")
cmd.set("ray_opaque_background", 1)
cmd.set("ray_opaque_background", 0)
cmd.bg_color("white") # For preview
# PNG will have transparent background
cmd.set("antialias", 2) # 0=off, 1=fast, 2=quality
# Clean, even lighting
cmd.set("direct", 0.5) # Direct light intensity
cmd.set("spec_reflect", 0.5) # Specular reflection
cmd.set("ambient", 0.4) # Ambient light
# For clean diagrams (no shadows)
cmd.set("ray_shadows", 0)
cmd.set("depth_cue", 0)
# For 3D effect (with shadows)
cmd.set("ray_shadows", 1)
cmd.set("ray_shadow_decay_factor", 0.1)
cmd.set("depth_cue", 1)
cmd.set("cartoon_fancy_helices", 1)
cmd.set("cartoon_smooth_loops", 1)
cmd.set("cartoon_flat_sheets", 1)
cmd.set("cartoon_cylindrical_helices", 1)
cmd.set("cartoon_tube_radius", 0.3)
cmd.set("cartoon_loop_radius", 0.3)
cmd.set("stick_radius", 0.15)
cmd.set("stick_ball", 1)
cmd.set("stick_ball_ratio", 1.5)
cmd.set("surface_quality", 1) # Higher = smoother
cmd.set("transparency", 0.5)
cmd.set("surface_color", "white")
cmd.viewport(1200, 900) # 4:3 aspect
cmd.viewport(1600, 900) # 16:9 aspect
| Use Case | Resolution | DPI |
|---|---|---|
| Web/slides | 1200x900 | 72-150 |
| Journal (1 col) | 1200x1200 | 300 |
| Journal (2 col) | 2400x1200 | 300 |
| Poster | 3000x2000 | 300 |
cmd.draw(1200, 900) # OpenGL render, fast
cmd.ray(1200, 900) # High quality, slower
cmd.set("ray_trace_mode", 1) # 0=normal, 1=color-only, 3=quantized
cmd.set("ray_trace_gain", 0.1) # Edge detection
# After ray tracing
cmd.ray(1200, 900)
cmd.png("/path/to/image.png", dpi=300)
# Without ray (faster, lower quality)
cmd.draw(1200, 900)
cmd.png("/path/to/image.png", dpi=150)
# Ray trace then save
cmd.ray(2400, 1800)
cmd.png("/path/to/figure.png", dpi=300)
cmd.scene("panel_A", "store", message="Overview")
cmd.scene("panel_B", "store", message="Active site")
cmd.scene("panel_C", "store", message="Close-up")
for panel in ["panel_A", "panel_B", "panel_C"]:
cmd.scene(panel, "recall")
cmd.ray(1200, 900)
cmd.png("/path/to/" + panel + ".png", dpi=300)
# 1. Load and style
cmd.fetch("1ubq")
cmd.show("cartoon")
cmd.hide("lines")
cmd.dss()
cmd.color("green", "ss h")
cmd.color("yellow", "ss s")
cmd.color("cyan", "ss l+")
# 2. Publication settings
cmd.bg_color("white")
cmd.set("ray_opaque_background", 1)
cmd.set("antialias", 2)
cmd.set("cartoon_fancy_helices", 1)
cmd.set("ray_shadows", 0)
cmd.set("depth_cue", 0)
# 3. View
cmd.orient()
cmd.zoom("all", 2)
# 4. Export
cmd.ray(2400, 1800)
cmd.png("/path/to/figure.png", dpi=300)
# Set up views
cmd.orient()
cmd.scene("overview", "store")
cmd.zoom("resi 45-50", 5)
cmd.scene("detail", "store")
# Export each
import os
output_dir = os.path.expanduser("~/Desktop")
for scene in ["overview", "detail"]:
cmd.scene(scene, "recall")
cmd.ray(1200, 900)
cmd.png(output_dir + "/" + scene + ".png", dpi=300)
# Blue/Orange (safe)
cmd.color("marine", "chain A")
cmd.color("orange", "chain B")
# Teal/Coral
cmd.color("teal", "chain A")
cmd.color("salmon", "chain B")
# Secondary structure
cmd.color("red", "ss h") # Helices
cmd.color("yellow", "ss s") # Sheets
cmd.color("green", "ss l+") # Loops
# By chain
cmd.do("util.cbc")
draw for previewscmd.remove("solvent") before making figures (removes water clutter)cmd.ray(w, h) then cmd.png(path) — never pass dimensions to cmd.png() (causes view corruption)cmd.set("specular", 0.2) for subtle shine without glare