Pymol Visualization

PyMOL Visualization Skill

Generate publication-quality molecular structure images using PyMOL.

Prerequisites

PyMOL must be installed. Check with:

pymol -c -q -e "print('ok')" 2>/dev/null && echo "PyMOL available" || echo "PyMOL not found"

If missing: conda install -c conda-forge pymol-open-source.

Workflow

1. Ask the User

Before writing any script, clarify:

• Structure: PDB ID, uploaded file path, or AlphaFold model?
• Goal: What does the figure show? (e.g. protein overview, binding site, PPI interface, active site, mutation, surface, alignment)
• Style preference: Any preferred colors or theme? Journal figure vs. presentation vs. artistic?

2. Write a .pml Script and Run It

pymol -c -q script.pml

-c = no GUI (headless), -q = quiet. For Python API logic, use pymol -c -q -r script.py.

3. Read the Reference Before Writing

Read references/recipes.md before writing — it contains scene-specific recipes and essential PyMOL commands organized by visualization goal.

4. Deliver Output

Always deliver three files:

1. PNG image — the rendered figure
2. PML script — so the user can reproduce or tweak
3. PSE session — so the user can open in PyMOL GUI and adjust interactively

Save all to user's desktop and use present_files.

Script Template

Every script should follow this structure:

reinitialize

# --- Load ---
fetch 4HHB, async=0
# or: load /path/to/structure.pdb, myprotein

# --- Clean ---
remove solvent
remove elem H
set valence, 0

# --- Base look ---
bg_color white
space cmyk
set ray_shadow, 0
set ray_trace_mode, 1
set antialias, 3
set ambient, 0.5
set spec_count, 5
set shininess, 50
set specular, 1
set reflect, 0.1
set orthoscopic, on
set opaque_background, off
set cartoon_oval_length, 1
set cartoon_rect_length, 1
set cartoon_discrete_colors, on
dss

# --- Representation (scene-specific) ---
hide everything
show cartoon
# ...

# --- Color ---
util.color_chains("(all) and elem C", _self=cmd)
util.cnc("all", _self=cmd)

# --- Camera ---
orient
# zoom sele, 8

# --- Save session BEFORE ray tracing ---
save /mnt/user-data/outputs/structure.pse

# --- Render ---
ray 2400, 1800
png /mnt/user-data/outputs/structure.png, dpi=150
quit

Essential Patterns

Show sidechains cleanly:

cmd.show("sticks", "((byres (sele)) & (sc. | (n. CA) | (n. N & r. PRO)))")

Molecule-agnostic coloring:

util.color_chains("(sele) and elem C", _self=cmd)
util.cnc("sele", _self=cmd)

Surface + cartoon as separate objects:

create surf_obj, sele, zoom=0
show surface, surf_obj
set transparency, 0.5, surf_obj
cmd.color_deep("white", "surf_obj", 0)

Ball-and-stick for ligands:

show sticks, ligand
show spheres, ligand
set sphere_scale, 0.25, ligand
set stick_radius, 0.15, ligand

Goodsell style (flat, illustrative):

set ray_trace_mode, 3
set ray_trace_color, black
unset specular
set ray_trace_gain, 0
unset depth_cue
set ambient, 1.0
set direct, 0.0
set reflect, 0.0

Key Rules

1. Always space cmyk for print colors
2. Always remove elem H unless user needs hydrogens
3. Always save .pse before ray tracing — this is the user's editable session
4. set valence, 0 unless showing ligand bond orders
5. Create separate objects for surface overlays (transparency is per-object)
6. Use async=0 with fetch — otherwise structure isn't loaded when next command runs
7. End script with quit — otherwise PyMOL hangs in batch mode
8. Render large (1200x900+) — downscale later for quality