pymol-academic-figures

PyMOL Academic Figures

Use PyMOL to make clean, reproducible molecular figures for papers, posters, talks, and reports. Prefer scripted .pml generation over manual GUI steps so figures can be regenerated after structure or style changes.

This skill is adapted for Codex from the PyMOL figure workflow in claudemol, with local command-line rendering added for this machine.

Local Environment

Use these commands directly:

pymol -cq figure.pml
claudemol --help

Known local paths:

C:\Users\dell\Downloads\PyMOL-3.1.6.1_appveyor2641-Win64-portable-py310\PyMOL\Scripts\pymol.exe
C:\Users\dell\Downloads\PyMOL-3.1.6.1_appveyor2641-Win64-portable-py310\PyMOL\pymol.cmd
C:\Users\dell\Downloads\PyMOL-3.1.6.1_appveyor2641-Win64-portable-py310\PyMOL\claudemol.cmd

For headless batch rendering, prefer:

python C:\Users\dell\.codex\skills\pymol-academic-figures\scripts\run_pymol_render.py --pml figure.pml --output figure.png

Workflow

1. Clarify the scientific message: binding site, conformational change, alignment, interaction network, surface property, mutation, epitope, or MD snapshot.
2. Identify the input: PDB ID, local .pdb/.cif, trajectory-derived snapshot, aligned structures, ligand/cofactor, or user-provided session.
3. Generate a .pml script with deterministic object names, selections, colors, camera, labels, image dimensions, and output path.
4. Render headlessly with run_pymol_render.py or pymol -cq.
5. Inspect the resulting PNG. Fix clipping, crowded labels, hidden ligand, low contrast, bad orientation, or excessive visual complexity.

Figure Standards

Default publication settings:

bg_color white
set ray_opaque_background, off
set antialias, 2
set ray_trace_mode, 1
set ray_shadows, off
set ambient, 0.35
set direct, 0.65
set spec_reflect, 0.15
set cartoon_fancy_helices, on
set cartoon_smooth_loops, on
set depth_cue, off
set orthoscopic, on

Use 2400 x 1800 for most single-panel figures. Use 3000 x 2400 or higher when labels or surfaces need extra room. Export transparent backgrounds only when the downstream layout needs it.