Pymol Visualization

What it does

When your agent uses it

• The user mentions PyMOL
• Molecular visualization
• Protein rendering
• Structure figures

Example prompts

• “t mention”
• “/pymol-visualization”

Requirements

• Python 3

Workflow steps

4 steps, taken from the step headings in SKILL.md.

1. 1Ask the User
2. 2Write a .pml Script and Run It
3. 3Read the Reference Before Writing
4. 4Deliver Output

What it can do on your machine

Read from SKILL.md and the folder at commit d376ccd. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Shell commands in SKILL.md call:

  • conda

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  No URLs in SKILL.md.

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Pymol Visualization loads about 1.2k tokens when it runs, and up to ~2.8k if it reads all its reference files. Until then it costs about 233 tokens; SKILL.md has 274 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~233

When it runs · the whole SKILL.md, loaded when a task matches

~1.2k

With references · SKILL.md plus every file in references/, read only if the agent opens them

~2.8k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ChatMol/ChatMol at commit d376ccd, republished under its MIT licence (© ChatMol). 274 words, ~1,154 tokens.

name

pymol-visualization

description

Generate publication-quality molecular visualization images using PyMOL. Use this skill whenever the user mentions PyMOL, molecular visualization, protein rendering, structure figures, PDB visualization, ray tracing molecules, or wants to create images of proteins, ligands, binding sites, protein-protein interactions, or any biomolecular structure. Also trigger when the user wants to: make a figure of a crystal structure for a paper or presentation; render a protein surface; show binding pockets; visualize protein-ligand interactions; create Goodsell-style illustrations; produce cartoon representations with highlighted residues; compare multiple structures side by side; or generate any molecular graphics output — even if they don't mention "PyMOL" by name. Trigger for any request involving PDB files, molecular surfaces, cartoon ribbons, stick models, electron density, or structural biology figures.

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

pymol -c -q script.pml

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

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

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

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

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

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

© ChatMol, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 1 other file (references) in pymol_skill of ChatMol/ChatMol.

• SKILL.md
• references/recipes.md

Open the folder on GitHubat commit d376ccd