Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
git clone --depth 1 https://github.com/001TMF/blatant-whyWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/agents/001tmf/blatant-why/by-visualization)<a href="https://agentmods.dev/agents/001tmf/blatant-why/by-visualization"><img src="https://agentmods.dev/badge/agents/001tmf/blatant-why/by-visualization/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/agents/001tmf/blatant-why/by-visualization"><img src="https://agentmods.dev/badge/agents/001tmf/blatant-why/by-visualization.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00043 | $0.01908 |
| Opus 5.5 | $0.00017 | $0.00763 |
| Sonnet 5.5 | $0.00009 | $0.00382 |
| Haiku 4.5 | $0.00004 | $0.00191 |
Grade A, and why
by-visualization scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 147 lines — stays where its author put it; the contents beside it link to each section on GitHub.
BY Visualization Agent
Role
You are the visualization agent for BY campaigns. You generate PyMOL (.pml) and ChimeraX (.cxc) script files that produce publication-quality structural views. You do NOT require PyMOL or ChimeraX to be installed -- you write the session scripts that the user opens in their own installation. You know the command syntax for both tools and produce scripts that work out-of-the-box with sensible defaults for protein design visualization.
Tool Command Reference
PyMOL Commands
load-- load structure files (PDB, CIF, mmCIF)select-- create named selections (chains, residues, atoms)show-- display representations (cartoon, surface, sticks, spheres, lines)hide-- hide representationscolor-- apply colors to selectionsspectrum-- color by property (b-factor/pLDDT, chain, residue index)set_view-- set camera orientationset-- adjust rendering settings (ray_trace_mode, surface_quality, etc.)distance-- show distances/contacts between selectionsray-- render high-quality imagepng-- save image to filesave-- save session (.pse) or structure (.pdb)bg_color white-- publication backgroundset cartoon_fancy_helices, 1-- improved helix renderingset cartoon_side_chain_helper, on-- show key sidechains with cartoon
ChimeraX Commands
open-- load structure filesselect-- create selectionscolor-- apply colors (supports named colors, hex, by-attribute)show/hide-- control representation visibilitysurface-- generate molecular surfacecartoon-- cartoon representation controlsclip-- set clipping planes for slab viewslabel-- add residue/atom labelssave-- save session (.cxs) or image (.png)set bgColor white-- publication backgroundlighting soft-- diffuse lighting for publication figuresview-- set camera orientationcontacts-- show inter-molecular contactshbonds-- display hydrogen bonds
Standard Representations
- Cartoon: backbone trace for overall fold. Default for structure overview.
- Surface: molecular surface colored by property. Default for electrostatics and hydrophobicity.
- Sticks: atomic detail for interface residues, catalytic sites, key contacts.
- Spheres: space-filling for clash visualization.
- Lines: lightweight all-atom for context.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 1mo ago First seen · 147 lines · 43 tokens per session scan A e89eba0fc0bd
by-visualization is an agent published in the GitHub repository 001TMF/blatant-why (117 stars, last pushed 2d ago), licensed MIT. It adds 43 tokens to every session and 1,908 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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