# Gaussian Molecular Box

> Export a Multiwfn molecular box PDB and render its length, width, and height as a PNG from Gaussian formatted checkpoint (.fch) files. Use for Gaussian FCH molecular dimensions and box visualization.

- **Type:** Skill
- **Install:** `agentstack add skill-nanhuai-x-gaussian-molecule-workflow-gaussian-molecular-box`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [Nanhuai-X](https://agentstack.voostack.com/s/nanhuai-x)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [Nanhuai-X](https://github.com/Nanhuai-X)
- **Source:** https://github.com/Nanhuai-X/gaussian-molecule-workflow/tree/main/skills/gaussian-molecular-box

## Install

```sh
agentstack add skill-nanhuai-x-gaussian-molecule-workflow-gaussian-molecular-box
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# Gaussian molecular box and dimensions

Use this skill when a Gaussian `.fch` file needs a PDB with box dimensions and a molecular-box image.

## Preconditions

- Inputs are `fch/.fch`; results go to `output//`.
- Resolve Multiwfn from `MULTIWFN_BIN`, then `PATH`, then a user-provided installation path.
- Python 3, NumPy, and Matplotlib are required for rendering `_BOX.png`.

## Isolated workflow

Run the bundled exporter from the analysis folder:

```powershell
python /scripts/run_box.py --input fch --output output
```

The bundled renderer and Multiwfn input template are self-contained.

1. Create an isolated working directory for exactly one molecule; do not allow a root-level or prior molecule's `new.pdb` to satisfy the run.
2. Run Multiwfn's molecular-box/PDB sequence and verify that a new `new.pdb` was generated in that isolated directory. Stop on a non-zero exit or a missing new file; never suppress Multiwfn failures. A known Multiwfn 3.8 Windows EOF return after the `Exporting new.pdb file finished!` marker is accepted only when the PDB is present and its `CRYST1` record is valid.
3. Copy the verified file into `output//new.pdb` and `output//.pdb`.
4. Read the `CRYST1` record in `.pdb` for X/Y/Z dimensions, save `_box_dimensions.txt`, and render an atom-plus-wireframe figure as `_BOX.png` with NumPy and Matplotlib.
5. Verify both PDB files and the PNG are readable, then report the three dimensions with their units.

## Meaning of dimensions

The PDB `CRYST1` box is the output of this skill. Electron-density-isosurface dimensions are a separate, optional quantity and should be generated and labelled through `$gaussian-esp-vmd`; never present the two definitions as interchangeable.

## Failure handling

- Missing NumPy or Matplotlib: retain the valid PDB outputs and report that only the PNG stage is unavailable.
- Missing `CRYST1`: stop before plotting and preserve the Multiwfn log for diagnosis.
- Preserve outputs unless overwrite was explicitly approved; use quiet per-molecule logs and a final summary. The box dimensions are distinct from the ESP isosurface dimensions.

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [Nanhuai-X](https://github.com/Nanhuai-X)
- **Source:** [Nanhuai-X/gaussian-molecule-workflow](https://github.com/Nanhuai-X/gaussian-molecule-workflow)
- **License:** MIT

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-nanhuai-x-gaussian-molecule-workflow-gaussian-molecular-box
- Seller: https://agentstack.voostack.com/s/nanhuai-x
- Browse the marketplace: https://agentstack.voostack.com/browse

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