# Send Molecular 3D Renderer to your agent
Hand the extracted package to your coding agent with a concrete install brief instead of figuring it out manually.
## Fast path
- Download the package from Yavira.
- Extract it into a folder your agent can access.
- Paste one of the prompts below and point your agent at the extracted folder.
## Suggested prompts
### New install

```text
I downloaded a skill package from Yavira. Read SKILL.md from the extracted folder and install it by following the included instructions. Tell me what you changed and call out any manual steps you could not complete.
```
### Upgrade existing

```text
I downloaded an updated skill package from Yavira. Read SKILL.md from the extracted folder, compare it with my current installation, and upgrade it while preserving any custom configuration unless the package docs explicitly say otherwise. Summarize what changed and any follow-up checks I should run.
```
## Machine-readable fields
```json
{
  "schemaVersion": "1.0",
  "item": {
    "slug": "mol-render",
    "name": "Molecular 3D Renderer",
    "source": "tencent",
    "type": "skill",
    "category": "AI 智能",
    "sourceUrl": "https://clawhub.ai/Zhao-Zehua/mol-render",
    "canonicalUrl": "https://clawhub.ai/Zhao-Zehua/mol-render",
    "targetPlatform": "OpenClaw"
  },
  "install": {
    "downloadUrl": "/downloads/mol-render",
    "sourceDownloadUrl": "https://wry-manatee-359.convex.site/api/v1/download?slug=mol-render",
    "sourcePlatform": "tencent",
    "targetPlatform": "OpenClaw",
    "packageFormat": "ZIP package",
    "primaryDoc": "SKILL.md",
    "includedAssets": [
      "SKILL.md",
      "scripts/pdb_to_3d.py",
      "scripts/smiles_to_3d.py"
    ],
    "downloadMode": "redirect",
    "sourceHealth": {
      "source": "tencent",
      "slug": "mol-render",
      "status": "healthy",
      "reason": "direct_download_ok",
      "recommendedAction": "download",
      "checkedAt": "2026-05-02T12:00:40.212Z",
      "expiresAt": "2026-05-09T12:00:40.212Z",
      "httpStatus": 200,
      "finalUrl": "https://wry-manatee-359.convex.site/api/v1/download?slug=mol-render",
      "contentType": "application/zip",
      "probeMethod": "head",
      "details": {
        "probeUrl": "https://wry-manatee-359.convex.site/api/v1/download?slug=mol-render",
        "contentDisposition": "attachment; filename=\"mol-render-1.0.0.zip\"",
        "redirectLocation": null,
        "bodySnippet": null,
        "slug": "mol-render"
      },
      "scope": "item",
      "summary": "Item download looks usable.",
      "detail": "Yavira can redirect you to the upstream package for this item.",
      "primaryActionLabel": "Download for OpenClaw",
      "primaryActionHref": "/downloads/mol-render"
    },
    "validation": {
      "installChecklist": [
        "Use the Yavira download entry.",
        "Review SKILL.md after the package is downloaded.",
        "Confirm the extracted package contains the expected setup assets."
      ],
      "postInstallChecks": [
        "Confirm the extracted package includes the expected docs or setup files.",
        "Validate the skill or prompts are available in your target agent workspace.",
        "Capture any manual follow-up steps the agent could not complete."
      ]
    }
  },
  "links": {
    "detailUrl": "https://openagent3.xyz/skills/mol-render",
    "downloadUrl": "https://openagent3.xyz/downloads/mol-render",
    "agentUrl": "https://openagent3.xyz/skills/mol-render/agent",
    "manifestUrl": "https://openagent3.xyz/skills/mol-render/agent.json",
    "briefUrl": "https://openagent3.xyz/skills/mol-render/agent.md"
  }
}
```
## Documentation

### mol-render

Generate high-quality 3D ball-and-stick model PNG images from SMILES strings or PDB structures, rendered with POV-Ray ray tracing.

### Dependencies

Required:

rdkit — SMILES parsing & 3D conformer generation
numpy — coordinate transforms
povray — ray tracing renderer

Optional (PDB mode only):

biopython — PDB file parsing

Install:

pip install rdkit numpy
apt-get install -y povray

# For PDB support:
pip install biopython

### SMILES Mode

python3 scripts/smiles_to_3d.py "SMILES" -o output.png

Arguments:

SMILES — (positional) SMILES string (required)
-o, --output — output PNG path (default: molecule.png)
--bg — background color: black / white / blue (default: blue)
--no-hydrogen — hide hydrogen atoms
--kekulize — convert aromatic bonds to alternating single/double bonds

Examples:

# Ethanol
python3 scripts/smiles_to_3d.py "CCO" -o ethanol.png

# Benzene (white background, Kekulé style)
python3 scripts/smiles_to_3d.py "c1ccccc1" -o benzene.png --bg white --kekulize

# Caffeine
python3 scripts/smiles_to_3d.py "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" -o caffeine.png

# Aspirin (no hydrogens)
python3 scripts/smiles_to_3d.py "CC(=O)OC1=CC=CC=C1C(=O)O" -o aspirin.png --no-hydrogen

### PDB Mode

python3 scripts/pdb_to_3d.py --pdb <PDB_ID_or_file> -o output.png

Arguments:

--pdb — PDB file path or 4-character PDB ID (auto-downloads from RCSB) (required)
-o, --output — output PNG path (default: pdb_molecule.png)
--chain — select specific chain (e.g., A)
--residues — residue range (e.g., 1-50 or 10,20,30-40)
--ligand-only — render only ligands (HETATM, excluding water)
--no-hydrogen — hide hydrogen atoms
--no-water / --keep-water — filter/keep water molecules (default: filter)
--bg — background color: black / white / blue (default: blue)
--view — viewing angle: auto / side / top / front or θ,φ in degrees (default: auto)
--resolution — resolution multiplier, e.g., 0.5 for half, 2.0 for double (default: 1.0)
--sphere-scale — override sphere scale factor (default: auto)
--bond-radius — override bond radius (default: auto)

Examples:

# Download and render G-quadruplex from RCSB
python3 scripts/pdb_to_3d.py --pdb 1KF1 --no-hydrogen -o g4.png

# Side view
python3 scripts/pdb_to_3d.py --pdb 1KF1 --no-hydrogen --view side -o g4_side.png

# Ligands only
python3 scripts/pdb_to_3d.py --pdb 1KF1 --ligand-only -o ligands.png

# Specific chain and residues
python3 scripts/pdb_to_3d.py --pdb 1KF1 --chain A --residues 1-12 -o partial.png

# Local PDB file
python3 scripts/pdb_to_3d.py --pdb structure.pdb -o out.png

# Large protein at lower resolution
python3 scripts/pdb_to_3d.py --pdb 2HYY --no-hydrogen --resolution 0.5 -o protein.png

### Output

1200×1200 PNG with POV-Ray ray tracing
CPK color scheme (C=dark gray, O=red, N=blue, H=white, P=orange, S=yellow, K=purple, ...)
Aromatic bonds rendered as solid + dashed lines (SMILES mode)
Double bonds rendered as two parallel solid lines
--kekulize option converts aromatic bonds to alternating single/double
Metal ions displayed with ionic radius (large spheres), no coordination bonds drawn
Auto-selects best viewing angle (PCA-based)
Auto-scales sphere/bond sizes for large molecules
Water molecules filtered by default (PDB mode)

### Known Limitations

Very large molecules (>2000 atoms) may be slow to render (use --resolution 0.5)
PDB mode renders all bonds as single bonds (no double/aromatic distinction)
Metal coordination bonds are not rendered
POV-Ray must be installed (which povray)
biopython required only for PDB mode (optional dependency)

### License

MIT
## Trust
- Source: tencent
- Verification: Indexed source record
- Publisher: Zhao-Zehua
- Version: 1.0.0
## Source health
- Status: healthy
- Item download looks usable.
- Yavira can redirect you to the upstream package for this item.
- Health scope: item
- Reason: direct_download_ok
- Checked at: 2026-05-02T12:00:40.212Z
- Expires at: 2026-05-09T12:00:40.212Z
- Recommended action: Download for OpenClaw
## Links
- [Detail page](https://openagent3.xyz/skills/mol-render)
- [Send to Agent page](https://openagent3.xyz/skills/mol-render/agent)
- [JSON manifest](https://openagent3.xyz/skills/mol-render/agent.json)
- [Markdown brief](https://openagent3.xyz/skills/mol-render/agent.md)
- [Download page](https://openagent3.xyz/downloads/mol-render)