PymolBLOCK
Overview
From the repository's own README, as read at the audited commit. Badges and raw HTML are left out.
PyMOL-MCP connects PyMOL to Claude AI through the Model Context Protocol (MCP), enabling Claude to directly interact with and control PyMOL. This powerful integration allows for conversational structural biology, molecular visualization, and analysis through natural language.
https://github.com/user-attachments/assets/687f43dc-d45e-477e-ac2b-7438e175cb36
Features
- Two-way communication: Connect Claude AI to PyMOL through a socket-based server
- Intelligent command parsing: Natural language processing for PyMOL commands
- Molecular visualization control: Manipulate representations, colors, and views
- Structural analysis: Perform measurements, alignments, and other analyses
- Code execution: Run arbitrary Python code in PyMOL from Claude
Installation Guide
Prerequisites
- PyMOL installed on your system
- Claude for Desktop
- Python 3.10 or newer
- Git
Step 1: Install the UV Package Manager
On macOS:
brew install uv
On Windows:
powershell -c "irm https://astral.sh/uv/install.ps1 | iex" set Path=C:\Users\[YourUsername]\.local\bin;%Path%
For other platforms, visit the UV installation guide.
Step 2: Clone the Repository
git clone https://github.com/vrtejus/pymol-mcp cd pymol-mcp
Step 3: Set Up the Environment
Create and activate a Python virtual environment:
python -m venv venv
On macOS/Linux:
source venv/bin/activate
On Windows:
venv\Scripts\activate
Step 4: Install Dependencies
With the virtual environment activated:
pip install mcp
Step 5: Configure Claude Desktop
- Open Claude Desktop
- Go to Claude > Settings > Developer > Edit Config
- This will open the
claude_desktop_config.jsonfile - Add the MCP server configuration:
{
"mcpServers": {
"pymol": {
"comman1f4675d87ae3OBSERVED · 2026-10-07Connect
Built from this server's own package name, version and transport as found in its source — not copied from anyone's documentation, so it cannot drift against a page we do not control.
claude mcp add mcp-rosetta -- uvx mcp-rosetta
{
"mcpServers": {
"mcp-rosetta": {
"command": "uvx",
"args": [
"mcp-rosetta"
]
}
}
}Exposed tools (1)
0 read · 1 write · 0 destructive.
| Tool | Risk | Description |
|---|---|---|
parse_and_execute | write |
Trust audit
BLOCKgrade D · trust 69/100 Do not install this without reading the findings. The audit found something that could harm you or your machine.
| Layer | What it checks | Result |
|---|---|---|
| L0 | Provenance & inventory | WARN |
| L1 | Static analysis of the code | FAIL |
| L2 | Instruction surface (what it tells the agent) | PASS |
| L3 | Class-specific surface | PASS |
| L4 | Behavioural (sandbox) | SKIPPED |
What the source does
- Filesystem
- none-observed
- Network
- none-observed
- Shell
- declared (1 observation(s))
- Dependencies
- pinned
- Secrets in source
- none-found
Findings (5)
exec(code, exec_globals)
.DS_Store
.DS_Store
.DS_Store
.DS_Store
Gates applied: no_behavioural_pass.
1f4675d87ae3full audit observations/trust-audit/mcp-server/vrtejus__pymol.json · Report an issue / request a re-scanAudit history
Every audit this server has had. A grade with a past is a grade somebody is still checking.
| Date | Source | Verdict | Grade | Score | Change |
|---|---|---|---|---|---|
| 2026-10-07 | 1f4675d87ae3 | BLOCK | D | 69 | first audit |
Questions
What tools does Pymol expose?
1 in total: 0 read-only, 1 that write, and 0 that can delete or overwrite. Every one is listed on this page with its risk.
Is Pymol safe to connect to an agent?
No — not without reading the findings first. The audit graded it D (69/100) and found 1 critical or high issue in the source. Each one is listed on this page with the file and line it is on.
What credentials does Pymol need?
No credential environment variables were found in its source, so it appears to need none.
How current is this page?
The grade is for one exact copy of the source (1f4675d87ae3), read on 2026-10-07. The repository is watched and re-audited when it changes.