Protein Struct Viz

Generate PyMOL scripts to highlight specific protein residues in PDB structures. Use this skill when the user needs to visualize specific amino acid residues...

This skill appears to do what it says (generate PyMOL scripts), but exercise caution before installing or running generated scripts. What to consider before using: - Do NOT run .pml files produced from untrusted inputs without inspection. The generator inserts user-provided residue specs directly into the script, so malicious text could inject PyMOL commands. - Restrict the output path: the tool writes the provided filename verbatim. Avoid running it with untrusted output paths and ensure the filename is normalized and confined to a safe workspace (prevent '../' escapes). - Validate inputs: only allow residue specs that match a safe pattern (example regex idea: ^(?:(?:[A-Za-z]|\*)?:)?\d{1,5}(?::[A-Z]{3})?$ with explicit handling of wildcards) and disallow characters like semicolons, newline, backticks, or other shell/command delimiters. Sanitize color names and style choices against allowed lists. - Review generated .pml before executing in PyMOL, and avoid executing scripts from unknown sources. Look for unexpected commands (e.g., system calls or file manipulation commands) inserted into the file. - Be aware that the generated scripts may include 'fetch <pdb_id>' which triggers network downloads when run inside PyMOL; if that is a privacy or network policy concern run PyMOL in an environment where network access is controlled. - If you plan to adopt this skill into automated workflows, either add input sanitization and path normalization to scripts/main.py or run the generator in a sandbox/VM and only transfer inspected outputs into production systems. If you want, I can provide a safe-sanitizing wrapper for this script (validate residue specs, restrict output path to workspace, and whitelist style/color inputs) or specific regex patterns and filename normalization code to reduce these risks.

Type: OpenClaw Skill Name: protein-struct-viz Version: 1.0.0 The protein-struct-viz skill is a legitimate bioinformatics tool designed to generate PyMOL visualization scripts (.pml). The core logic in scripts/main.py safely constructs PyMOL commands based on user-provided residue specifications and structural data, with no evidence of malicious intent, data exfiltration, or unauthorized execution. While the SKILL.md documentation self-identifies as 'High' risk due to the nature of script generation and network fetching of PDB files, these behaviors are standard for the stated purpose and are handled transparently.