dbcve.org
Code InjectionWeakness · CWE-94

CVE-2024-50636

CRITICAL · 9.8 CVSS v3.1 Published 2024-11-11
Mitigation only
No fix yet — a mitigation exists. There is no fixed release. A documented workaround reduces exposure in the meantime.
See remediation →
100/100
Remediation priority · Urgent
Remotely reachable No privileges Zero-click

Official description Straight from the sourceThe vendor's or NVD's own wording, published unedited. Authoritative, but often terse — it says what broke, rarely what to do.

NVD · unedited
PyMOL 2.5.0 contains a vulnerability in its "Run Script" function, which allows the execution of arbitrary Python code embedded within .PYM files. Attackers can craft a malicious .PYM file containing a Python reverse shell payload and exploit the function to achieve Remote Command Execution (RCE). This vulnerability arises because PyMOL treats .PYM files as Python scripts without properly validating or restricting the commands within the script, enabling attackers to run unauthorized commands in the context of the user running the application.

Technical summary Written by usOur analysis, written from the advisory, the CVSS vector and the affected-version data. It adds context the advisory leaves out, and never invents facts that are not in the source.

dbcve analysis · high confidence

PyMOL 2.5.0's 'Run Script' function treats .PYM files as executable Python scripts without validation, allowing attackers to embed arbitrary Python code (including reverse shell payloads) that executes with the privileges of the user running PyMOL, resulting in Remote Command Execution.

MitigationUsers should avoid opening untrusted .PYM files and disable or restrict the Run Script function until a patch is available that implements proper input validation or sandboxing for embedded Python code.

Verify against the referenced sources before acting — the references below are authoritative for this CVE, this summary is not.

CVSS breakdown How the score is builtThe industry scoring standard. It rates how the flaw is reached, what it takes to exploit, and what an attacker gains — the score is derived from those, not the other way round.

From the vector
Attack vector
Network
Complexity
Low
Privileges
None
User interaction
None
Scope
Unchanged
Confidentiality
High
Integrity
High
Availability
High

CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:H/A:H

Am I affected? How to checkSteps we derive from the advisory and the affected-version data, so you can decide whether this CVE reaches your setup. They are a guide, not a scan — your own configuration is the authority.

dbcve checks

Work through these to decide whether this CVE applies to you.

  1. Identify installed PyMOL version
    Run 'pymol --version' from command line, or open PyMOL and check Help > About PyMOL
    Affected if Version is 2.5.0 or falls within any other affected version range for this CVE
  2. Confirm Run Script function is present
    In PyMOL GUI, locate the 'Run Script' option (typically under File menu or as a toolbar button)
    Affected if The Run Script function exists and is accessible in the installation
  3. Check .PYM file association
    Verify that .PYM files are registered to open with PyMOL by checking system file associations or running 'pymol -c "print cmd.get_version()"' and testing .PYM file handling
    Affected if PYM files are associated with PyMOL and treated as executable scripts rather than data files
  4. Review recent .PYM file activity
    Check system logs, recent documents, or PyMOL's recent files list for any .PYM scripts that have been opened or executed
    Affected if Untrusted or external .PYM files have been loaded into PyMOL

User is affected if running a vulnerable PyMOL version where the Run Script function can execute unvalidated .PYM files as Python code.

Generated from the published advisory. Verify against your own configuration.

Check your environment

Paste your version and any relevant configuration and it will be compared against the affected criteria above. Do not include secrets or credentials.

AI-assisted, checked against the advisory. Informational, not a guarantee.

Remediation Closing itWhat it takes to close this. Where a vendor fix exists we point at it; where none exists we say so plainly, and can build one. Effort estimates are scoped from the advisory, not from your codebase.

dbcve · scoped
Mitigation available No clean upgrade yet — mitigate in the meantime
Mitigation

Users should avoid opening untrusted .PYM files and disable or restrict the Run Script function until a patch is available that implements proper input validation or sandboxing for embedded Python code.

Recommended fix Moderate confidence

Latest stable PyMOL 3.x release (currently 3.0.0 or later)

  1. 1. Back up any existing PyMOL configurations, plugins, and custom scripts before upgrading
  2. 2. Uninstall the current PyMOL 2.5.0 installation
  3. 3. Download the latest stable PyMOL release from the official GitHub repository (github.com/schrodinger/pymol-open-source)
  4. 4. Install the new version following standard installation procedures for your operating system
  5. 5. After installation, verify the version number matches the expected stable release
  6. 6. Test that legitimate .PYM scripts still function correctly
  7. 7. Review and apply any updated security settings or recommendations from the release notes
Caveat Newer major versions may have minor changes to the Python API and command syntax used in .PYM scripts; test custom scripts after upgrade

Generated from the published advisory — verify against the referenced sources before acting.

Have this fixed Scoped from the published advisory
  • Consultation8.0 h
  • Implementation24.0 h
  • Testing12.0 h
  • Review / QA8.0 h
52.0 hours of engineering $9,160
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References Go to the primary sourcePrimary sources — vendor advisories, patches and trackers. Where our summary and a reference disagree, the reference wins.

Primary sources

Practitioner notes

Contributed

Peer-ranked notes from engineers who’ve handled CVE-2024-50636 in production — separate from our analysis above.

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What this is

A place for practitioners to share what actually worked: a mitigation you’ve tested, a configuration change, a version- or environment-specific caveat, or a link to a verified patch. The most useful notes rise to the top as peers upvote them, so the signal stays high.

What belongs here
  • Verified mitigations, workarounds, and config changes
  • Version or environment caveats, and links to real fixes
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