PyMOL is a source-available molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. As the original software license was a permissive licence, they were able to remove it; new versions are no longer released under the Python license, but under a custom license (granting broad use, redistribution, and modification rights, but assigning copyright to any version to Schrödinger, LLC.), and some of the source code is no longer released. PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. PyMOL is widely used.
PyMOL is one of the few mostly open-source model visualization tools available for use in structural biology. The Py part of the software's name refers to the program having been written in the programming language Python.
What is PyMOL?
PyMOL is a proprietary languages & sdk program for Windows from Schrodinger, Inc. (developed by Schrödinger). The first release dates back to 2010. It is written in Python. Besides Windows, it is available for cross-platform.
Installation and requirements
Official installers exist for 64-bit as EXE (NSIS). The main installer is 427.9 MB. Installation asks for administrator rights. The installer supports unattended (silent) installation.
Updates and version history
The current version is 3.1.9, released on October 7, 2026. 9 versions are listed since February 5, 2025, each with links to its own installer files. That is about 5.4 releases a year. The last update is less than a month old.
Popularity and file types
Wikipedia has an article about it in 15 of our languages. On Windows it registers 11 file types, including .pdb, .xyz, .cif, .mol and .sdf. Similar programs include Go Programming Language, LLVM and Deno.
Pros / Cons
Pros
- Documented silent install
- Updated in the last two months
- Also runs on cross-platform
- Mature project (since 2010)
Cons
- Proprietary licence: check the terms and price
- No native ARM64 build
- Installation needs administrator rights
- Large download (427.9 MB)
In short: PyMOL is a languages & sdk tool for 64-bit PCs. It is actively maintained. Administrators can deploy it unattended.
Is PyMOL safe to download?
- The file is served by storage.googleapis.com; check that it is the publisher’s official mirror
- The download link uses HTTPS
- A SHA256 hash is published, so you can verify the file:
C36FE9B4DFF44E286F72A3119DBB362BD97C892ECD9DB2E14408ECB74F325442· Open the VirusTotal report for this hash - The link answered when we last checked it (October 27, 2026)
- ExeAtlas does not host, wrap or modify installers
Related guide: How to check a file’s SHA256 hash on Windows
Recent versions
All 9 versions ›9 versions over 2 years · about 5.4 a year
| Version | Date | Size | Files |
|---|---|---|---|
| 3.1.9Latest | October 7, 2026 | 427.9 MB | 64-bit EXE (NSIS)64-bit EXE (NSIS) |
| 3.1.8 | March 18, 2026 | 385.3 MB | 64-bit EXE (NSIS)64-bit EXE (NSIS) |
| 3.1.7.2 | March 4, 2026 | — | 64-bit EXE (NSIS)64-bit EXE (NSIS) |
| 3.1.6.1 | June 9, 2025 | — | 64-bit EXE (NSIS)64-bit EXE (NSIS) |
| 3.1.6 | June 6, 2025 | — | 64-bit EXE (NSIS)64-bit EXE (NSIS) |
| 3.1.5.1 | May 8, 2025 | — | 64-bit EXE (NSIS)64-bit EXE (NSIS) |
| 3.1.4.1 | March 26, 2025 | — | 64-bit EXE (NSIS)64-bit EXE (NSIS) |
| 3.1.4 | March 14, 2025 | — | 64-bit EXE (NSIS)64-bit EXE (NSIS) |
Install from the command line
Silent install ›winget install --id Schrodinger.PyMOL -ePyMOL-3.1.9-Windows-x86_64.exe /SRelated guide: How to use winget: install and update apps
Also for other systems
brew install pymolInformation
- Publisher
- Schrodinger, Inc.
- Developer
- Schrödinger
- Category
- Languages & SDKs
- Licence
- Proprietary
- Price
- See the publisher’s site
- Written in
- Python
- Requires
- Windows 11 / 10
- Architecture
- 64-bit
- Installer
- EXE (NSIS)
- Other platforms
- cross-platform
- Version
- 3.1.9
- Released
- October 7, 2026
- First release
- 2010
- Added to the catalogue
- February 6, 2025
- Versions listed
- 9
- Updates / year
- 5.4
- Website
- pymol.org
- winget ID
- Schrodinger.PyMOL
File types it opens (11)
Ratings and reviews
No reviews yet. Be the first to rate it.
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Frequently asked questions
Is PyMOL free?
PyMOL is proprietary (closed-source) software (licence: Proprietary). Whether it costs money depends on the edition: check the publisher’s site for prices and free tiers.
Is PyMOL safe to download?
The download comes from storage.googleapis.com; ExeAtlas does not host or change the file. Compare its SHA256 hash with the one shown here, or open the VirusTotal report for that hash.
How do I install PyMOL with winget?
Open PowerShell or Windows Terminal and run the winget command shown on this page. winget downloads the official installer and checks its SHA256 hash before running it.
Can PyMOL be installed silently?
Yes. The silent install page lists the exact command for each installer.
Does PyMOL run on ARM (Windows on Arm)?
There is no ARM64 build; Windows 11 on Arm can run the 64-bit version through emulation.
Where can I download an older version of PyMOL?
The versions page lists all 9 versions with links to their official installer files, back to February 5, 2025.
Can I use PyMOL without administrator rights?
Yes, there is a per-user installer that does not need administrator rights.
What are alternatives to PyMOL?
Go Programming Language, LLVM, Deno, CMake and Yarn. The alternatives page compares them.
