Free software for viewing 3D molecular structures

PyMOL is a free educational software that lets you view high-quality 3D images of biological macromolecules and small molecules. It’s an open-source model visualization tool for use in the field of science, specifically in molecular biology. Originally developed by Warren Lyford Delano, the software is now maintained and distributed by Schrödinger, Inc.

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The developers have created PyMOL with the goal of providing professionals and students an advanced and accurate software that can render 3D molecular structures. It features precise measuring tools for better analysis, realistic graphics for advanced rendering, customizable coloring to highlight specific residues, and many more tools that make it reliable.

View, analyze, and study molecular structures

PyMOL allows scientists, educators, and students to explore 3D structures of molecules, DNA, and proteins. With its built-in ray-tracing graphics technology, the molecule models have smoother surfaces, enhanced shadows, and reflections—making it realistic when publishing images. There is a rotational camera and other adjustable options included, allowing you to choose what angle you want to capture. Additionally, the export feature supports multiple image formats. 

Upon using the software, you are greeted with an interface that looks overwhelming at first glance, but as soon as you familiarize yourself with its layout, you’ll realize how intuitive and useful it is with the amount of advanced features—from customizable visualizations to precise measuring tools, it’s a user-friendly experience for exploring complex molecular structures. Beginners and experienced users should have no problems using the software in the long run.

The software was written using the Python programming language, which allows for deep customization and scripting. This makes it easy for users to create complex visualizations and extend the software’s functionality to suit specific research needs. While the software can handle most molecules smoothly, larger models can slow down loading times, especially on less powerful computers. Higher end computers shouldn’t experience this issue.

Powerful and reliable

Overall, PyMOL is a useful and reliable software for professionals, educators, and students working in the field of molecular biology. With its comprehensive set of advanced tools, it allows users to visualize complex molecular structures, analyze them, and create high-quality images and animations. Its combination of flexibility, precision, and powerful features makes it a highly sought-after resource for learning, research, and scientific presentations.

  • Pros

    • High-quality 3D images of molecular structures
    • Supports multiple image formats
    • Tons of options to customize
    • Easily scripted and coded
  • Cons

    • Overwhelming interface at first glance
    • Slow loading times for less powerful computers
 0/7

App specs

Also available in other platforms

Program available in other languages


Icon of program: PyMOL

PyMOL for PC

  • Free
  • 3.8
    53
  • 53.9K
  • V3.1.8

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Laws concerning the use of this software vary from country to country. We do not encourage or condone the use of this program if it is in violation of these laws.
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Is PyMOL safe?

100/100

Score result: Clean

This file passed a comprehensive security scan using VirusTotal technology. It is safe to download.

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Scan Info

Last scan
Tuesday, April 14, 2026
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File Integrity

File
3.1.8.exe
SHA256
615512c63c6a35c73c7e59d91a2cc0525a9e796836c406759ca8aa66e9279cf3
SHA1
25b79abddd6f3da339475dd1394071b6b09dc07d

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PyMOL has been thoroughly scanned by our advanced security systems and verified by industry-leading partners. This file comes from the official developer and has passed all our security checks, showing no signs of viruses, malware, or spyware. For more information, visit our Security and Trust Center