PyMOL facts for kids
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A PyMOL instance, with the Viewer and GUI visible.
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| Original author(s) | Warren Lyford DeLano |
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| Developer(s) | Schrödinger, Inc. |
| Initial release | 2000 |
| Stable release |
2.5.5 / 17 April 2023
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| Written in | C, C++, Python |
| Operating system | Cross-platform: macOS, Unix, Linux, Windows |
| Platform | IA-32, x86-64 |
| Available in | English |
| Type | Molecular modelling |
| License | Originally the Python License, now proprietary |
PyMOL is a special computer program that helps scientists and students see tiny molecules in 3D. It was created by a person named Warren Lyford DeLano. Think of it like a powerful microscope for molecules, but on your computer screen!
PyMOL is great for making high-quality 3D pictures of very small molecules and larger biological molecules, like proteins. Proteins are super important for how living things work. In fact, by 2009, nearly a quarter of all 3D protein pictures in science papers were made using PyMOL.
The "Py" in PyMOL stands for Python. This means the program was mostly written using the Python computer language. PyMOL is also one of the few tools that lets you see molecules and is mostly available for free or at a low cost. This makes it very helpful for people studying structural biology, which is about understanding the shapes of molecules.
PyMOL uses special computer graphics tools like OpenGL Extension Wrangler Library (GLEW) to create its amazing 3D views. It also used to have a user interface built with Tk, but now it uses PyQt for its menus and buttons on all types of computers.
How PyMOL Started and Grew
Early versions of PyMOL were available under a special kind of license called the Python License. This meant many people could use and change the program freely.
- Early Days: In 2006, the company that made PyMOL started to control how people downloaded the ready-to-use versions of the program.
- Paying for Access: Now, if you want the newest versions that are already put together, you usually need to be a paying customer.
- Free for Students: But good news! Students and teachers can often get these versions for free.
- Open Source Still Available: Most of the program's source code (the instructions that make it work) is still available for free. This means if you know how, you can build the program yourself!
In 2010, a company called Schrödinger, Inc. bought PyMOL. They now handle making, updating, and selling PyMOL. They also keep supporting the community of people who use the free, open-source version of PyMOL.
- Newer Versions: In 2017, Schrödinger released PyMOL version 2. This version brought a new look and made it easier to manage the program.
- Trial Periods: If you use the newest versions without a license, they might have a watermark (a faint image) on your pictures after a 30-day trial.
- Source Code Still Open: Even with these changes, most of the source code is still available for free.
How PyMOL Colors Elements
PyMOL has a cool feature: it colors different chemical elements in molecules with specific colors. This helps scientists easily tell which atoms are which in a complex 3D structure. For example, carbon atoms might be grey, oxygen atoms red, and nitrogen atoms blue. This makes it much easier to understand the shape and parts of a molecule.
Gallery
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This picture shows the same protein, called TEV protease, in eight different ways using PyMOL. You can see it as a cartoon, a solid surface, a cut-through view, and more. Each view helps scientists understand different things about the protein's shape and how it works.
See also
- Comparison of software for molecular mechanics modeling
- List of molecular graphics systems
- Molecular modelling
- Abalone
- Gabedit
- Molden
- Molekel
- RasMol
- SAMSON
- UCSF Chimera
- List of free and open-source software packages
