PyMOL is a

source-available Source-available software is software released through a source code distribution model that includes arrangements where the source can be viewed, and in some cases modified, but without necessarily meeting the criteria to be called ''open-source ...

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 A software license is a legal instrument governing the use or redistribution of software. Since the 1970s, software copyright has been recognized in the United States. Despite the copyright being recognized, most companies prefer to sell lic ...

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

molecule A molecule is a group of two or more atoms that are held together by Force, attractive forces known as chemical bonds; depending on context, the term may or may not include ions that satisfy this criterion. In quantum physics, organic chemi ...

s and biological

macromolecule A macromolecule is a "molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." Polymers are physi ...

s, such as

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

s. PyMOL is widely used. PyMOL is one of the few mostly

open-source model Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use and view the source code, design documents, or content of the product. The open source model is a decentrali ...

visualization tools available for use in

structural biology Structural biology deals with structural analysis of living material (formed, composed of, and/or maintained and refined by living cells) at every level of organization. Early structural biologists throughout the 19th and early 20th centuries we ...

. The ''Py'' part of the

software Software consists of computer programs that instruct the Execution (computing), execution of a computer. Software also includes design documents and specifications. The history of software is closely tied to the development of digital comput ...

's name refers to the program having been written in the programming language Python. PyMOL uses OpenGL Extension Wrangler Library (GLEW) and FreeGLUT, and can solve Poisson–Boltzmann equations using the Adaptive Poisson Boltzmann Solver. PyMOL used Tk for the GUI widgets and had native Aqua binaries for

macOS macOS, previously OS X and originally Mac OS X, is a Unix, Unix-based operating system developed and marketed by Apple Inc., Apple since 2001. It is the current operating system for Apple's Mac (computer), Mac computers. With ...

through Schrödinger, which were replaced with a PyQt user interface on all platforms with the release of version 2.0.

History and commercialization

Early versions of PyMol were released under the Python License. On 1 August 2006, DeLano Scientific adopted a controlled-access download system for precompiled PyMOL builds (including betas) distributed by the company. Access to these

executable In computer science, executable code, an executable file, or an executable program, sometimes simply referred to as an executable or binary, causes a computer "to perform indicated tasks according to encoded instruction (computer science), in ...

s is now limited to registered users who are paying customers; educational builds are available free to students and teachers. However, most of the current

source code In computing, source code, or simply code or source, is a plain text computer program written in a programming language. A programmer writes the human readable source code to control the behavior of a computer. Since a computer, at base, only ...

continues to be available for free, as are older precompiled builds. While the build systems for other platforms are open, the

Windows API The Windows API, informally WinAPI, is the foundational application programming interface (API) that allows a computer program to access the features of the Microsoft Windows operating system in which the program is running. Programs can acces ...

(WinAPI, Win32) build system is not, although unofficial Windows binaries are available online. Anyone can either compile an executable from the Python-licensed source code or pay for a subscription to support services to obtain access to precompiled executables. On 8 January 2010, Schrödinger, Inc. reached an agreement to acquire PyMOL. The firm assumed development, maintenance, support, and sales of PyMOL, including all then-valid subscriptions. They also continue to actively support the PyMOL open-source community. In 2017, Schrödinger revamped the distribution system to unify the user interface under Qt and the package management under Anaconda, and released it as PyMol v2. This version restricts some new functionalities and adds a watermark to the visualization if used unlicensed beyond the 30-day trial period; the overall license policy is similar to the DeLano system. The source code remains mostly available, this time under a BSD-like license. As with the previous distribution, unofficial Windows binaries in the wheel format are available, and indeed

Linux distribution A Linux distribution, often abbreviated as distro, is an operating system that includes the Linux kernel for its kernel functionality. Although the name does not imply product distribution per se, a distro—if distributed on its own—is oft ...

s continue to provide their own builds of the open-source code.

Element colors

PyMOL applies ball-coloring by element.

Gallery

File:PyMOL.ogv, Example of some molecule editing features of PyMOL, dihedral bond rotation and interactive molecular relaxation with ''Sculpting mode''. These are useful features to prepare input geometry for quantum chemistry software File:Pymol 8 view.png, The same protein structure ( TEV protease - ) rendered in different modes. Standard cartoon, surface, cut-through of surface, highlighted barrels, ' QuteMol'-like, ' Goodsell'-like, glossy-surface, and b-factor putty.

References

External links

*
PyMOL WikiRead-only PyMOL Wiki MirrorSchrödinger LLC

{{DEFAULTSORT:Pymol Color codes Articles containing video clips Chemistry software for Linux Molecular modelling software Proprietary software that uses Tk (software) Formerly open-source or free software

History and commercialization

Element colors

Gallery

See also

References

External links