PyMOL

PyMOL is an open source but proprietary[3] 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 Schrodinger, LLC.),[3] and some of the source code is no longer released.[4] PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. According to the original author, by 2009, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL.

PyMOL
Original author(s)Warren Lyford DeLano
Developer(s)Schrödinger, Inc.
Initial release2000 (2000)
Stable release
2.5.5[1] / 17 April 2023 (2023-04-17)
Repository
Written inC, C++, Python
Operating systemCross-platform: macOS, Unix, Linux, Windows
PlatformIA-32, x86-64
Available inEnglish
TypeMolecular modelling
LicenseOriginally the Python License,[2] now proprietary[3]
Websitepymol.org/2/

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.

PyMOL uses OpenGL Extension Wrangler Library (GLEW) and FreeGLUT, and can solve Poisson–Boltzmann equations using the Adaptive Poisson Boltzmann Solver.[5] PyMOL used Tk for the GUI widgets and had native Aqua binaries for macOS through Schrödinger, which were replaced with a PyQt user interface on all platforms with the release of version 2.0.[6]

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 executables 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 continues to be available for free, as are older precompiled builds. While the build systems for other platforms are open, the Windows API (WinAPI, Win32) build system is not, although unofficial Windows binaries are available online.[7] 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.[6] 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.[8] As with the previous distribution, unofficial Windows binaries in the wheel format are available,[7] and indeed Linux distributions continue to provide their own builds of the open-source code.

Element colors

PyMOL applies ball-coloring by element.

Periodic table using PyMOL element colors as background[9]
① Hydro­genH#e5e5e5 He­liumHe#d8ffff
② Lith­iumLi#cc7fff Beryl­liumBe#c2ff00 BoronB#ffb5b5 CarbonC#33ff33 Nitro­genN#3333ff Oxy­genO#ff4c4c Fluor­ineF#b2ffff NeonNe#b2e2f5
③ So­diumNa#aa5cf2 Magne­siumMg#8aff00 Alumin­iumAl#bfa5a5 Sili­conSi#f0c79f Phos­phorusP#ff7f00 SulfurS#e5c53f Chlor­ineCl#1ef01e ArgonAr#7fd0e2
④ Potas­siumK#8f3fd3 Cal­ciumCa#3cff00 Scan­diumSc#e5e5e5 Tita­niumTi#bfc2c7 Vana­diumV#a5a5aa Chrom­iumCr#8a99c7 Manga­neseMn#9c7ac7 IronFe#e06633 CobaltCo#f08f9f NickelNi#4fd04f CopperCu#c77f33 ZincZn#7c7faf GalliumGa#c28f8f Germa­niumGe#668f8f ArsenicAs#bd7fe2 Sele­niumSe#ffa000 BromineBr#a52929 Kryp­tonKr#5cb7d0
⑤ Rubid­iumRb#6f2eaf Stront­iumSr#00ff00 YttriumY#94ffff Zirco­niumZr#94e0e0 Nio­biumNb#72c2c8 Molyb­denumMo#54b5b5 Tech­netiumTc#3a9d9d Ruthe­niumRu#248f8f Rho­diumRh#097c8c Pallad­iumPd#006984 SilverAg#bfbfbf Cad­miumCd#ffd88f IndiumIn#a57472 TinSn#667f7f Anti­monySb#9d62b5 Tellur­iumTe#d37a00 IodineI#940094 XenonXe#419daf
⑥ Cae­siumCs#57168f Ba­riumBa#00c800 1 asterisk Lute­tiumLu#00aa24 Haf­niumHf#4cc2ff Tanta­lumTa#4ca5ff Tung­stenW#2194d5 Rhe­niumRe#267caa Os­miumOs#266695 IridiumIr#165487 Plat­inumPt#d0d0e0 GoldAu#ffd023 Mer­curyHg#b7b7d0 ThalliumTl#a5544c LeadPb#575961 Bis­muthBi#9d4fb5 Polo­niumPo#aa5c00 Asta­tineAt#744f44 RadonRn#418295
⑦ Fran­ciumFr#410066 Ra­diumRa#007c00 1 asterisk Lawren­ciumLr#c70066 Ruther­fordiumRf#cc0059 Dub­niumDb#d0004f Sea­borgiumSg#d80044 Bohr­iumBh#e00037 Has­siumHs#e5002e Meit­neriumMt#ea0026 Darm­stadtiumDs– Roent­geniumRg– Coper­niciumCn– Nihon­iumNh– Flerov­iumFl– Moscov­iumMc– Liver­moriumLv– Tenness­ineTs– Oga­nessonOg–

1 asterisk Lan­thanumLa#6fd3ff CeriumCe#ffffc7 Praseo­dymiumPr#d8ffc7 Neo­dymiumNd#c7ffc7 Prome­thiumPm#a2ffc7 Sama­riumSm#8fffc7 Europ­iumEu#61ffc7 Gadolin­iumGd#44ffc7 Ter­biumTb#2fffc7 Dyspro­siumDy#1effc7 Hol­miumHo#00ff9c ErbiumEr#00e574 ThuliumTm#00d351 Ytter­biumYb#00bf37
1 asterisk Actin­iumAc#6faafa Thor­iumTh#00baff Protac­tiniumPa#00a0ff Ura­niumU#008fff Neptu­niumNp#007fff Pluto­niumPu#006aff Ameri­ciumAm#545cf2 CuriumCm#775ce2 Berkel­iumBk#8a4fe2 Califor­niumCf#a036d3 Einstei­niumEs#b21ed3 Fer­miumFm#b21eba Mende­leviumMd#b20ca5 Nobel­iumNo#bd0c87
  • 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
  • The same protein structure (TEV protease - PDB: 1LVB​) rendered in different modes. Standard cartoon, surface, cut-through of surface, highlighted barrels, 'QuteMol'-like, 'Goodsell'-like, glossy-surface, and b-factor putty.
    The same protein structure (TEV protease - PDB: 1LVB​) rendered in different modes. Standard cartoon, surface, cut-through of surface, highlighted barrels, 'QuteMol'-like, 'Goodsell'-like, glossy-surface, and b-factor putty.

See also

References
  1. "Download PyMol". PyMol. Retrieved 12 January 2023.
  2. "PyMOL Molecular Graphics System". SourceForge.
  3. "Open-Source PyMOL". Schrodinger, Inc. 5 November 2021. Retrieved 7 November 2021.
  4. "PyMOL | pymol.org". pymol.org. Retrieved 7 November 2021. Open-Source Philosophy
    PyMOL is a commercial product, but we make most of its source code freely available under a permissive license. The open source project is maintained by Schrödinger and ultimately funded by everyone who purchases a PyMOL license.
    Open source enables open science.
    This was the vision of the original PyMOL author Warren L. DeLano.
  5. "APBS". poissonboltzmann.org. Archived from the original on 24 February 2020. Retrieved 7 October 2020.
  6. "PyMOL v2.0 Release Notes".
  7. "Python Extension Packages for Windows - Christoph Gohlke". lfd.uci.edu. Retrieved 26 October 2019.
  8. "schrodinger/pymol-open-source". GitHub. Retrieved 24 June 2019.
  9. "Color Values". pymolwiki. 2010. Retrieved 4 September 2021.
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