Пимол
 | Эта статья требует дополнительных цитат для проверки . ( июнь 2008 г. ) |
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 A PyMOL instance, with the Viewer and GUI visible. | |
| Original author(s) | Warren Lyford DeLano |
|---|---|
| Developer(s) | Schrödinger, Inc. |
| Initial release | 2000 |
| Stable release | 2.5.5[1]
/ 17 April 2023 |
| Repository | |
| 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,[2] now proprietary[3] |
| Website | pymol |
Пимол источник -доступный [ 3 ] Молекулярная система визуализации, созданная Уорреном Лайфордом Делано . Первоначально он был коммерциализирован Delano Scientific LLC, которая была частной компанией по программному обеспечению, занимающейся созданием полезных инструментов, которые становятся универсально доступными для научных и образовательных сообществ. В настоящее время он коммерциализируется Schrödinger, Inc. Поскольку оригинальная лицензия на программное обеспечение была разрешающей лицензией , они смогли удалить ее; Новые версии больше не выпускаются по лицензии на Python , а по пользовательской лицензии (предоставление прав на широкое использование, перераспределение и модификацию, но присвоение авторским правом любой версии Schrödinger, LLC.), [ 3 ] И некоторые из исходного кода больше не выпущены. [ 4 ] Pymol может продуцировать высококачественные 3D-изображения мелких молекул и биологических макромолекул , таких как белки . Согласно первоначальному автору, к 2009 году, почти четверть всех опубликованных изображений трехмерных белковых структур в научной литературе были сделаны с использованием Pymol. [citation needed]
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
[edit]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
[edit]PyMOL applies ball-coloring by element.
| Periodic table using PyMOL element colors as background[9] | |||||||||||||||||||
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| ⑥ | 
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| ⑦ | 
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Gallery
[edit]-
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
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See also
[edit]
- 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
References
[edit]- ^ "Download PyMol". PyMol. Retrieved 12 January 2023.
- ^ "PyMOL Molecular Graphics System". SourceForge.
- ^ Jump up to: a b c "Open-Source PyMOL". Schrodinger, Inc. 5 November 2021. Retrieved 7 November 2021.
- ^ "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. - ^ "APBS". poissonboltzmann.org. Archived from the original on 24 February 2020. Retrieved 7 October 2020.
- ^ Jump up to: a b "PyMOL v2.0 Release Notes".
- ^ Jump up to: a b "Python Extension Packages for Windows - Christoph Gohlke". lfd.uci.edu. Retrieved 26 October 2019.
- ^ "schrodinger/pymol-open-source". GitHub. Retrieved 24 June 2019.
- ^ "Color Values". pymolwiki. 2010. Retrieved 4 September 2021.
External links
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