View source for PyMOL

{{Short description|Biology structure visualization software}}
{{More citations needed|date=June 2008}}
{{Use dmy dates|date=February 2021}}
{{Infobox software
| name = PyMOL
| logo = PyMOL logo.svg
| screenshot = PyMOL large.png
| caption = A PyMOL instance, with the Viewer and GUI visible.
| author = [[Warren Lyford DeLano]]
| developer = [[Schrödinger (company)|Schrödinger, Inc.]]
| released = {{Start date and age|2000}}
| latest release version ={{wikidata|property|preferred|single|P348|P548=Q2804309|P348}}
| latest release date = {{wikidata|qualifier|preferred|single|P348|P548=Q2804309|P577}}
| programming language = [[C (programming language)|C]], [[C++]], [[Python (programming language)|Python]]
| operating system = [[Cross-platform]]: [[macOS]], [[Unix]], [[Linux]], [[Microsoft Windows|Windows]]
| platform = [[IA-32]], [[x86-64]]
| size = 
| language = English
| genre = [[Molecular modelling]]
| license = Originally the [[Python License]],<ref>{{cite web|url=http://sourceforge.net/projects/pymol/|title=PyMOL Molecular Graphics System|date=2 June 2020 |publisher=[[SourceForge]]}}</ref> now proprietary<ref name=proprietary/>
| website = {{URL|https://pymol.org/2/}}
}}
'''PyMOL''' is a [[source-available software|source-available]]<ref name=proprietary>{{cite web |title=Open-Source PyMOL |url=https://github.com/schrodinger/pymol-open-source/blob/master/LICENSE |publisher=Schrodinger, Inc. |access-date=7 November 2021 |date=5 November 2021}}</ref> 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 (company)|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 Schrödinger, LLC.),<ref name=proprietary/> and some of the source code is no longer released.<ref>{{cite web |title=PyMOL {{!}} pymol.org |url=https://pymol.org/2/ |website=pymol.org |access-date=7 November 2021|quote=Open-Source Philosophy<br/> 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.<br/>Open source enables open science.<br/>This was the vision of the original PyMOL author Warren L. DeLano.}}</ref> PyMOL can produce high-quality 3D images of small [[molecule]]s and biological [[macromolecule]]s, such as [[protein]]s. PyMOL is widely used.

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 (programming language)|Python]].

PyMOL uses [[OpenGL Extension Wrangler Library]] (GLEW) and [[FreeGLUT]], and can solve [[Poisson–Boltzmann equation]]s using the Adaptive Poisson Boltzmann Solver.<ref>{{cite web |url=http://www.poissonboltzmann.org/apbs/ |title=APBS|url-status=dead|archive-url=https://web.archive.org/web/20200224180932/http://www.poissonboltzmann.org/apbs/|archive-date=24 February 2020|access-date=7 October 2020|website=poissonboltzmann.org}}</ref> PyMOL used [[Tk (software)|Tk]] for the [[Widget (GUI)|GUI widgets]] and had native [[Aqua (user interface)|Aqua]] binaries for [[macOS]] through [[Schrödinger (company)|Schrödinger]], which were replaced with a [[PyQt]] user interface on all platforms with the release of version 2.0.<ref name=Pymol2>{{cite web |url=https://pymol.org/dokuwiki/?id=media:new2 |title=PyMOL v2.0 Release Notes}}</ref>

== 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]]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]] 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.<ref name=builds/> Anyone can either [[compiler|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 (company)|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 (software)|Qt]] and the package management under [[Anaconda (Python distribution)|Anaconda]], and released it as PyMol v2.<ref name=Pymol2/> 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.<ref>{{cite web |title=schrodinger/pymol-open-source |url=https://github.com/schrodinger/pymol-open-source |website=GitHub |access-date=24 June 2019}}</ref> As with the previous distribution, unofficial Windows binaries in the [[Setuptools|wheel format]] are available,<ref name="builds">{{Cite web|url=https://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol|title=Python Extension Packages for Windows - Christoph Gohlke|website=lfd.uci.edu|access-date=2019-10-26}}</ref> and indeed [[Linux distribution]]s continue to provide their own builds of the open-source code.

==Element colors==
PyMOL applies ball-coloring by element.
{| class="collapsible {{{state|uncollapsed}}}" style="text-align:center; background:{{Element color|table background}}; border:1px solid {{Element color|table border}}; margin:0 auto; padding:2px;"
|-
! colspan=20 style="background:{{Element color|table title}}; padding:2px 4px;" | [[Periodic table]] using PyMOL element colors as background<ref>{{cite web|url=https://pymolwiki.org/index.php/Color_Values#Chemical_element_colours |volume=Color_Values#Chemical_element_colours|title=Color Values|publisher=pymolwiki|date=2010|access-date=4 September 2021}}</ref>
|-
| {{Element cell/period|1}}
| {{element cell-PyMOL|symbol=H }}
| colspan="17" |
| {{element cell-PyMOL|symbol=He}}
|-
| {{Element cell/period|2}}
| {{element cell-PyMOL|symbol=Li}}
| {{element cell-PyMOL|symbol=Be}}
| colspan="11" |
| {{element cell-PyMOL|symbol=B }}
| {{element cell-PyMOL|symbol=C }}
| {{element cell-PyMOL|symbol=N }}
| {{element cell-PyMOL|symbol=O }}
| {{element cell-PyMOL|symbol=F }}
| {{element cell-PyMOL|symbol=Ne}}
|-
| {{Element cell/period|3}}
| {{element cell-PyMOL|symbol=Na}}
| {{element cell-PyMOL|symbol=Mg}}
| colspan="11" |
| {{element cell-PyMOL|symbol=Al}}
| {{element cell-PyMOL|symbol=Si}}
| {{element cell-PyMOL|symbol=P }}
| {{element cell-PyMOL|symbol=S }}
| {{element cell-PyMOL|symbol=Cl}}
| {{element cell-PyMOL|symbol=Ar}}
|-
| {{Element cell/period|4}}
| {{element cell-PyMOL|symbol=K }}
| {{element cell-PyMOL|symbol=Ca}}
| 
| {{element cell-PyMOL|symbol=Sc}}
| {{element cell-PyMOL|symbol=Ti}}
| {{element cell-PyMOL|symbol=V }}
| {{element cell-PyMOL|symbol=Cr}}
| {{element cell-PyMOL|symbol=Mn}}
| {{element cell-PyMOL|symbol=Fe}}
| {{element cell-PyMOL|symbol=Co}}
| {{element cell-PyMOL|symbol=Ni}}
| {{element cell-PyMOL|symbol=Cu}}
| {{element cell-PyMOL|symbol=Zn}}

| {{element cell-PyMOL|symbol=Ga}}
| {{element cell-PyMOL|symbol=Ge}}
| {{element cell-PyMOL|symbol=As}}
| {{element cell-PyMOL|symbol=Se}}
| {{element cell-PyMOL|symbol=Br}}
| {{element cell-PyMOL|symbol=Kr}}
|-
| {{Element cell/period|5}}
| {{element cell-PyMOL|symbol=Rb}}
| {{element cell-PyMOL|symbol=Sr}}
| 
| {{element cell-PyMOL|symbol=Y }}
| {{element cell-PyMOL|symbol=Zr}}
| {{element cell-PyMOL|symbol=Nb}}
| {{element cell-PyMOL|symbol=Mo}}
| {{element cell-PyMOL|symbol=Tc}}
| {{element cell-PyMOL|symbol=Ru}}
| {{element cell-PyMOL|symbol=Rh}}
| {{element cell-PyMOL|symbol=Pd}}
| {{element cell-PyMOL|symbol=Ag}}
| {{element cell-PyMOL|symbol=Cd}}
| {{element cell-PyMOL|symbol=In}}
| {{element cell-PyMOL|symbol=Sn}}
| {{element cell-PyMOL|symbol=Sb}}
| {{element cell-PyMOL|symbol=Te}}
| {{element cell-PyMOL|symbol=I }}
| {{element cell-PyMOL|symbol=Xe}}
|-
| {{Element cell/period|6}}
| {{element cell-PyMOL|symbol=Cs}}
| {{element cell-PyMOL|symbol=Ba}}
| {{element cell-asterisk|1}}
| {{element cell-PyMOL|symbol=Lu}}
| {{element cell-PyMOL|symbol=Hf}}
| {{element cell-PyMOL|symbol=Ta}}
| {{element cell-PyMOL|symbol=W }}
| {{element cell-PyMOL|symbol=Re}}
| {{element cell-PyMOL|symbol=Os}}
| {{element cell-PyMOL|symbol=Ir}}
| {{element cell-PyMOL|symbol=Pt}}
| {{element cell-PyMOL|symbol=Au}}
| {{element cell-PyMOL|symbol=Hg}}
| {{element cell-PyMOL|symbol=Tl}}
| {{element cell-PyMOL|symbol=Pb}}
| {{element cell-PyMOL|symbol=Bi}}
| {{element cell-PyMOL|symbol=Po}}
| {{element cell-PyMOL|symbol=At}}
| {{element cell-PyMOL|symbol=Rn}}
|-
| {{Element cell/period|7}}
| {{element cell-PyMOL|symbol=Fr}}
| {{element cell-PyMOL|symbol=Ra}}
| {{element cell-asterisk|2vertical}}
| {{element cell-PyMOL|symbol=Lr}}
| {{element cell-PyMOL|symbol=Rf}}
| {{element cell-PyMOL|symbol=Db}}
| {{element cell-PyMOL|symbol=Sg}}
| {{element cell-PyMOL|symbol=Bh}}
| {{element cell-PyMOL|symbol=Hs}}
| {{element cell-PyMOL|symbol=Mt}}
| {{element cell-PyMOL|symbol=Ds}}
| {{element cell-PyMOL|symbol=Rg}}
| {{element cell-PyMOL|symbol=Cn}}
| {{element cell-PyMOL|symbol=Nh}}
| {{element cell-PyMOL|symbol=Fl}}
| {{element cell-PyMOL|symbol=Mc}}
| {{element cell-PyMOL|symbol=Lv}}
| {{element cell-PyMOL|symbol=Ts}}
| {{element cell-PyMOL|symbol=Og}}
|-
| <br />
|-
| colspan="3" | <!-- lanthanides -->
| {{element cell-asterisk|1}}
| {{element cell-PyMOL|symbol=La}}
| {{element cell-PyMOL|symbol=Ce}}
| {{element cell-PyMOL|symbol=Pr}}
| {{element cell-PyMOL|symbol=Nd}}
| {{element cell-PyMOL|symbol=Pm}}
| {{element cell-PyMOL|symbol=Sm}}
| {{element cell-PyMOL|symbol=Eu}}
| {{element cell-PyMOL|symbol=Gd}}
| {{element cell-PyMOL|symbol=Tb}}
| {{element cell-PyMOL|symbol=Dy}}
| {{element cell-PyMOL|symbol=Ho}}
| {{element cell-PyMOL|symbol=Er}}
| {{element cell-PyMOL|symbol=Tm}}
| {{element cell-PyMOL|symbol=Yb}}
|-
| colspan="1" |
|- <!-- actinides -->
| colspan="3" |
| {{element cell-asterisk|2vertical}}
| {{element cell-PyMOL|symbol=Ac}}
| {{element cell-PyMOL|symbol=Th}}
| {{element cell-PyMOL|symbol=Pa}}
| {{element cell-PyMOL|symbol=U }}
| {{element cell-PyMOL|symbol=Np}}
| {{element cell-PyMOL|symbol=Pu}}
| {{element cell-PyMOL|symbol=Am}}
| {{element cell-PyMOL|symbol=Cm}}
| {{element cell-PyMOL|symbol=Bk}}
| {{element cell-PyMOL|symbol=Cf}}
| {{element cell-PyMOL|symbol=Es}}
| {{element cell-PyMOL|symbol=Fm}}
| {{element cell-PyMOL|symbol=Md}}
| {{element cell-PyMOL|symbol=No}}
|
|}

==Gallery==
<gallery mode="packed" heights="250px">
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]] - {{PDB|1LVB}}) rendered in different modes. Standard cartoon, surface, cut-through of surface, highlighted barrels, '[[QuteMol]]'-like, '[[David Goodsell|Goodsell]]'-like, glossy-surface,<!-- Would be good to find proper name for this rendering mode. See talk page. --> and [[b-factor]] putty.
</gallery>

==See also==
{{Portal|Free and open-source software}}
* [[List of molecular graphics systems]]
* [[Molecular modelling]]
* [[Gabedit]]
* [[Molden]]
* [[Molekel]]
* [[RasMol]]
* [[SAMSON]]
* [[UCSF Chimera]]
*[[List of free and open-source software packages]]

==References==
{{Reflist}}

==External links==
{{Commons category|PyMOL}}
* {{Official website|https://pymol.org/2/}}
*[https://pymolwiki.org/index.php/Main_Page PyMOL Wiki]
*[https://wiki.pymol.org/index.php/Main_Page Read-only PyMOL Wiki Mirror]
*[https://www.schrodinger.com/ Schrödinger LLC]
* [https://web.archive.org/web/20071025054743/http://www.weizmann.ac.il/ISPC/eMovie.html Molecular movie-making with PyMOL]

{{Chemistry software}}

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