PyMOL

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PyMOL

Pymol logo.png
The graphical user interfaces of PyMOL with the rendered representation of a protein structure.
Basic data

developer DeLano Scientific LLC, Schrödinger
Publishing year 2010
Current  version 2.4
(May 19, 2020)
operating system Linux , macOS , Windows
programming language python
category 3D computer graphics
License Python License
German speaking No
pymol.org

PyMOL is free 3D graphics software that is used to represent biomolecules in biochemistry and bioinformatics . Besides the use of the most important in the structural biology common data formats PyMOL allowed on different operating systems, the rendering of graphics with high quality.

history

The American biophysicist Warren L. DeLano developed PyMOL from 1998 and presented it on the Internet in 2000. His intention was to create a freely available, user-friendly program for academic research and the pharmaceutical industry that can produce high-resolution 3D graphics of small molecules and large proteins or nucleic acids. A prerequisite for the success of PyMOL was the design for different computer operating systems. With the establishment of DeLano Scientific LLC in 2003, PyMOL was marketed for the first time without giving up the open source strategy, which DeLano regards as an important basis for scientific work in research and teaching. In August 2006, DeLano Scientific introduced the so-called controlled-access download of precompiled versions of PyMOL. Access to these versions is regulated by purchasing licenses. The prices are staggered according to the type of user, for example an academic researcher pays $ 50 per year, whereas an industrial user pays $ 1000 per year. In addition, the latest PyMOL version is also freely available, whereby the user is asked to make a voluntary contribution ( sponsorship ). In general, free use by students and teachers in schools and universities is permitted. On January 8, 2010, after DeLano's death, the PyMOL project was bought by Schrödinger LLC and is to be continued in his favor.

Program description

PyMOL is comparable in its functions to the freeware programs DeepView (formerly Swiss-PDBViewer ) and VMD and combines the advantages of some programs that were created in the 1990s, such as Molscript , Bobscript or GRASP , but which were almost exclusively available for Unix . The Py in PyMOL relates that a Python - interpreter is involved, can also expand the functions of the PyMOL. In addition to versions for Linux , Windows and macOS, there are also versions for IRIX and Solaris . The program is normally set up on individual computers, but can also be installed on a file server for a local network , especially under Linux and UNIX .

Communication with other programs

If PyMOL is started with the -p option, it can receive commands from the standard input. This mechanism allows other programs to control PyMOL directly. An example of this type of interprocess communication is the coupling of PyMOL with a sequence alignment program. The Java class, which is responsible for the installation of PyMOL and the communication between the two programs, can be used freely.

A PyMOL session

For the three-dimensional representation of molecules, a molecule file with the information on the type and position of the atoms and bonds as well as the molecule representation program is required. After starting the program, the graphical user interface opens, which is divided into two main segments: the actual graphics window ( PyMOL Viewer ) and a window that has menus that can be activated by mouse click as well as an input line for the PyMOL commands ( PyMOL Tcl / Tk GUI ). Then the desired data files are loaded, e.g. B. Atomic coordinates of a protein structure in PDB format or CIF format and an electron density map . PyMOL supports most of the relevant data formats and allows rapid interactive visualization of the molecular models. It is worth highlighting the various options for designing the individual atoms, amino acids and the secondary structure of a protein up to the molecular surface with shape and color. The selection of suitable views of the molecule by rotating, shifting and enlarging the model is also very easy. Finally, the selected image section is rendered, i. H. reproduced by calculating a three-dimensional scenery with light and shadow effects. These images can be saved in PNG format and, if necessary, edited with other graphics programs such as Adobe Photoshop or GIMP and then converted into TIFF or JPEG graphics. Also noteworthy is the property of PyMOL to be able to generate sophisticated 3D animations of the displayed molecules and corresponding films in a very simple way.

MacPyMOL

The Mac OS X versions of PyMOL use either the X Window System of OS X Tiger directly or a so-called hybrid X11 mode. The former starts OpenGL with GUI and Tcl / Tk directly in X11 and is therefore fully compatible with the Linux or UNIX versions. In contrast, MacPyMOL is adapted to the Aqua graphic user interface of Mac OS X. MacPyMOL can be installed on computers with Panther (MAC OS X 10.3) and Tiger (OS X 10.4). In order for PyMOL to run without restrictions on a Macintosh , a mouse with three buttons is required and the buttons should be reconfigured.

development

Major versions for several operating systems are listed.

  • 1998: First PyMOL
  • 2000: PyMOL available as open source software on the Internet
  • February 6, 2002: v0.78 with RPM Package Manager for Linux, (16.06.) V0.82 with cross-eye stereo function, hardware stereo under Linux
  • June 1, 2003: v0.88 allows stand-alone installation without external Python for MS Windows, electrostatic surface display (.phi format), CMYK color code, (1.11.) V0.93 with improved rendering and secondary structure calculation
  • April 3, 2004: v0.95 additionally first MacPyMOL v0.95, (15.07.) V0.97 with sequence display for the selection of molecular units
  • May 5, 2005: v0.98
  • February 14, 2006: v0.99
  • July 24, 2018: v2.20
  • February 11, 2019: v2.30
  • May 20, 2020: v2.40

See also

Web links

Commons : Created with PyMOL  - collection of images, videos and audio files

Individual evidence

  1. Python License
  2. News. In: pymol.org. Retrieved July 7, 2016 .
  3. News. In: schrodinger.com. Retrieved July 7, 2016 .