PyMOL (visualization tool for structural biology)

PyMOL


www.pymol.org




visible.
Original author(s) Warren Lyford DeLano
Developer(s) Schrödinger, Inc.
Initial release 2000; 17 years ago

Stable release
1.8.6.2 / 26 June 2017; 3 months ago
Development status Active
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 Python[1]
Website www.pymol.org



PyMOL is computer software, a molecular visualization system created by Warren Lyford DeLano. It is user-sponsored, open-source software, released under the Python License. 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. 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.[citation needed]
PyMOL is one of a few open-source model visualization tools available for use in structural biology. The Py part of the software's name refers to that it extends, and is extensible by, 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.[2] PyMOL uses Tk for the GUI widgets; Native Aqua binaries are available for macOS through Schrödinger.

Contents

Nonfree binaries

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.[3] Anyone can either compile an executable from the source code or pay for a subscription to support services to obtain access to precompiled executables.

Acquisition by Schrödinger

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.

Gallery

  • 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.

See also

References



  • "PyMOL Molecular Graphics System". SourceForge.

  • "poissonboltzmann".


    1. Unofficial Windows Binaries for Python Extension Packages

    External links





    -----------
    PyMOL is an OpenGL molecular graphics system written in Python.
    PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations.
    It is fully extensible and available free to everyone via the "Python" license. Although a newcomer to the field, PyMOL can already be used to generate stunning images and animations with unprecedented ease. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research.
     PyMOL 1.7.6.0
    Price
    Free to download
    Size
    8.3MB
    License
    Open-source, user-sponsored
    Developer
    DeLano Scientific LLC

    Website
    www.pymol.org
    System Requirements
    3D OpenGL graphics acceleration
    Python
    tcl
    tk
    libpng
    zlib
    glut
    glut-devel
    pmw
    numeric
    Support:
    Wiki, Tutorials, eMovie, PyMOL Plugins, Cams PyMOL Page
    Selected Reviews:
    wordpress
    Features include:
    • Real-Time 3D visualization
    • Publication quality renderings
    • Extensive animation capabilities
    • Support for X-ray crystallography
    • Modular Architechture
    • Volume visualization for unique display of volumetric data and simultaneous visualization of multiple iso-surfaces
    • Electron density map generation from reflection data
    • Stereochemical labeling
    • Atom Typing; MacroModel and SYBYL/MOL2 support
    • OpenGL Shaders (GLSL) for improved on-screen rendering (cartoons, sticks, surfaces, volumes)
    • Dynamic measurements (distances, bond angles and dihedral angles)
    • Flexible API for custom applications
    • Support for bg_gradient when ray tracing
    • Many non-standard nucleic acids (PSU, 5MU, 7MG, MIA, H2U, 4SU, MA6, UR3, 5MC, 40C, 2MG, TM2, 2MG) render correctly as cartoons
    • Surface color smoothing
    • Frame buffer-based antialiasing for real-time rendering
    • Optimized anaglyph colors and intensities for an improved 3D viewing experience
    • Real-time and ray-traced ambient occlusion
    • Support for reading compressed Maestro (.maegz)** and PyMOL session files (.pze, pzw, .pse.gz, .psw.gz)
    • Written in C and Python





    ------------


    Installing:






    No comments:

    Post a Comment

    Subscribe to: Posts (Atom)