PyMOL

In the free software PyMOL is a 3D graphics software that is used to represent biomolecules in biochemistry and bioinformatics. In addition to the use of the most important currently used in structural biology 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 put it in 2000 on the internet before. His intention was to create a freely available user-friendly program for academic research and the pharmaceutical industry, which can generate 3D graphics of small molecules and large proteins or nucleic acids with high resolution. A prerequisite for the success of PyMOL was the design for different computer operating systems. With the founding of the company DeLano Scientific LLC in 2003 PyMOL was first marketed without the open source strategy to abandon that sees DeLano as an important basis of scientific work in research and teaching. In August 2006, DeLano Scientific introduced the so-called controlled download (controlled -access download) precompiled versions of PyMOL. Access to these versions is controlled via the acquisition of licenses. The prices are graded depending on the user type, such as an academic researcher pays $ 50 per year, while a user from the industry $ 1000. In addition, the latest PyMOL version is also available for free, and the user is asked for a voluntary contribution ( sponsorship). In general, the free use by students and teachers is permitted in schools and universities. On January 8, 2010 the PyMOL project was bought after the death of DeLano of the company Schrödinger LLC and is to be continued in his senses.

Program Description

PyMOL is comparable in its capabilities with the available freeware programs Deep View (formerly Swiss- PDBViewer ) and VMD and combines the advantages of some costs incurred in the 1990s, programs such as Molscript, Bobscript or GRASP that were available almost exclusively for UNIX but. The Py in PyMOL refers to the fact that a Python interpreter is involved, can the also expand the functions of PyMOL. Minor versions for Linux, Microsoft Windows and Mac OS X there are also those for IRIX and Solaris. The program is usually set up on individual computers, but can be installed especially on Linux and UNIX on a file server for a local network.

Communication with other programs

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

A PyMOL session

After starting the program the main graphical user interface that is divided into two main segments: the actual graphics window ( PyMOL Viewer) and a window that can be activated by both mouse click menus, and an input line for the PyMOL commands owns ( PyMOL Tcl / Tk GUI). Thereafter, the desired data files to be loaded, for example, the atomic coordinates of a protein structure in the PDB format, and an electron density map. PyMOL supports most relevant data formats and allows rapid interactive visualization of molecular models. These are a variety of ways to make the individual atoms, amino acids and the secondary structure of a protein to the molecular surface with shape and color. Very simply this is also the selection of appropriate views of the molecule by rotation, translation and magnification of the model. Finally, the selected image portion is rendered, ie represented by the computation of a three-dimensional scene with light and shadow effects. These images can be saved in PNG format, and optionally edit with other graphics programs such as Adobe Photoshop or GIMP and then convert to TIFF or JPEG images. Also noteworthy is the property of PyMOL to be able to create sophisticated 3D animations of the molecules shown and corresponding films on fairly simple way.

MacPyMOL

Using the Mac OS X versions of PyMOL either directly the X Window System of Mac OS X Tiger or a so-called hybrid -X11 mode. The former starts with OpenGL GUI and Tcl / Tk directly into X11 and is therefore fully compatible with Linux or UNIX versions. In contrast MacPyMOL the graphical user interface of the Mac OS X Aqua is adjusted. MacPyMOL can on machines with Panther ( Mac OS X 10.3) and Tiger (OS X 10.4) to be installed. This PyMOL runs without restrictions on a Macintosh, a three-button mouse is required, where you should configure the new keys.

Development

Listed are major versions for multiple operating systems.