Pymol open source license

Grosse-Kunstleve's generous contribution of the SgLite package 9. PyMOL contains a rudimentary electron density "wizard" written in Python which can be used to quickly navigate through one or more electron density maps surrounding an atomic model. This wizard enables one to move and regenerate multiple meshes merely by CTRL-middle-clicking on the atom to center.

A powerful time-saving feature found in PyMOL is its integrated ray-tracing engine. With PyMOL, what you construct in real-time 3D is exactly what you will get when you ray-trace except for labels , and you can import the resulting images directly into Microsoft PowerPoint. Although PyMOL's built-in ray-tracer is quite good, PovRay 11 support has recently been added, and it can now be used as a replacement renderer for generation of the highest quality images.

The advantage of using PyMOL instead of Raster3D is that it allows users to orient and combine multiple objects in real-time 3D prior to rendering. PyMOL supports molecular editing at several different levels. PyMOL also supports conformational editing within objects using an intuitive click-and-drag interface when in "editing" mode.

PyMOL also enables rudimentary chemical editing of structures on an atomic basis using mouse clicks and CTRL-key combinations to delete, replace, or grow new molecular structures. Some ambitious users are already using PyMOL to carry out limited conformational changes late in refinement.

PyMOL was designed from the ground-up to accommodate multiple atomic coordinates for each atom. PyMOL does not require a graphical user interface in order to run. The PyMOL command language is merely a series of Python function calls with implicit quoted arguments and implicit parentheses.

This syntax makes the power of Python directly accessible to non-programmers, and it provides a familiar feel for experienced users of crystallographic software.

Because the PyMOL scripting language falls back on Python for evaluation, it can be thought of as a superset of the Python language. By default, PyMOL starts up like a typical stand-alone molecular graphics program.

However, command line options can be used to change this behavior. Other applications can simply utilize PyMOL as a molecular display window and provide their own external menus, windows, dialog boxes, and controls.

So long as external applications are developed using PyMOL's Python-based application programming interface API , it should be possible for packages to maintain compatibility even as each package evolves independently. Unlike comparable academic open-source software development efforts, DeLano Scientific receives no direct support from university or government sources for PyMOL. Nearly all biomolecular scientists will benefit from the existence of a powerful and universally available graphics program, so everyone has a reason to contribute.

According to the original author, by , almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL. PyMOL is one of the few 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. Early versions of PyMol were released under the Python License.

On 1 August , 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.

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.

The source code remains mostly available, this time under a BSD-like license. Example of some molecule editing features of PyMOL, dihedral bond rotation and interactive molecular relaxation with Sculpting mode.