A kinemage is an interactive graphic scientific illustration. It often is used to visualize molecules, especially proteins although it can also represent other types of 3-dimensional data. The kinemage system is designed to optimize ease of use, interactive performance, and the perception and communication of detailed 3D information. The kinemage information is stored in a text file, human- and machine-readable, that describes the hierarchy of display objects and their properties, and includes optional explanatory text. The kinemage format is a defined chemical MIME type of 'chemical/x-kinemage' with the file extension '.kin'.
Visual Molecular Dynamics (VMD) is a molecular modelling and visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, RenderMan, Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge.
In scientific visualization and computer graphics, volume rendering is a set of techniques used to display a 2D projection of a 3D discretely sampled data set, typically a 3D scalar field.
RasMol is a computer program written for molecular graphics visualization intended and used mainly to depict and explore biological macromolecule structures, such as those found in the Protein Data Bank (PDB).
PyMOL is a source-available 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, 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, and some of the source code is no longer released. 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.
In computer graphics, per-pixel lighting refers to any technique for lighting an image or scene that calculates illumination for each pixel on a rendered image. This is in contrast to other popular methods of lighting such as vertex lighting, which calculates illumination at each vertex of a 3D model and then interpolates the resulting values over the model's faces to calculate the final per-pixel color values.
OpenEye Scientific Software is an American software company founded by Anthony Nicholls in 1997. It develops large-scale molecular modelling applications and toolkits. Following OpenEye's acquisition by Cadence Design Systems for $500 million in September 2022, the company was rebranded to OpenEye Cadence Molecular Sciences and operates as a business unit under Cadence.
UNIGINE is a proprietary cross-platform game engine developed by UNIGINE Company used in simulators, virtual reality systems, serious games and visualization. It supports OpenGL 4, Vulkan and DirectX 12.
3D rendering is the 3D computer graphics process of converting 3D models into 2D images on a computer. 3D renders may include photorealistic effects or non-photorealistic styles.
BALL is a C++ class framework and set of algorithms and data structures for molecular modelling and computational structural bioinformatics, a Python interface to this library, and a graphical user interface to BALL, the molecule viewer BALLView.
3D computer graphics, sometimes called CGI, 3-D-CGI or three-dimensional computer graphics, are graphics that use a three-dimensional representation of geometric data that is stored in the computer for the purposes of performing calculations and rendering digital images, usually 2D images but sometimes 3D images. The resulting images may be stored for viewing later or displayed in real time.
Sirius is a molecular modelling and analysis system developed at San Diego Supercomputer Center. Sirius is designed to support advanced user requirements that go beyond simple display of small molecules and proteins. Sirius supports high quality interactive 3D graphics, structure building, displaying protein or DNA primary sequences, access to remote data sources, and visualizing molecular dynamics trajectories. It can be used for scientific visualization and analysis, and chemistry and biology instruction.
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
Screen space ambient occlusion (SSAO) is a computer graphics technique for efficiently approximating the ambient occlusion effect in real time. It was developed by Vladimir Kajalin while working at Crytek and was used for the first time in 2007 by the video game Crysis, also developed by Crytek.
Avogadro is a molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It is extensible via a plugin architecture.
Biological data visualization is a branch of bioinformatics concerned with the application of computer graphics, scientific visualization, and information visualization to different areas of the life sciences. This includes visualization of sequences, genomes, alignments, phylogenies, macromolecular structures, systems biology, microscopy, and magnetic resonance imaging data. Software tools used for visualizing biological data range from simple, standalone programs to complex, integrated systems.
Voreen is an open-source volume visualization library and development platform. Through the use of GPU-based volume rendering techniques it allows high frame rates on standard graphics hardware to support interactive volume exploration.
Tachyon is a parallel/multiprocessor ray tracing software. It is a parallel ray tracing library for use on distributed memory parallel computers, shared memory computers, and clusters of workstations. Tachyon implements rendering features such as ambient occlusion lighting, depth-of-field focal blur, shadows, reflections, and others. It was originally developed for the Intel iPSC/860 by John Stone for his M.S. thesis at University of Missouri-Rolla. Tachyon subsequently became a more functional and complete ray tracing engine, and it is now incorporated into a number of other open source software packages such as VMD, and SageMath. Tachyon is released under a permissive license.
