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RasMol is a computer program written for
molecular graphics Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and Keku ...
visualization intended and used mainly to depict and explore biological macromolecule structures, such as those found in the
Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cry ...
. It was originally developed by Roger Sayle in the early 1990s. Historically, it was an important tool for molecular biologists since the extremely optimized program allowed the software to run on (then) modestly powerful
personal computer A personal computer (PC) is a multi-purpose microcomputer whose size, capabilities, and price make it feasible for individual use. Personal computers are intended to be operated directly by an end user, rather than by a computer expert or tec ...
s. Before RasMol, visualization software ran on graphics workstations that, due to their cost, were less accessible to scholars. RasMol continues to be important for research in structural biology, and has become important in education. RasMol has a complex
licensing A license (or licence) is an official permission or permit to do, use, or own something (as well as the document of that permission or permit). A license is granted by a party (licensor) to another party (licensee) as an element of an agreeme ...
version history. Starting with the version 2.7 series, RasMol
source code In computing, source code, or simply code, is any collection of code, with or without comments, written using a human-readable programming language, usually as plain text. The source code of a program is specially designed to facilitate the ...
is dual-licensed under a
GNU General Public License The GNU General Public License (GNU GPL or simply GPL) is a series of widely used free software licenses that guarantee end users the four freedoms to run, study, share, and modify the software. The license was the first copyleft for general ...
(GPL), or custom license ''RASLIC''. Starting with version 2.7.5, a GPL is the only license valid for binary distributions. RasMol includes a
scripting language A scripting language or script language is a programming language that is used to manipulate, customize, and automate the facilities of an existing system. Scripting languages are usually interpreted at runtime rather than compiled. A scriptin ...
, to perform many functions such as selecting certain
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
chains, changing colors, etc.
Jmol Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g., in chemistry and biochemistry. It is written in the ...
and
Sirius Sirius is the brightest star in the night sky. Its name is derived from the Greek word , or , meaning 'glowing' or 'scorching'. The star is designated α Canis Majoris, Latinized to Alpha Canis Majoris, and abbreviated Alpha CMa ...
software have incorporated this language into their commands.
Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cry ...
(PDB) files can be downloaded for visualization from members of the
Worldwide Protein Data Bank The Worldwide Protein Data Bank, wwPDB, is an organization that maintains the archive of macromolecular structure. Its mission is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly avail ...
(wwPDB). These have been uploaded by researchers who have characterized the structure of
molecule A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioch ...
s usually by
X-ray crystallography X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles ...
,
protein NMR Nuclear magnetic resonance spectroscopy of proteins (usually abbreviated protein NMR) is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and ...
spectroscopy, or
cryo-electron microscopy Cryogenic electron microscopy (cryo-EM) is a cryomicroscopy technique applied on samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An aqueous sample sol ...
.


Interprocess communication

Rasmol can communicate with other programs via Tcl/ Tk on
Unix Unix (; trademarked as UNIX) is a family of multitasking, multiuser computer operating systems that derive from the original AT&T Unix, whose development started in 1969 at the Bell Labs research center by Ken Thompson, Dennis Ritchie, an ...
platforms, and via
Dynamic Data Exchange In computing, Dynamic Data Exchange (DDE) is a technology for interprocess communication used in early versions of Microsoft Windows and OS/2. DDE allows programs to manipulate objects provided by other programs, and respond to user actions affect ...
(DDE) on
Microsoft Windows Windows is a group of several Proprietary software, proprietary graphical user interface, graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, W ...
. With a
multiple sequence alignment Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolut ...
program, the responsible Java class can be freely used in other applications.Multiple alignment program
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See also

*
List of molecular graphics systems This is a list of notable software systems that are used for visualizing macromolecules. Key The tables below indicate which types of data can be visualized in each system: See also * Biological data visualization * Comparison of nucleic ...
*
Comparison of software for molecular mechanics modeling This is a list of computer programs that are predominantly used for molecular mechanics calculations. See also *Car–Parrinello molecular dynamics * Comparison of force-field implementations *Comparison of nucleic acid simulation software ...
*
Molecular graphics Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and Keku ...
*
Molecule editor A molecule editor is a computer program for creating and modifying representations of chemical structures. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, ...
*
List of free and open-source software packages This is a list of free and open-source software packages, computer software licensed under free software licenses and open-source licenses. Software that fits the Free Software Definition may be more appropriately called free software; the G ...


References


External links

*{{Official website, www.rasmol.org
Download RasMol
(production releases)
Source repository
(stable)
Source repository
(development) *Protein databanks and files
RCSB
( Research Collaboratory for Structural Bioinformatics)
Europe

Japan
*RasMol development history
Early


Molecular modelling software Free science software Free software programmed in C Free educational software