RasMol
Encyclopedia
RasMol is a computer program written for molecular graphics
visualization intended and used primarily for the depiction and exploration of biological macromolecule structures
, such as those found in the Protein Data Bank
. It was originally developed by Roger Sayle in the early 90s .
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
s. Before RasMol, visualization software ran on graphics workstations that, due to their expense, were less accessible to scholars. RasMol has become an important educational tool as well as continuing to be an important tool for research in structural biology.
RasMol has a complex version history. Starting with the series of 2.7 versions
, RasMol is licensed under a dual license (GPL
or custom license RASLIC).
RasMol includes a language (for selecting certain protein
chains, or changing colors etc). Jmol
and Sirius
has incorporated the RasMol scripting language into its commands.
Protein Databank
(PDB) files can be downloaded for visualization from the Research Collaboratory for Structural Bioinformatics
(RCSB) bank. These have been uploaded by researchers who have characterized the structure of molecules usually by X-ray crystallography
or NMR spectroscopy.
/Tk
.
Under Microsoft Windows
, Dynamic Data Exchange
(DDE) is used.
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"...
visualization intended and used primarily for the depiction and exploration of biological macromolecule structures
Structural biology
Structural biology is a branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macromolecules, especially proteins and nucleic acids, how they acquire the structures they have, and how alterations in their structures affect their function...
, such as those found in the Protein Data Bank
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
. It was originally developed by Roger Sayle in the early 90s .
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
Personal computer
A personal computer is any general-purpose computer whose size, capabilities, and original sales price make it useful for individuals, and which is intended to be operated directly by an end-user with no intervening computer operator...
s. Before RasMol, visualization software ran on graphics workstations that, due to their expense, were less accessible to scholars. RasMol has become an important educational tool as well as continuing to be an important tool for research in structural biology.
RasMol has a complex version history. Starting with the series of 2.7 versions
, RasMol is licensed under a dual license (GPL
GNU General Public License
The GNU General Public License is the most widely used free software license, originally written by Richard Stallman for the GNU Project....
or custom license RASLIC).
RasMol includes a language (for selecting certain protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
chains, or changing colors etc). Jmol
Jmol
Jmol is an open-source Java viewer for chemical structures in 3D,that does not require 3D acceleration plugins.Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g...
and Sirius
Sirius visualization software
Sirius is a molecular modeling 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...
has incorporated the RasMol scripting language into its commands.
Protein Databank
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
(PDB) files can be downloaded for visualization from the Research Collaboratory for Structural Bioinformatics
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
(RCSB) bank. These have been uploaded by researchers who have characterized the structure of molecules usually by X-ray crystallography
X-ray crystallography
X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...
or NMR spectroscopy.
Inter-process Communication
On UNIX platforms Rasmol can communicate with other programs via TclTcl
Tcl is a scripting language created by John Ousterhout. Originally "born out of frustration", according to the author, with programmers devising their own languages intended to be embedded into applications, Tcl gained acceptance on its own...
/Tk
Tk (framework)
Tk is an open source, cross-platform widget toolkit that provides a library of basic elements for building a graphical user interface in many different programming languages....
.
Under Microsoft Windows
Microsoft Windows
Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal...
, Dynamic Data Exchange
Dynamic Data Exchange
Dynamic Data Exchange is a technology for interprocess communication under Microsoft Windows or OS/2.- Overview :Dynamic Data Exchange was first introduced in 1987 with the release of Windows 2.0 as a method of interprocess communication so that one program can communicate with or control another...
(DDE) is used.
- multiple alignment program. The responsible Java class can be freely used in other applications.
See also
- List of molecular graphics systems
- List of software for molecular mechanics modeling
- Molecular graphicsMolecular graphicsMolecular 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"...