Sirius visualization software
Encyclopedia
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 molecule
s and protein
s. In addition to high quality interactive 3D graphics, Sirius supports structure building, displaying protein
or DNA
primary sequences, access to remote data sources and visualization of molecular dynamics
trajectories. Sirius can be used for scientific visualization
and analysis, as well as for chemistry
and biology
instruction.
Sirius is based on molecular graphics code and data structures developed as a part of Molecular Biology Toolkit.
, so it's fully compatible with existing scripts. Additional commands introduced in Sirius have been added to provide support for manipulation of multiple structures loaded at the same time, and to enable more flexible selection.
Existing RasMol scripts can be imported and run within Sirius to produce high quality representations of encoded molecular scenes. Since RasMol uses a coordinate system that differs from that Sirius, internal conversion is performed when RasMol scripts are imported, so that any orientation changes are shown correctly. Any manually entered commands, however, are executed according to the Sirius coordinate system. For details, refer to Sirius help.
Sirius supports a number of predefined atom/residue sets and color schemes, as well as allows for editing of scripts using the Command Panel interface. In addition, logical operators and parentheses can be used to create complex selection commands.
and CHARMM
simulations, including compressed and AMBER out files. RMSD changes along the trajectory can be calculated using user-defined atom subsets and displayed in an interactively updated graph. In order to reduce memory requirements, large multifile simulations may be loaded in a buffered mode. If a simulation involves changes in protein
fold, Sirius can be set to track and recompute displayed secondary structure
features in real time, which provides a convenient way to observe transformations of the structure. The full trajectory or selected frames can be exported as QuickTime
video or a set of POV-Ray
scene snapshots that can later be converted to a high quality movie.
, Linux
and Mac OS X
. In addition to providing the downloads, the project site contains Sirius help system, tutorials and screenshots.
San Diego Supercomputer Center
The San Diego Supercomputer Center is an organized research unit of the University of California, San Diego . Physically, SDSC is located on the east end of Eleanor Roosevelt College on the campus of UCSD....
. Sirius is designed to support advanced user requirements that go beyond simple display of small molecule
Molecule
A molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...
s and 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...
s. In addition to high quality interactive 3D graphics, Sirius supports structure building, displaying 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...
or DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
primary sequences, access to remote data sources and visualization of molecular dynamics
Molecular dynamics
Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...
trajectories. Sirius can be used for scientific visualization
Scientific visualization
Scientific visualization is an interdisciplinary branch of science according to Friendly "primarily concerned with the visualization of three-dimensional phenomena , where the emphasis is on realistic renderings of volumes, surfaces, illumination sources, and so forth, perhaps...
and analysis, as well as for chemistry
Chemistry
Chemistry is the science of matter, especially its chemical reactions, but also its composition, structure and properties. Chemistry is concerned with atoms and their interactions with other atoms, and particularly with the properties of chemical bonds....
and biology
Biology
Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy. Biology is a vast subject containing many subdivisions, topics, and disciplines...
instruction.
The key features
Sirius supports a variety of applications with a set of features that include- Building and editing chemical structures using a library of fragments
- Protein structure and sequence alignmentSequence alignmentIn bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are...
- Command line interpreter and scripting support fully compatible with existing RasMolRasMolRasMol 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...
scripts - Full support for molecular dynamicsMolecular dynamicsMolecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...
trajectory visualization - BLASTBLASTIn bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
search directly in Protein Data BankProtein Data BankThe Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
and UniprotUniProtUniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many of which are derived from genome sequencing projects...
databases - Ability to move parts of the loaded data while freezing the rest
- Interactive calculation of hydrogen bondHydrogen bondA hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen must be covalently bonded to another electronegative atom to create the bond...
ing, steric clashes, Ramachandran plotRamachandran plot-Introduction and early history:A Ramachandran plot , originally developed in 1963 by G. N. Ramachandran C. Ramakrishnan and V...
s - Support for all major structure and sequence formats
- Bundled POV-RayPOV-RayThe Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program available for a variety of computer platforms. It was originally based on DKBTrace, written by David Kirk Buck and Aaron A. Collins. There are also influences from the earlier Polyray raytracer contributed by its author...
for creating photorealistic images - Integrated selection and coloring across individual visualization components
Sirius is based on molecular graphics code and data structures developed as a part of Molecular Biology Toolkit.
RasMol-compatible scripting
Sirius features a command line interpreter that can be used to quickly manipulate structure appearance and orientation. The set of commands has been patterned after RasMolRasMol
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...
, so it's fully compatible with existing scripts. Additional commands introduced in Sirius have been added to provide support for manipulation of multiple structures loaded at the same time, and to enable more flexible selection.
Existing RasMol scripts can be imported and run within Sirius to produce high quality representations of encoded molecular scenes. Since RasMol uses a coordinate system that differs from that Sirius, internal conversion is performed when RasMol scripts are imported, so that any orientation changes are shown correctly. Any manually entered commands, however, are executed according to the Sirius coordinate system. For details, refer to Sirius help.
Sirius supports a number of predefined atom/residue sets and color schemes, as well as allows for editing of scripts using the Command Panel interface. In addition, logical operators and parentheses can be used to create complex selection commands.
Visualization of molecular dynamics trajectories
Sirius contains a full-featured molecular dynamics (MD) visualization component. It can read output files from AMBERAMBER
AMBER is a family of force fields for molecular dynamics of biomolecules originally developed by the late Peter Kollman's group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields...
and CHARMM
CHARMM
CHARMM is the name of a widely used set of force fields for molecular dynamics as well as the name for the molecular dynamics simulation and analysis package associated with them...
simulations, including compressed and AMBER out files. RMSD changes along the trajectory can be calculated using user-defined atom subsets and displayed in an interactively updated graph. In order to reduce memory requirements, large multifile simulations may be loaded in a buffered mode. If a simulation involves changes in 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...
fold, Sirius can be set to track and recompute displayed secondary structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
features in real time, which provides a convenient way to observe transformations of the structure. The full trajectory or selected frames can be exported as QuickTime
QuickTime
QuickTime is an extensible proprietary multimedia framework developed by Apple Inc., capable of handling various formats of digital video, picture, sound, panoramic images, and interactivity. The classic version of QuickTime is available for Windows XP and later, as well as Mac OS X Leopard and...
video or a set of POV-Ray
POV-Ray
The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program available for a variety of computer platforms. It was originally based on DKBTrace, written by David Kirk Buck and Aaron A. Collins. There are also influences from the earlier Polyray raytracer contributed by its author...
scene snapshots that can later be converted to a high quality movie.
Sirius access and download
Sirius is distributed freely from the project website to individuals affiliated with academic and non-profit organizations. Native desktop application installers are available for WindowsMicrosoft 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...
, Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...
and Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...
. In addition to providing the downloads, the project site contains Sirius help system, tutorials and screenshots.
See also
- List of molecular graphics systems
- List of web resources for visualizing molecular dynamics
- Molecular modellingMolecular modellingMolecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...
- 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"...
- Molecular dynamicsMolecular dynamicsMolecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...