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Bsoft
{{Short description, Structural biology software Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in structural biology are approached with a highly modular design, allowing fast development of new algorithms without the burden of issues such as file I/O. It provides an easily accessible interface, a resource that can be and has been used in other packages. Several workflows such as for single particle analysis and tomography are supported with parameter exchange as well as the ability to do distributed processing across heterogeneous clusters of computers. Technical details Version: 1.8.8 OS support: Unix (Mac OS X, IRIX, Linux, AIX, Solaris, Tru64), OpenVMS Format support: * Images: BioRad, Brix, CCP4, Digital Instruments, Digital Micrograph, DSN6, EM, Goodford, GRD, Imagic, JPEG, MFF, Image Magick, MRC, PIC, PIF, PNG, Spider, Suprim, TIFF, RAW * Micrograph parameters: STAR (Bsoft ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CCP4 (file Format)
The CCP4 file format is file generated by the Collaborative Computational Project Number 4 in 1979. The file format for electron density has become industry standard in X-ray crystallography and Cryo-electron microscopy where the result of the technique is a three-dimensional grid of voxels each with a value corresponding to density of electrons (see wave function) The CCP4 format is supported by almost every molecular graphics suite that supports volumetric data. The major packages include: *Visual molecular dynamics *PyMOL *UCSF Chimera *Bsoft *Coot *MOE See also *MTZ (file format) *MRC (file format) * EZD (file format) *Chemical file format **Protein Data Bank (file format) *Voxel In 3D computer graphics, a voxel represents a value on a regular grid in three-dimensional space. As with pixels in a 2D bitmap, voxels themselves do not typically have their position (i.e. coordinates) explicitly encoded with their values. Ins ... - one way of presenting 3D densities Externa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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, and others. Initially intended for use inside the Bell System, AT&T licensed Unix to outside parties in the late 1970s, leading to a variety of both academic and commercial Unix variants from vendors including University of California, Berkeley (Berkeley Software Distribution, BSD), Microsoft (Xenix), Sun Microsystems (SunOS/Solaris (operating system), Solaris), Hewlett-Packard, HP/Hewlett Packard Enterprise, HPE (HP-UX), and IBM (IBM AIX, AIX). In the early 1990s, AT&T sold its rights in Unix to Novell, which then sold the UNIX trademark to The Open Group, an industry consortium founded in 1996. The Open Group allows the use of the mark for certified operating systems that comply with the Single UNIX Specification (SUS). Unix systems are chara ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OpenVMS
OpenVMS, often referred to as just VMS, is a multi-user, multiprocessing and virtual memory-based operating system. It is designed to support time-sharing, batch processing, transaction processing and workstation applications. Customers using OpenVMS include banks and financial services, hospitals and healthcare, telecommunications operators, network information services, and industrial manufacturers. During the 1990s and 2000s, there were approximately half a million VMS systems in operation worldwide. It was first announced by Digital Equipment Corporation (DEC) as VAX/VMS (''Virtual Address eXtension/Virtual Memory System'') alongside the VAX-11/780 minicomputer in 1977. OpenVMS has subsequently been ported to run on DEC Alpha systems, the Itanium-based HPE Integrity Servers, and select x86-64 hardware and hypervisors. Since 2014, OpenVMS is developed and supported by VMS Software Inc. (VSI). OpenVMS offers high availability through clustering — the ability to distribute the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
JPEG
JPEG ( ) is a commonly used method of lossy compression for digital images, particularly for those images produced by digital photography. The degree of compression can be adjusted, allowing a selectable tradeoff between storage size and image quality. JPEG typically achieves 10:1 compression with little perceptible loss in image quality. Since its introduction in 1992, JPEG has been the most widely used image compression standard in the world, and the most widely used digital image format, with several billion JPEG images produced every day as of 2015. The term "JPEG" is an acronym for the Joint Photographic Experts Group, which created the standard in 1992. JPEG was largely responsible for the proliferation of digital images and digital photos across the Internet, and later social media. JPEG compression is used in a number of image file formats. JPEG/Exif is the most common image format used by digital cameras and other photographic image capture devices; along with JPEG ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Image Magick
ImageMagick, invoked from the command line as magick, is a free and open-source cross-platform software suite for displaying, creating, converting, modifying, and editing raster images. Created in 1987 by John Cristy, it can read and write over 200 image file formats. It is widely used in open-source applications. History ImageMagick was created in 1987 by John Cristy when working at DuPont, to convert 24-bit images (16 million colors) to 8-bit images (256 colors), so they could be displayed on most screens at the time. It was freely released in 1990 when DuPont agreed to transfer copyright to ''ImageMagick Studio LLC'', still currently the project maintainer organization. In May 2016, it was reported that ImageMagick had a vulnerability through which an attacker can execute arbitrary code on servers that use the application to edit user-uploaded images. Security experts including CloudFlare researchers observed actual use of the vulnerability in active hacking attempts. Th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MRC (file Format)
MRC is a file format that has become an industry standard in cryo-electron microscopy (cryoEM) and electron tomography (ET), where the result of the technique is a three-dimensional grid of voxels each with a value corresponding to electron density or electric potential. It was developed by the MRC ( Medical Research Council, UK) Laboratory of Molecular Biology. In 2014, the format was standardised. The format specification is available on thCCP-EM website The MRC format is supported by many of the software packages listed in b:Software Tools For Molecular Microscopy. See also *CCP4 (file format) The CCP4 file format is file generated by the Collaborative Computational Project Number 4 in 1979. The file format for electron density has become industry standard in X-ray crystallography and Cryo-electron microscopy where the result of the ... References External links MRC specification Computational chemistry Structural biology Computer file formats {{Biophy ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Portable Network Graphics
Portable Network Graphics (PNG, officially pronounced , colloquially pronounced ) is a raster-graphics file format that supports lossless data compression. PNG was developed as an improved, non-patented replacement for Graphics Interchange Format (GIF) — unofficially, the initials PNG stood for the recursive acronym "PNG's not GIF". PNG supports palette-based images (with palettes of 24-bit RGB or 32-bit RGBA colors), grayscale images (with or without an alpha channel for transparency), and full-color non-palette-based RGB or RGBA images. The PNG working group designed the format for transferring images on the Internet, not for professional-quality print graphics; therefore non-RGB color spaces such as CMYK are not supported. A PNG file contains a single image in an extensible structure of ''chunks'', encoding the basic pixels and other information such as textual comments and integrity checks documented in RFC 2083. PNG files use the file extension PNG or png and hav ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
TIFF
Tag Image File Format, abbreviated TIFF or TIF, is an image file format for storing raster graphics images, popular among graphic artists, the publishing industry, and photographers. TIFF is widely supported by scanning, faxing, word processing, optical character recognition, image manipulation, desktop publishing, and page-layout applications. The format was created by the Aldus Corporation for use in desktop publishing. It published the latest version 6.0 in 1992, subsequently updated with an Adobe Systems copyright after the latter acquired Aldus in 1994. Several Aldus or Adobe technical notes have been published with minor extensions to the format, and several specifications have been based on TIFF 6.0, including TIFF/EP (ISO 12234-2), TIFF/IT (ISO 12639), TIFF-F (RFC 2306) and TIFF-FX (RFC 3949). History TIFF was created as an attempt to get desktop scanner vendors of the mid-1980s to agree on a common scanned image file format, in place of a multitude of proprietary for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Data Bank (file Format)
The Protein Data Bank (PDB) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank. The PDB format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, secondary structure assignments, as well as atomic connectivity. In addition experimental metadata are stored. The PDB format is the legacy file format for the Protein Data Bank which now keeps data on biological macromolecules in the newer mmCIF file format. History The PDB file format was invented in 1976 as a human-readable file that would allow researchers to exchange protein coordinates through a database system. Its fixed-column width format is limited to 80 columns, which was based on the width of the computer punch cards that were previously used to exchange the coordinates.Berman, Helen M. "The protein data bank: a historical perspective." Acta Crystallographica Section A 64.1 (2007): 88-9 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
EM Data Bank
The EM Data Bank or Electron Microscopy Data Bank (EMDB) collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens. It was established in 2002 at the MSD/PDBe group of the European Bioinformatics Institute (EBI), where the European site of the EMDataBank.org consortium is located. , the resource contained over 2,600 entries with a mean resolution of 15Å. Deposition of data was originally via the EMdep deposition interface, but since 2016 deposition of data has been incorporated into the wwPDB OneDep interface. Under the NIH Unified Data Resource for CryoEM, the Research Collaboration for Structural Biology (RCSB) also acts as a deposition, data processing and distribution center for EMDB data, while the National Center for Macromolecular Imaging (NCMI) is a collaborative partner in providing services and tools concerning the EMDB. EM Data Bank also provides the EMsearch search tool and data can also be queried at RCSB, EM ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Software Tools For Molecular Microscopy
Transmission electron cryomicroscopy (CryoTEM), commonly known as cryo-EM, is a form of cryogenic electron microscopy, more specifically a type of transmission electron microscopy (TEM) where the sample is studied at cryogenic temperatures (generally liquid-nitrogen temperatures). Cryo-EM is gaining popularity in structural biology. The utility of transmission electron cryomicroscopy stems from the fact that it allows the observation of specimens that have not been stained or fixed in any way, showing them in their native environment. This is in contrast to X-ray crystallography, which requires crystallizing the specimen, which can be difficult, and placing them in non-physiological environments, which can occasionally lead to functionally irrelevant conformational changes. Advances in electron detector technology, particularly DED (Direct Electron Detectors) as well as more powerful software imaging algorithms have allowed for the determination of macromolecular structures at n ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
