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AppCiter

AppCiter will help you create a bibliography of the programs you wish to cite. Use the "AppCiter+1" button in the Name column to choose your programs. Proceed to Step 2 to view available citations.

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Name Description Links  
3DNA
  • Xiang-Jun Lu
- a package for analyzing, visualizing and rebuilding 3-dimensional nucleic acid structures. 3DNA was created by Dr. Xiang-Jun Lu in the laboratory of Professor Wilma K. Olson at the Department of Chemistry and Chemical Biology, Rutgers-the State University of New Jersey.
adxv
  • Andy Arvai
- displays protein crystallography X-ray diffraction data. The data may be displayed as a 2-D image, 3-D wire mesh or as integer pixel values. Data files may be saved in tiff or postscript format. adxv was written by Andrew Arvai.
ARP/wARP
  • Victor Lamzin
  • Anastassis Perrakis
An interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models. At the request of the developer, this software is licensed on a per-user basis. To obtain an ARP/wARP license and enable use in the SBGrid environment, each user should: - visit the [ARP/wARP website](http://www.embl-hamburg.de/ARP/) to request a license. - download any of the current ...
autoPROC
autoPROC combines third-party processing programs with new tools and an automated workflow script for automated treatment of multi-sweep X-ray diffraction data.

autoPROC is freely available to academic labs, but each lab must register with Global Phasing before this software can be used. To include this software in your installation, please submit a license request to http://www.globalphasing.com/autoproc/licence/request.html, then ...
BALBES
  • Fei Long
  • Garib Murshudov
- aims to integrate into one system all the components necessary for finding a solution structure by MR. It consists of a database, scientific programs and a python pipeline. The system is automated and needs no user intervention when running a complicated combination of jobs, such as model searching, molecular replacement and refinement.
BEST
  • Gleb Bourenkov
  • Alexander Popov
- a program for optimal planning of X-ray data collection from protein crystals.

BEST is freely available to non-profit labs, but each lab must register with EMBL before we can install the software. To include this software in your installation, please register here http://www.embl-hamburg.de/BEST/download_request3.1.html, then send a copy of your registration confirmation to us at licensing@sbgrid.org.

BnP
  • William Furey
  • Charles Weeks
- Buffalo and Pittsburgh) an interface for complete protein phasing suite includes SnB and Phases.
BUSTER
  • Gerard Bricogne
  • Claus Flensberg
BUSTER is a software system for crystallographic structure determination by Bayesian statistical methods

BUSTER is freely available to academic labs, but each lab must register with Global Phasing before this software can be used. To enable this software in your installation, please submit a license request to: http://www.globalphasing.com/autoproc/licence/request.html. Then copy your license file to /programs/local/buster ...
CCP4
  • Charles Ballard
  • Ronan Keegan
- (Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries which can be used for macromolecular structure determination by X-ray crystallography.

CCP4 is freely available to non-profit labs, but each lab must complete the CCP4 license and return the executed document directly to the STFC Daresbury Laboratory, as specified on the CCP4 webpage.
CNS
  • Axel Brunger
- an X-ray crystallography suite used for refinement, phasing, and molecular replacement
COMO
- is a program for molecular replacement calculations, using the combined molecular replacement method.
Coot
  • Paul Emsley
- (Crystallographic Object-Oriented Toolkit) supports model building and real space refinement. The application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.
crop
  • Niko Grigorieff
crop is a program for cutting sections out of 2D and 3D density maps.
CrystFEL
  • Thomas White
CrystFEL is a suite of programs for processing diffraction data acquired "serially" in a "snapshot" manner, such as when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser source.
diffmap
  • Niko Grigorieff
diffmap is a program to calculate difference maps between two density maps. The maps must have the same overall dimensions and need to be aligned with each other.
DPS
  • Marian Szebenyi
- (Data Processing Suite) a suite of programs for processing of single crystal X-ray diffraction data of proteins, viruses, nucleic acids and other large biological complexes with an emphasis on data collected at synchrotron sources. The software website has not been updated since 2000, but software updates are posted on a regular basis.
d*TREK
- a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors.

d*TREK is a commercial software application that we can include in your installation for ease of use, but that requires you or your institute to have a current license in place. To enable the SBGrid installation for d*TREK please send an email to licensing@sbgrid ...
Eden
  • Hanna Szoke
- a crystallographic real-space electron-density refinement and optimization program that produces electron density maps with minimal model bias in a robust manner.
Elves
  • Tom Alber
  • James Holton
- automates most of the repetitive and mindless procedures used in solving macromolecular crystal structures, and is capable of autonomously carrying out all the steps needed to convert raw X-ray diffraction image data to a phased electron density map.
EPMR
  • Charles Kissinger
- a program that finds crystallographic molecular replacement solutions using an evolutionary search algorithm. The program directly optimizes three rotational and three positional parameters for the search model with respect to the correlation coefficient between Fo and Fc.
HKL2000
  • Wladek Minor
- A data processing suite for X-ray crystallography that provides a sleek interface for devising a data collection strategy and processing data. HKL is based on the extended versions of Denzo, Xdisplayf and Scalepack.HKL was developed and is maintained by Wladek Minor (University of Virginia).

HKL2000 is a commercial software application that we can include in your installation for ease of use, but that ...
HKL2MAP
  • Thomas Schneider
A graphical user-interface for macromolecular phasing. HKL2MAP is freely available to non-profit labs, but each lab must register with EMBL before we can install the software. To include this software in your installation, please register [here][1], then send a copy of your registration confirmation to us at licensing@sbgrid.org . [1]: http://webapps.embl-hamburg.de/bundle/download.php?hkl2mp=true&sitcom=false
iMosflm
  • Harry Powell
- a data processing application for macromolecular crystallography. iMosflm (Graphical User Interface) and Mosflm (data processing application) are distributed with this package. iMosflm is maintained by Harry Powell and distributed under a CCP4 license.
knuspr
knuspr finds the positions of phosphates and bases in electron density maps with a fairly high degree of reliability.
LAFIRE
  • Lafire Developer Group
  • M Yao
- (Local-correlation-coefficient-based Automatic FItting for REfinement) is an automatic refinement system for protein crystallography. The system starts with an initial model (approximate or partial model) and finishes with the final structure including water molecules. LAFIRE uses the refinement programs CNS or Refmac5.
MAIN
  • Dusan Turk
- a model building application for X-ray crystallography.
MIExpert
  • John Badger
- an expert system for running molecular replacement and refinement applications, and analyzing the data obtained from high-throughput co-crystallography and fragment screening projects. MIExpert is a module of MIFit.
MIFit
  • John Badger
  • Bradley Smith
- an interactive graphics application for molecular modeling, fitting, and refinement of protein structures from X-ray crystallography developed by Bradley Smith as an Open Source project while working for Rigaku/MSC Inc. A particular focus of the MIFit software is the efficient solution and analysis of protein:ligand complexes.
MMTSB Toolset
  • Charles L Brooks
Multiscale Modeling Tools for Structural Biology
MOSFLM
  • Harry Powell
- a package for processing film and image plate data.
mrtailor
mrtailor - PDB preparation tool for use with ProSmart or for Molecular Replacement
O
  • Alwyn Jones
- a model building application for X-ray crystallography.
pdb-care
The pdb-care program is able to identify and assign carbohydrate structures using only atom types and their 3D atom coordinates given in PDB-files. Looking up a translation table where systematic names and the respective PDB residue codes are listed, both assignments are compared and inconsistencies are reported. Additionally, the reliability of reported and calculated connectivities for molecules listed within the HETATOM records is checked ...
PDB_REDO
  • Robbie Joosten
PDB_REDO refines any structural model you are working on, by optimising REFMAC refinement and by partial model rebuilding. The process is fully automated so you only need to provide an initial structure model and your reflection data.
PDB Validation Suite
  • RCSB
- a set of tools used by the PDB for processing and checking structure data.
PHASES
  • William Furey
- computes phase angles for diffraction data from macromolecular crystals. The package contains programs for merging and scaling of native and derivative data sets; analyzing difference statistics; computing Patterson and electron density maps; searching for peaks; refining heavy atoms (or protein domains as rigid groups); computing phases by MIR (multiple isomorphous replacement), SIR (single isomorphous replacement), SAS (single wavelength anomalous scattering), SIRAS (single isomorphous replacement ...
PHENIX
  • Paul Adams
  • Pavel Afonine
  • Nat Echols
  • Ralf Grosse-Kunstleve
- (Python-based Hierarchical Environment for INtegrated Xtallography) provides tools for automated structure solution by X-ray crystallography. The PHENIX software provides algorithms to proceed from reduced intensity data to a refined molecular model, and facilitate structure solution for both the novice and expert crystallographer. We also maintain a recent PHENIX nightly build in the software suite.
PROFphd
  • Burkhard Rost
- a new package added as part of the pipeline to create fragments for Rosetta. For commercial users, Biosof LLC (www.bio-sof.com) offers additional customization and data analysis of PROFphd.
Python Macromolecular Library
  • E.A. Merritt
  • Jay Painter
is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.
RCrane
  • Kevin Keating
  • Anna Pyle
- allows for semi-automated building of RNA structure within Coot.
Reduce
  • David Richardson
  • Jane Richardson
- a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided.
REFMAC
  • Garib Murshudov
  • Rob Nicholls
- carries out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. There are options to use different minimization methods. (At the moment only CGMAT is active.) REFMAC also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc ...
Remediator
  • Dave Richardson
  • Jane Richardson
Remediator converts PDB files between PDBv2.3 and PDBv3.2 formats. It can accurately and rapidly convert in either direction: old to new OR new to old. Atom records of type ATOM, HETATM, TER, ANISOU, SIGATM, SIGUIJ, and LINK are converted, as are DNA residue names (e.g., A, C, T, G of v2.3 cf. DA, DC, DT, DG of v3.2).
REPLACE
  • Liang Tong
a suite of programs for molecular replacement calculations. It currently consists of two major programs, GLRF for rotation function calculations and TF for translation function calculations. In addition, a small program (ANGCAL) is a convenient tool for conversions between angles and matrices.
Ringer
  • Ringer Developer Group
  • Terry Lang
- a program to detect molecular motions by automatic electron density sampling.
RMERGE
  • Manfred Weiss
RMERGE can calculate Rpim for merging, which HKL (scalepack) does not. There's no official manual right now but you can see Cell 147, 199-208 for more information.
RSRef2000
  • Michael Chapman
  • RSRef Developer Group
- supports real-space simulated annealing refinement with X-ray data. RSRef uses an electron density function that is resolution dependent, so that it accurately models a medium resolution map. When combined with TNT’s Geometry, or CNS, full stereochemical refinement is possible. RSRef can be used to quickly pre-refine a protein structure during or after model building, or to completely refine structures with high non-crystallographic symmetry ...
SHARP/autoSHARP
  • Gerard Bricogne
  • Clemens Vonrhein
- an automated structure solution pipeline built around the heavy-atom refinement and phasing program SHARP, the density modification program SOLOMON, and the ARP/wARP package for automated model building and refinement (using REFMAC). It allows fully automated structure solution, from merged reflection data to an initial model, without any user intervention.
SHELX-2013
  • George Sheldrick
A set of programs for macromolecular phasing. SHELXC is designed to provide a simple and fast way of setting up the files for the programs SHELXD (heavy atom location) and SHELXE (phasing and density modification) for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods. hkl2map provides a simple user interface to SHELX and is installed separately. SHELX was written and is actively ...
SHELX-97
  • George Sheldrick
- a set of programs for macromolecular phasing. SHELXC is designed to provide a simple and fast way of setting up the files for the programs SHELXD (heavy atom location) and SHELXE (phasing and density modification) for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods. hkl2map provides a simple user interface to SHELX and is installed separately. SHELX was written and is actively ...
SITUS
  • Situs Developer Team
  • Willy Wriggers
- a program package for modeling of atomic resolution structures into low-resolution density maps. The software supports both rigid-body and flexible docking using a variety of fitting strategies.
SnB
  • SnB Developer Group
  • Russ Miller
- determination of the anomalously scattering substructures of selenomethionyl-substituted proteins containing as many as 160 Se sites. SnB is based on Shake-and-Bake, a dual-space direct-methods procedure.
SOLVE/RESOLVE
  • Tom Terwilliger
- a program that can automatically search for heavy atom sites, calculate initial phases and perform density modification.
SOMoRe
  • Diane Jamrog
- 6D global search and multi-start optimization molecular replacement package.
Untangle
  • Liev Buts
- a program designed to separate overlapping diffraction patterns from a set of crystals with slightly different orientations. The program can read x files from the HKL Package and CCP4 MTZ files. It can output data files from which the offending reflections have been removed. A case study for a dataset from an aggregate with three dominant subcrystals can be found here.
USF Gerard Utilities
  • Gerard Kleywegt
- the Swiss Army knife of crystallography tools. The installation includes the packages from RAVE, SBIN, X-UTIL, VOIDOO, DEJAVU and SPASM.
WASP
  • Enrico DiCera
  • David Gohara
- searches PDB files for misidentified water molecules that should be modeled as cations.
XDS
  • Wolfgang Kabsch
- X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method. Written by Wolfgang Kabsch (see Tales about Developers section on SBGrid website).
XDSAPP
  • Uwe Mueller
- XDSAPP (Krug et al., 2012) is a graphical user interface for the easy and convenient processing of diffraction data sets using XDS. It is available for all our experimental end-stations. It automates the data processing and generates graphical plots of various data set statistics provided by XDS. By incorporating additional software, further information on certain features of the dataset, such as radiation decay or ...
XDSGUI
  • Wolfgang Brehm
  • Michael Hoffer
XDSGUI is a GUI (graphical user interface) for XDS that is supposed to help both novice and experienced users. It graphically displays the ASCII and cbf files that XDS writes, and can run useful shell commands with a simple mouse click. The design goal of the program is to enable XDS data processing without the command line, and to supply additional graphical information, in ...
XDSi
  • Petri Kursula
- allows processing of datasets in a given directory with minimum effort when you supply it with a result directory and the directory where your frames are stored. All datasets consisting of more than 100 frames within the given directory and all its subdirectories will be processed. For each dataset a space group assignment is done using POINTLESS from the CCP4 software package. Plots of ...
xdsme
xdsme is a collection of python scripts made to simplify the processing of crystal diffraction images with the XDS Program Package (X-ray Detector Software, http://xds.mpimf-heidelberg.mpg.de/). Provided that the diffraction parameters are well recorded in the diffraction image headers, XDS data processing can be started with a simple command lines (see manual for details).
XDSSTAT
  • Kay Diederichs
- a home-brewn program that prints various statistics (that are not available from XDS itself) in the form of tables and images.
XDS-Viewer
  • Michael Hoffer
  • Wolfgang Kabsch
- an X-ray diffraction and control image viewing utility for data processed using the XDS program package.
XIA2
  • Graeme Winter
- an automated data reduction system designed to work from raw diffraction data and a little metadata, and produce usefully reduced data in a form suitable to immediately start phasing and structure solution, e.g. through Mr BUMP or your favorite experimental phasing suite.
XRayView
  • George Phillips
XRayView uses interactive computer graphics to introduce basic concepts of X-ray diffraction by crystals, including the reciprocal lattice, the Ewald sphere construction, Laue cones, the wavelength dependence of the reciprocal lattice, primitive and centered lattices and systematic extinctions, rotation photography, Laue photography, space group determination and Laue group symmetry, and the alignment of crystals by examination of reciprocal space.