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a versatile, integrated software system for the analysis, rebuilding and visualization of 3-dimensional nucleic acid structures.
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.
consists of the standalone program ALBULA VIEWER, a fast and easy-to-use program that allows optimal visualization of PILATUS and EIGER data, and ALBULA API, a Python programming interface for displaying images and performing operations and calculations. The API enables you to easily integrate the viewer functionality into your beamline infrastructure or experimental setup.
the structure-solution program that constitutes a general crystallographic Ab Initio macromolecular phasing method for 2Å data, based on the combination of location of model fragments like small α-helices with PHASER and density modification with SHELXE.
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 enable ARP/wARP license in the SBGrid environment, each user should:

- visit the ARP/wARP website.
- download any of the current versions via your web browser.
- in the shell run 'sbgrid-register -r path/to ...
combines third-party processing programs with new tools for automated data processing of single-sweep, multi-sweep and multi-crystal X-ray diffraction data.
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.
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.
(Buffalo n' Pittsburgh Interface) for complete protein phasing; combines SnB and the Phases Suite.
a software system containing crystallographic structure refinement using Bayesian statistical methods (BUSTER), ligand fitting (rhofit) and a fully automated pipeline (Pipedream) to drive a structure based fragment/ligand screening pathway.

(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography. All SBGrid members must complete the CCP4 license and return the executed document directly to The Science and Technology Facilities Council as specified on the CCP4 licensing page located here: http://www.ccp4.ac.uk/ccp4license.php.
(Crystallography & NMR System) an X-ray crystallography suite used for refinement, phasing, and molecular replacement.
a program for molecular replacement calculations, using the combined molecular replacement method.
(Crystallographic Object-Oriented Toolkit) supports model building and real space refinement. This application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.
a program for cutting sections out of 2D and 3D density maps.
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.
(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images designed to cope with the ever increasing volumes and rates of data collection, and with the developments in experimental methodology, from shutterless, fine-sliced rotation scans through to the randomly-oriented snapshots of serial crystallography. This software utilizes techniques of parallel processing using multiple CPU and GPU machines, facilitating not ...
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.
(Data Processing Suite) a suite of programs for processing 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.
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 ...
a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors. This entry is for the free version of d*TREK, contains neither the Reqab absorption correction nor the absorption correction written by Higashi. It also does not make any use of collision file information during the strategy generation.
a crystallographic real-space electron-density refinement and optimization program that produces electron density maps with minimal model bias in a robust manner.
a simple program that converts diffraction images from EIGER in the HDF5 format to the miniCBF format.
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.
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.
used by the XDS package for the processing of EIGER HDF5 data.
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 ...
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
a data processing application for macromolecular crystallography. iMosflm (Graphical User Interface) and Mosflm (data processing application) are distributed with this package.
finds the positions of phosphates and bases in electron density maps with a fairly high degree of reliability.
(Local-correlation-coefficient-based Automatic FItting for REfinement) 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.
a model building application for X-ray crystallography.
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.
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.
(Multiscale Modeling Tools for Structural Biology) a collection of perl-based user-level utilities as well as programming libraries for multiscale protein structure modeling. Intended applications include protein structure prediction, loop modeling, structure refinement, and structure evaluation/scoring.
a protein structure analysis platform offering quality validation for 3D structures of proteins, nucleic acids and complexes.
a package for processing film and image plate data.
a PDB preparation tool for use with ProSmart or for Molecular Replacement
an HDF5 read plugin for XDS. NEGGIA presents HDF5 data to XDS in a fully parallelized way, directly and without interconversion and speeds up the processing of HDF5 data.
a model building application for X-ray crystallography.
identifies and assigns 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.
The pdb_extract Program Suite contains tools and examples for extracting mmCIF data from structure determination applications.
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.
a set of tools used by the PDB for processing and checking structure data.
computes phase angles for diffraction data from macromolecular crystals with 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, SIR, SAS, SIRAS, MIRAS, or from atomic coordinates for an input model; noncrystallographic symmetry averaging; combining phases from ...
(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.
a linear-scaling, semiempirical quantum mechanics (SE-QM) program DivCon with the Phenix X-ray refinement engine. Phenix/DivCon does not utilize CIF(s), link restraints and other refinement parameters so there are fewer assumptions about the model. Accurate energy and density scoring tools also allow tautomer/protomer and “flip state” determination.
creates fragments for Rosetta. For commercial users, Biosof LLC (www.bio-sof.com) offers additional customization and data analysis of PROFphd.
a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.
allows for semi-automated building of RNA structure within Coot.
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.
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 ...
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).
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.
A program to detect molecular motions by automatic electron density sampling.
calculates 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.
a program for the fitting of atomic models into electron density maps derived from x-ray crystallography or electron microscopy (EM).
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 ...
an automated structure solution pipeline built around the heavy-atom refinement and phasing program SHARP, the substructure determination program SHELXD, the density modification program SOLOMON and the model building programs BUCCANEER and ARP/wARP. It allows fully automated structure solution by experimental phasing, from merged reflection data to an initial model, without any user intervention.
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 ...
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 ...
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.
based on Shake-and-Bake (a dual-space direct-methods procedure), a computer program for the determination of the anomalously scattering substructures of selenomethionyl-substituted proteins containing as many as 160 Se sites.
a program that can automatically search for heavy atom sites, calculate initial phases and perform density modification.
6D global search and multi-start optimization molecular replacement package.
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.
the Swiss Army knife of crystallography tools. The installation includes the packages from RAVE, SBIN, X-UTIL, VOIDOO, DEJAVU and SPASM. And includes the following binaries: * aconio * cello * comap * crave * essens * flood * lsqman * mama.debug * mapman * mave * moleman2 * o2d * oops * prof * site2rt * solex * ssencs * xpand
searches PDB files for misidentified water molecules that should be modeled as cations.
(X-ray Detector Software) a software tool for processing single-crystal monochromatic diffraction data recorded by the rotation method.
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 the presence of pseudo-translational symmetry and ...
a program for generating delta-CC1/2 values, for individual frames, or groups of frames, from a single dataset collected with the rotation method and processed by XDS.
a GUI (graphical user interface) for XDS designed to help both novice and experienced users; it enable XDS data processing without the command line and supplies additional graphical information in a simple, user-modifiable and user-extensible way. It graphically displays the ASCII and cbf files that XDS writes and can run useful shell commands with a simple mouse click.
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 ...
a collection of python scripts made to simplify the processing of crystal diffraction images with the XDS Program Package. 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).
a home-brewn program that prints various statistics (that are not available from XDS itself) in the form of tables and images.
an X-ray diffraction and control image viewing utility for data processed using the XDS program package.
an expert system for automated reduction of X-Ray diffraction data from macromolecular crystals, making use of existing software (CCP4, XDS, Phenix, CCTBX.) XIA2 is now included with DIALS.
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.