X-ray Crystallography

SBGrid supports 44 x-ray crystallography software titles. The following software packages are supported by SBGrid; availability of a specific software package may be limited based on license requirements.

Software Title Description Linux 32-bit Linux 64-bit OS X Intel Links

3DNA

- a package for analyzing, visualizing and rebuilding 3-dimensional nucleic acid structures. 3DNA was created by Dr. Xiang-Jun ...

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  • 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.

Developers

Wilma Olson

Xiang-Jun Lu

Categories

X-ray Crystallography

Structure Analysis

Structure Visualization

Nucleic Acids

Versions

Citations

Xiang-Jun Lu and Wilma K Olson (2008) "3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures." Nature Protocols, 3, 1213-1227.


Static link to the SBGrid 3DNA page.

adxv

- displays protein crystallography X-ray diffraction data. The data may be displayed as a 2-D image, 3-D wire ...

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  • 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.

Developers

Andy Arvai

Categories

X-ray Crystallography

Versions

Technical Notes

Adxv will display data from most current detectors:

  • ADSC ccd
  • Mar ccd
  • APS 3x3 ccd
  • Mar image plate (old and new format)
  • Raxis II & IV
  • Fuji image plate
  • Crystallographic Binary Format (CBF)
  • XDS .pck files
  • Raw binary 8, 16 & 32 bit integer data


Static link to the SBGrid adxv page.

ARP/wARP

an interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models. This software is ...

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an interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models.

This software is licensed on a per-lab basis. Please visit the ARP/wARP website to request a license, and then email help@sbgrid.org to have it added to your installation.

The following authors developed this software: Victor Lamzin, Gerrit Langer, Ciaran Carolan, Saul Hazledine, Philipp Heuser, Tim Wiegels, Anastassis Perrakis, Krista Joosten.

Developers

Martin Raditsch

Anastassis Perrakis

Victor Lamzin

Categories

X-ray Crystallography

Versions

Citations

Langer et al. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc (2008) vol. 3 (7) pp. 1171-9


Static link to the SBGrid ARP/wARP page.

BALBES

- aims to integrate into one system all the components necessary for finding a solution structure by MR. ...

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  • 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.

Developers

Fei Long

Garib Murshudov

Categories

X-ray Crystallography

Versions

Citations

Long et al. BALBES: a molecular-replacement pipeline. Acta Crystallogr D Biol Crystallogr (2008) vol. 64 (Pt 1) pp. 125-32


Static link to the SBGrid BALBES page.

BEST

- a program for optimal planning of X-ray data collection from protein crystals. This software is licensed on ...

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  • a program for optimal planning of X-ray data collection from protein crystals.

This software is licensed on a per-lab basis. Please visit the BEST website to request a license, and then email help@sbgrid.org to have it added to your installation.

Developers

Gleb Bourenkov

Alexander Popov

Martin Raditsch

Categories

X-ray Crystallography

Versions

Citations

Bourenkov and Popov. Optimization of data collection taking radiation damage into account. Acta Crystallogr D Biol Crystallogr (2010) vol. 66 (Pt 4) pp. 409-19


Static link to the SBGrid BEST page.

BnP

- Buffalo and Pittsburgh) an interface for complete protein phasing suite includes SnB and Phases.

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  • Buffalo and Pittsburgh) an interface for complete protein phasing suite includes SnB and Phases.

Developers

William Furey

Charles Weeks

Categories

X-ray Crystallography

Versions

Technical Notes

Test the package with BnP test data (can be downloaded from BnP web page)


Static link to the SBGrid BnP page.

CCP4

- (Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries which can ...

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  • (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.

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.

Developers

Ronan Keegan

Charles Ballard

Categories

X-ray Crystallography

Versions

Citations

CCP4: COLLABORATIVE COMPUTATIONAL PROJECT, NUMBER 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763.

Winn et al. Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr (2011) vol. 67 (Pt 4) pp. 235-42


Static link to the SBGrid CCP4 page.

CNS

- an X-ray crystallography suite used for refinement, phasing, and molecular replacement

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  • an X-ray crystallography suite used for refinement, phasing, and molecular replacement

Developers

Axel Brunger

Categories

X-ray Crystallography

Versions

Citations

Brunger. Version 1.2 of the Crystallography and NMR system. Nat Protoc (2007) vol. 2 (11) pp. 2728-33

Brünger et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr (1998) vol. 54 (Pt 5) pp. 905-21


Static link to the SBGrid CNS page.

Coot

- (Crystallographic Object-Oriented Toolkit) supports model building and real space refinement. The application interfaces with refmac, Phenix, and ...

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  • (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.

Developers

Paul Emsley

Categories

X-ray Crystallography

Versions

Citations

Emsley et al. Features and development of Coot. Acta Crystallogr D Biol Crystallogr (2010) vol. 66 (Pt 4) pp. 486-501

Emsley and Cowtan. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr (2004) vol. 60 (Pt 12 Pt 1) pp. 2126-32

Technical Notes

Versions later than 0.3.3 will not work on Fedora Core 3 or older machines due to a change in the GLIBC ABI.


Static link to the SBGrid Coot page.

d*TREK

- a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors.

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  • a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors.

Categories

X-ray Crystallography

Versions

Citations

Pflugrath. The finer things in X-ray diffraction data collection. Acta Crystallogr D Biol Crystallogr (1999) vol. 55 (Pt 10) pp. 1718-25

Technical Notes

We can provide updated d*TREK binaries for your installation, but this software requires an individual license for each lab. Please contact license-request@Rigaku.com to procure a license.


Static link to the SBGrid d*TREK page.

DPS

- (Data Processing Suite) a suite of programs for processing of single crystal X-ray diffraction data of proteins, ...

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  • (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.

Developers

Marian Szebenyi

Categories

X-ray Crystallography

Versions

Citations

Rossmann and van Beek. Data processing. Acta Crystallogr D Biol Crystallogr (1999) vol. 55 (Pt 10) pp. 1631-40


Static link to the SBGrid DPS page.

Eden

- a crystallographic real-space electron-density refinement and optimization program that produces electron density maps with minimal model bias ...

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  • a crystallographic real-space electron-density refinement and optimization program that produces electron density maps with minimal model bias in a robust manner.

Developers

Hanna Szoke

Categories

X-ray Crystallography

Versions

Citations

Murray et al. Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction. Mol Cell (2000) vol. 5 (2) pp. 279-87


Static link to the SBGrid Eden page.

Elves

- automates most of the repetitive and mindless procedures used in solving macromolecular crystal structures, and is capable ...

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  • 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.

Developers

Tom Alber

Categories

X-ray Crystallography

Versions

Citations

Holton and Alber. Automated protein crystal structure determination using ELVES. Proceedings of the National Academy of Sciences of the United States of America (2004) vol. 101 (6) pp. 1537-42


Static link to the SBGrid Elves page.

EPMR

- a program that finds crystallographic molecular replacement solutions using an evolutionary search algorithm. The program directly optimizes ...

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  • 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.

Developers

Charles Kissinger

Categories

X-ray Crystallography

Versions

Citations

Kissinger et al. Rapid automated molecular replacement by evolutionary search. Acta crystallographica Section D, Biological crystallography (1999) vol. 55 (Pt 2) pp. 484-91


Static link to the SBGrid EPMR page.

HKL2000

- a data processing suite for X-ray crystallography that provides a sleek interface for devising a data collection ...

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  • 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. The newest version, HKL3000, supports all steps of the structure determination process. HKL was developed and is maintained by Wladek Minor (University of Virginia).

Categories

X-ray Crystallography

Versions

Citations

Minor et al. HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes. Acta crystallographica Section D, Biological crystallography (2006) vol. 62 (Pt 8) pp. 859-66

Technical Notes

Once you have received your license file from HKL Software, copy the file to /usr/local/lib/cr_info and the HKL2000 package will start working.

The default directory for detector profiles is $HOME/hklint. To override this default and use your own detector profiles, set the HKLPATH variable to the directory containing your detector profiles after sourcing an SBGrid shell initialization file.

The HKLPATH line will override the defaults for your site.


Static link to the SBGrid HKL2000 page.

HKL2MAP

- a graphical user-interface for macromolecular phasing.

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  • a graphical user-interface for macromolecular phasing.

Developers

Thomas Schneider

Categories

X-ray Crystallography

Versions

Citations

Thomas Pape & Thomas R. Schneider HKL2MAP: a graphical user interface for phasing with SHELX programs. J. Appl. Cryst. 2004. 37:843-844.

Technical Notes

To use HKL2MAP, you need to have licenced versions of SHELXC/D/E and Xfit in the executable path of your computer.


Static link to the SBGrid HKL2MAP page.

iMosflm

- a data processing application for macromolecular crystallography. iMosflm (Graphical User Interface) and Mosflm (data processing application) are ...

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  • 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.

Developers

Harry Powell

Categories

X-ray Crystallography

Versions

Citations

Battye et al. iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM. Acta Crystallogr D Biol Crystallogr (2011) vol. 67 (Pt 4) pp. 271-81


Static link to the SBGrid iMosflm page.

LAFIRE

- (Local-correlation-coefficient-based Automatic FItting for REfinement) is an automatic refinement system for protein crystallography. The system starts with ...

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  • (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.

Developers

Lafire Developer Group

M Yao

Categories

X-ray Crystallography

Versions

Citations

Yao et al. LAFIRE: software for automating the refinement process of protein-structure analysis. Acta Crystallogr D Biol Crystallogr (2006) vol. 62 (Pt 2) pp. 189-96


Static link to the SBGrid LAFIRE page.

MAIN

- a model building application for X-ray crystallography.

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  • a model building application for X-ray crystallography.

Developers

Dusan Turk

Categories

X-ray Crystallography

Versions

Citations

D.Turk: "MAIN 96: An interactive software for density modifications, model building, structure refinement and analysis." Proceedings from the 1996 meeting of the International Union of Crystallography Macromolecular Macromolecular Computing School, eds


Static link to the SBGrid MAIN page.

MIExpert

- an expert system for running molecular replacement and refinement applications, and analyzing the data obtained from high-throughput ...

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  • 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.

Developers

John Badger

Categories

X-ray Crystallography

Versions


Static link to the SBGrid MIExpert page.

MIFit

- an interactive graphics application for molecular modeling, fitting, and refinement of protein structures from X-ray crystallography developed ...

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  • 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.

Developers

Bradley Smith

John Badger

Categories

X-ray Crystallography

Structure Visualization

Versions


Static link to the SBGrid MIFit page.

MOSFLM

- a package for processing film and image plate data.

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  • a package for processing film and image plate data.

Developers

Harry Powell

Categories

X-ray Crystallography

Versions

Citations

Leslie. The integration of macromolecular diffraction data. Acta crystallographica Section D, Biological crystallography (2006) vol. 62 (Pt 1) pp. 48-57

Battye et al. iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM. Acta crystallographica Section D, Biological crystallography (2011) vol. 67 (Pt 4) pp. 271-81

Technical Notes

A graphical user interface to MOSFLM is provided by iMosflm.


Static link to the SBGrid MOSFLM page.

O

- a model building application for X-ray crystallography.

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  • a model building application for X-ray crystallography.

Developers

Alwyn Jones

Categories

X-ray Crystallography

Versions

Citations

Jones. Interactive electron-density map interpretation: from INTER to O. Acta crystallographica Section D, Biological crystallography (2004) vol. 60 (Pt 12 Pt 1) pp. 2115-25

Jones et al. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta crystallographica Section A, Foundations of crystallography (1991) vol. 47 ( Pt 2) pp. 110-9

Technical Notes

As of version 12.0, O no longer requires a license file.

To use custom O data files (rotamer database, interface files, etc), you must override the ODAT environmental variable to point to your own directory.

  • Open a tcsh new shell and source /programs/labcshrc
  • echo $ODAT (note the current O data directory
  • cp -Rp $ODAT ~/o_data (copy the current O data files to your home directory)
  • setenv ODAT ~/o_data (you can add this to your ~/.cshrc after the 'source /programs/labcshrc" line)

Copy your custom files to ~/o_data and then run your newly customized O.

O works with SGI Dials. If you're using OS X, you should download and install the most recent USB<->Serial adapter driver for dials use from David Gohara's website. The download file contains a PDF with instructions on installation and set up.


Static link to the SBGrid O page.

PHENIX

- (Python-based Hierarchical Environment for INtegrated Xtallography) provides tools for automated structure solution by X-ray crystallography. The PHENIX ...

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  • (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.

Developers

Pavel Afonine

Ralf Grosse-Kunstleve

Nat Echols

Paul Adams

Categories

X-ray Crystallography

Versions

Citations

Adams et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. 2010. D66: 213-221.

Technical Notes

If you use PHENIX to solve a structure please cite this publication:

PHENIX: building new software for automated crystallographic structure determination P.D. Adams, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter and T.C. Terwilliger. Acta Cryst. D58, 1948-1954 (2002)


Static link to the SBGrid PHENIX page.

PROFphd

- a new package added as part of the pipeline to create fragments for Rosetta. For commercial users, ...

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  • 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.

Developers

Burkhard Rost

Guy Yachdav

Categories

X-ray Crystallography

Versions

Citations

Rost and Sander. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins (1994) vol. 19 (1) pp. 55-72


Static link to the SBGrid PROFphd page.

RCrane

- allows for semi-automated building of RNA structure within Coot.

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  • allows for semi-automated building of RNA structure within Coot.

Developers

Anna Pyle

Kevin Keating

Categories

X-ray Crystallography

Nucleic Acids

Versions

Citations

Keating and Pyle. Semiautomated model building for RNA crystallography using a directed rotameric approach. Proc Natl Acad Sci USA (2010) vol. 107 (18) pp. 8177-82


Static link to the SBGrid RCrane page.

Reduce

- a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in ...

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  • 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.

Developers

Jane Richardson

David Richardson

Categories

X-ray Crystallography

Versions

Citations

Word, et al. Asparagine and glutamine: using hydrogen atom contacts in the choice of sidechain amide orientation. J. Mol. Biol. 1999. 285:1733-1745.

Chen VB, Arendall WB III, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC (2010) "MolProbity: all-atom structure validation for macromolecular crystallography", Acta Crystallogr D66:12-21, open access, PMC2803126

Davis, Leaver-Fay, Chen, Block, Kapral, Wang, Murray, Arendall, Snoeyink, J Richardson, D Richardson (2007) "MolProbity: All-atom contacts and structure validation for proteins and nucleic acids." Nucleic Acids Res. 35: W375-W383, open access, PMC1933162

Technical Notes

A slightly modified version of the connectivity table published by the PDB is available below. Note that the HET dictionary is available in two "flavors" - new and old (again). Which one to use is dependent upon which type of reduced PDB you want as output.


Static link to the SBGrid Reduce page.

REFMAC

- carries out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular ...

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  • 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 maps, where missing data have been restored.

Developers

Garib Murshudov

Rob Nicholls

Categories

X-ray Crystallography

Versions

Citations

Winn et al. Macromolecular TLS refinement in REFMAC at moderate resolutions. Meth Enzymol (2003) vol. 374 pp. 300-21

Vagin et al. REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr D Biol Crystallogr (2004) vol. 60 (Pt 12 Pt 1) pp. 2184-95

Technical Notes

How to cite: Click here.


Static link to the SBGrid REFMAC page.

REPLACE (GLRF and TF)

- a suite of programs for molecular replacement calculations. It currently consists of two major programs, GLRF for ...

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  • 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.

Developers

Liang Tong

Categories

X-ray Crystallography

Versions

Citations

Tong and Rossmann. Rotation function calculations with GLRF program. Meth Enzymol (1997) vol. 276 pp. 594-611


Static link to the SBGrid REPLACE (GLRF and TF) page.

Ringer

- a program to detect molecular motions by automatic electron density sampling.

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  • a program to detect molecular motions by automatic electron density sampling.

Developers

Ringer Licensing

Ringer Developer Group

Terry Lang

Categories

X-ray Crystallography

Versions

Citations

Lang et al. Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Protein Sci (2010) vol. 19 (7) pp. 1420-31


Static link to the SBGrid Ringer page.

RSRef2000

- supports real-space simulated annealing refinement with X-ray data. RSRef uses an electron density function that is resolution ...

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  • 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, that have good electron density. Application developed by Michael Chapman at Florida State University.

Developers

Michael Chapman

RSRef Developer Group

Categories

X-ray Crystallography

Versions

Citations

Korostelev et al. Simulated-annealing real-space refinement as a tool in model building. Acta Cryst. 2002. D58: 761-767.


Static link to the SBGrid RSRef2000 page.

SHARP/autoSHARP

- an automated structure solution pipeline built around the heavy-atom refinement and phasing program SHARP, the density modification ...

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  • 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.

Developers

Gerard Bricogne

Clemens Vonrhein

Categories

X-ray Crystallography

Versions

Citations

SHARP: Bricogne et al. Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Cryst. 2003. D59: 2023-2030.

autoSHARP: Vonrhein et al. Automated structure solution with autoSHARP. Methods Mol Biol. 2007. 364:215-30.

Technical Notes

SHARP/autoSHARP is installed on our server at Harvard Medical School. Please email accounts@sbgrid.org to gain access.


Static link to the SBGrid SHARP/autoSHARP page.

SHELX-97

- a set of programs for macromolecular phasing. SHELXC is designed to provide a simple and fast way ...

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  • 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 maintained by George Sheldrick and his group at the University of Gottingen.

All users must first obtain license from George Sheldrick, and then request software installation by writing to bugs@sbgrid.org.

Developers

George Sheldrick

Categories

X-ray Crystallography

Versions

Citations

Sheldrick. A short history of SHELX. Acta Cryst. 2008. A64:112-122.

Technical Notes

All users must first obtain license from George Sheldrick, and then request software installation by writing to bugs@sbgrid.org.


Static link to the SBGrid SHELX-97 page.

SnB

- determination of the anomalously scattering substructures of selenomethionyl-substituted proteins containing as many as 160 Se sites. SnB ...

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  • 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.

Developers

SnB Developer Group

Russ Miller

Categories

X-ray Crystallography

Versions

Citations

Version 1.5: Miller et al. SnB: crystal structure determination via Shake-and-Bake. J. Appl. Cryst. 1994. 27: 613-621.

Version 2.0: Weeks & Miller. The design and implementation of SnB v2.0. J. Appl. Cryst. 1999. 32: 120-124.

Rappleye et al. SnB version 2.2: an example of crystallographic multiprocessing. J. Appl. Cryst. 2002. 35: 374-376.

Miller et al. Shake-and-Bake on the grid, J. Appl. Cryst. 2007. 40: 938-944.

Technical Notes

Requires the libXp libraries (yum -y install libXp)


Static link to the SBGrid SnB page.

SOLVE/RESOLVE

- a program that can automatically search for heavy atom sites, calculate initial phases and perform density modification.

 yes yes yes

  • a program that can automatically search for heavy atom sites, calculate initial phases and perform density modification.

Developers

Tom Terwilliger

Categories

X-ray Crystallography

Versions

Citations

SOLVE: Terwilliger and Berendzen. Automated MAD and MIR structure solution. Acta Crystallographica. 1999. D55:849-861.

RESOLVE: Terwilliger. Maximum likelihood density modification. Acta Cryst. 2000. D56:965-972.

RESOLVE model-building: Terwilliger. Automated main-chain model building by template matching and iterative fragment extension. Acta. Cryst. 2003. D59:38-44.


Static link to the SBGrid SOLVE/RESOLVE page.

SOMoRe

- 6D global search and multi-start optimization molecular replacement package.

 yes yes yes

  • 6D global search and multi-start optimization molecular replacement package.

Developers

Diane Jamrog

Categories

X-ray Crystallography

Versions

Citations

Jamrog et al. SOMoRe: a multi-dimensional search and optimization approach to molecular replacement. Acta Cryst. 2003. D59: 304-314.


Static link to the SBGrid SOMoRe page.

Untangle

- a program designed to separate overlapping diffraction patterns from a set of crystals with slightly different orientations. ...

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  • 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.

Developers

Liev Buts

Categories

X-ray Crystallography

Versions

Citations

Buts et al. Untangle, a tool for filtering overlapping diffraction patterns from multicrystals. Acta. Crystallogr. D. Biol. Crystallogr. 2004. 60(Pt 5):983-4.


Static link to the SBGrid Untangle page.

USF Gerard Utilities

- the Swiss Army knife of crystallography tools. The installation includes the packages from RAVE, SBIN, X-UTIL, VOIDOO, ...

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  • the Swiss Army knife of crystallography tools. The installation includes the packages from RAVE, SBIN, X-UTIL, VOIDOO, DEJAVU and SPASM.

Developers

Gerard Kleywegt

Categories

X-ray Crystallography

Structure Analysis

Versions

Citations

See list of literature references here: http://www.hhmi.swmed.edu/Manuals/gerard/gerard_manuals.html


Static link to the SBGrid USF Gerard Utilities page.

WASP

- searches PDB files for misidentified water molecules that should be modeled as cations.

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  • searches PDB files for misidentified water molecules that should be modeled as cations.

Developers

David Gohara

Enrico DiCera

Categories

X-ray Crystallography

Structure Analysis

Versions

Citations

Nayal, M., & Di Cera, E. (1996) J. Mol. Biol. 256: 228-234


Static link to the SBGrid WASP page.

XDS

- X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method. Written by Wolfgang ...

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  • 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).

Developers

Wolfgang Kabsch

Categories

X-ray Crystallography

Versions

Citations

Kabsch. XDS. Acta Cryst. 2010. D66: 125-132. Additional references found at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/references.html


Static link to the SBGrid XDS page.

XDS-Viewer

- an X-ray diffraction and control image viewing utility for data processed using the XDS program package.

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  • an X-ray diffraction and control image viewing utility for data processed using the XDS program package.

Developers

Wolfgang Kabsch

Categories

X-ray Crystallography

Versions

Citations

Kabsch. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 1993. 26: 795-800.


Static link to the SBGrid XDS-Viewer page.

XDSi

- allows processing of datasets in a given directory with minimum effort when you supply it with a ...

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  • 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 the most informative statistics of INTEGRATE.LP, CORRECT.LP and XDSSTAT.LP are generated for each dataset. A plot comparing Rmeas, I/sig and Completeness of all the processed datasets is generated. You can also generate plots for datasets that have been processed using XDS without XDSi.

Note that this software requires 'kpdf' to display its output.

Developers

Petri Kursula

Categories

X-ray Crystallography

Versions

Citations

Kursula P. XDSi - a graphical interface for the data processing program XDS. J. Appl. Cryst. 2004. 37: 347-348.


Static link to the SBGrid XDSi page.

XDSSTAT

- a home-brewn program that prints various statistics (that are not available from XDS itself) in the form ...

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  • a home-brewn program that prints various statistics (that are not available from XDS itself) in the form of tables and images.

Developers

Kay Diederichs

Categories

X-ray Crystallography

Versions


Static link to the SBGrid XDSSTAT page.

XIA2

- an automated data reduction system designed to work from raw diffraction data and a little metadata, and ...

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  • 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.

Developers

Graeme Winter

Categories

X-ray Crystallography

Versions


Static link to the SBGrid XIA2 page.