SBGrid Consortium - Supported Software

X-ray Crystallography

SBGrid supports 50 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	HiddenDetail
3DNA	- a package for analyzing, visualizing and rebuilding 3-dimensional nucleic acid structures. 3DNA was created by Dr. Xiang-Jun ...	check	check	check	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 Linux 32: 2.1 Linux 64: 2.1 OSX Intel: 2.1 OSX PPC: 2.0 SGI Irix: 1.5 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. License Type This software is distributed under a Non-Profit license.
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 Linux 32: 2.1 Linux 64: 2.1 OSX Intel: 2.1 OSX PPC: 2.0 SGI Irix: 1.5 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. License Type This software is distributed under a Non-Profit license. 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 ...	check	check	check	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 Linux 32: 1.9.8 Linux 64: 1.9.8 OSX Intel: 1.9.8 OSX PPC: 1.9.8 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 License Type This software is distributed under an Open license.
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 Linux 32: 1.9.8 Linux 64: 1.9.8 OSX Intel: 1.9.8 OSX PPC: 1.9.8 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 License Type This software is distributed under an Open license. 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 ...	check		check	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 bugs@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 Linux 32: 7.2 OSX Intel: 7.2 OSX PPC: 7.1.1 SGI Irix: 6.1.1 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 License Type This software is distributed under a Commercial license.
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 bugs@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 Linux 32: 7.2 OSX Intel: 7.2 OSX PPC: 7.1.1 SGI Irix: 6.1.1 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 License Type This software is distributed under a Commercial license. 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. ...	check	check	check	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 Categories X-ray Crystallography Versions Linux 32: 1.0.0 Linux 64: 1.0.0 OSX Intel: 1.0.0 OSX PPC: 1.0.0 Citations Long et al. BALBES: a molecular-replacement pipeline. Acta Crystallogr D Biol Crystallogr (2008) vol. 64 (Pt 1) pp. 125-32 License Type This software is distributed under a Non-Profit license.
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 Categories X-ray Crystallography Versions Linux 32: 1.0.0 Linux 64: 1.0.0 OSX Intel: 1.0.0 OSX PPC: 1.0.0 Citations Long et al. BALBES: a molecular-replacement pipeline. Acta Crystallogr D Biol Crystallogr (2008) vol. 64 (Pt 1) pp. 125-32 License Type This software is distributed under a Non-Profit license. Static link to the SBGrid BALBES page.
BEST	- a program for optimal planning of X-ray data collection from protein crystals.	check	check	check	a program for optimal planning of X-ray data collection from protein crystals. Developers Martin Raditsch Gleb Bourenkov Categories X-ray Crystallography Versions Linux 32: 3.4.4 Linux 64: 3.4.4 OSX Intel: 3.2.0 OSX PPC: 3.2.0 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 License Type This software is distributed under a Non-Profit license.
a program for optimal planning of X-ray data collection from protein crystals. Developers Martin Raditsch Gleb Bourenkov Categories X-ray Crystallography Versions Linux 32: 3.4.4 Linux 64: 3.4.4 OSX Intel: 3.2.0 OSX PPC: 3.2.0 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 License Type This software is distributed under a Non-Profit license. Static link to the SBGrid BEST page.
BnP	- Buffalo and Pittsburgh) an interface for complete protein phasing suite includes SnB and Phases.	check			Buffalo and Pittsburgh) an interface for complete protein phasing suite includes SnB and Phases. Developers William Furey Charles Weeks Categories X-ray Crystallography Versions Linux 32: 1.02 OSX PPC: 1.02 Technical Notes Test the package with BnP test data (can be downloaded from BnP web page) License Type This software is distributed under a Non-Profit license.
Buffalo and Pittsburgh) an interface for complete protein phasing suite includes SnB and Phases. Developers William Furey Charles Weeks Categories X-ray Crystallography Versions Linux 32: 1.02 OSX PPC: 1.02 Technical Notes Test the package with BnP test data (can be downloaded from BnP web page) License Type This software is distributed under a Non-Profit license. 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 ...	check		check	(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. Developers Ronan Keegan Charles Ballard Categories X-ray Crystallography Versions Linux 32: 6.2.0 OSX Intel: 6.2.0 OSX PPC: 6.1.13 SGI Irix: 5.0.2 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 License Type This software is distributed under a Non-Profit license.
(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. Developers Ronan Keegan Charles Ballard Categories X-ray Crystallography Versions Linux 32: 6.2.0 OSX Intel: 6.2.0 OSX PPC: 6.1.13 SGI Irix: 5.0.2 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 License Type This software is distributed under a Non-Profit license. Static link to the SBGrid CCP4 page.
CNS	- an X-ray crystallography suite used for refinement, phasing, and molecular replacement	check	check	check	an X-ray crystallography suite used for refinement, phasing, and molecular replacement Developers Axel Brunger Categories X-ray Crystallography Versions Linux 32: 1.3r7 Linux 64: 1.3r7 OSX Intel: 1.3r7 OSX PPC: 1.3 SGI Irix: 1.1 Citations Brunger. Version 1.2 of the Crystallography and NMR system. Nat Protoc (2007) vol. 2 (11) pp. 2728-33 BrÃ¼nger 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 License Type This software is distributed under a Non-Profit license.
an X-ray crystallography suite used for refinement, phasing, and molecular replacement Developers Axel Brunger Categories X-ray Crystallography Versions Linux 32: 1.3r7 Linux 64: 1.3r7 OSX Intel: 1.3r7 OSX PPC: 1.3 SGI Irix: 1.1 Citations Brunger. Version 1.2 of the Crystallography and NMR system. Nat Protoc (2007) vol. 2 (11) pp. 2728-33 BrÃ¼nger 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 License Type This software is distributed under a Non-Profit license. 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 ...	check	check	check	(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 Linux 32: 0.7-pre-1-r4135 Linux 64: 0.7-pre-1-r4135 OSX Intel: 0.7-pre-1-4122 OSX PPC: 0.6.2-pre-1-65 SGI Irix: 0.0.33 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. License Type This software is distributed under an Open license.
(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 Linux 32: 0.7-pre-1-r4135 Linux 64: 0.7-pre-1-r4135 OSX Intel: 0.7-pre-1-4122 OSX PPC: 0.6.2-pre-1-65 SGI Irix: 0.0.33 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. License Type This software is distributed under an Open license. Static link to the SBGrid Coot page.
Crank	- provides a user-friendly, automated system incorporating the latest computational developments in all stages of structure solution by ...	check		check	provides a user-friendly, automated system incorporating the latest computational developments in all stages of structure solution by experimental phasing. Users can define pipelines from a choice of many different programs. Developers Crank Developer Group Categories X-ray Crystallography Versions Linux 32: 1.2.0 OSX Intel: 1.2.0 Citations Pannu et al. Recent advances in the CRANK software suite for experimental phasing. Acta Crystallogr D Biol Crystallogr (2011) vol. 67 (Pt 4) pp. 331-7 License Type This software is distributed under a Non-Profit license.
provides a user-friendly, automated system incorporating the latest computational developments in all stages of structure solution by experimental phasing. Users can define pipelines from a choice of many different programs. Developers Crank Developer Group Categories X-ray Crystallography Versions Linux 32: 1.2.0 OSX Intel: 1.2.0 Citations Pannu et al. Recent advances in the CRANK software suite for experimental phasing. Acta Crystallogr D Biol Crystallogr (2011) vol. 67 (Pt 4) pp. 331-7 License Type This software is distributed under a Non-Profit license. Static link to the SBGrid Crank page.
d*TREK	- a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors.	check		check	a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors. Categories X-ray Crystallography Versions Linux 32: various OSX Intel: various 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. License Type This software is distributed under a Commercial license.
a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors. Categories X-ray Crystallography Versions Linux 32: various OSX Intel: various 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 dTREK binaries for your installation, but this software requires an individual license for each lab. Please contact license-request@Rigaku.com to procure a license. License Type This software is distributed under a Commercial license. Static link to the SBGrid dTREK page.
DPS	- (Data Processing Suite) a suite of programs for processing of single crystal X-ray diffraction data of proteins, ...	check	check		(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 Linux 32: 2.13 Linux 64: 2.13 Citations Rossmann and van Beek. Data processing. Acta Crystallogr D Biol Crystallogr (1999) vol. 55 (Pt 10) pp. 1631-40 License Type This software is distributed under an Open license.
(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 Linux 32: 2.13 Linux 64: 2.13 Citations Rossmann and van Beek. Data processing. Acta Crystallogr D Biol Crystallogr (1999) vol. 55 (Pt 10) pp. 1631-40 License Type This software is distributed under an Open license. 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 ...	check	check	check	a crystallographic real-space electron-density refinement and optimization program that produces electron density maps with minimal model bias in a robust manner. Categories X-ray Crystallography Versions Linux 32: 5.3 Linux 64: 5.3 OSX Intel: 5.3 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 License Type This software is distributed under an Open license.
a crystallographic real-space electron-density refinement and optimization program that produces electron density maps with minimal model bias in a robust manner. Categories X-ray Crystallography Versions Linux 32: 5.3 Linux 64: 5.3 OSX Intel: 5.3 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 License Type This software is distributed under an Open license. 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 ...	check	check	check	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 Curt Theisen Categories X-ray Crystallography Versions Linux 32: 1.3.6.1.2 Linux 64: 1.3.6.1.2 OSX Intel: 1.3.6.1.2 OSX PPC: 1.3.6.1.1 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 License Type This software is distributed under a Non-Profit license.
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 Curt Theisen Categories X-ray Crystallography Versions Linux 32: 1.3.6.1.2 Linux 64: 1.3.6.1.2 OSX Intel: 1.3.6.1.2 OSX PPC: 1.3.6.1.1 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 License Type This software is distributed under a Non-Profit license. 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 ...	check	check	check	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 Linux 32: 11.02 Linux 64: 11.02 OSX Intel: 11.02 SGI Irix: 3.1 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 License Type This software is distributed under an Open license.
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 Linux 32: 11.02 Linux 64: 11.02 OSX Intel: 11.02 SGI Irix: 3.1 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 License Type This software is distributed under an Open license. 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 ...	check	check	check	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 Linux 32: 2000.0.98.703x Linux 64: 2000.0.98.703x OSX Intel: 2000.0.98.703x OSX PPC: HKL2000_mac_0.692i 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, add this line to your $HOME/.cshrc file after sourcing the SBGrid labcshrc: source /programs/labcshrc setenv HKLPATH /path/to/your/hklint The HKLPATH line will override the defaults for your site. License Type This software is distributed under a Non-Profit license.
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 Linux 32: 2000.0.98.703x Linux 64: 2000.0.98.703x OSX Intel: 2000.0.98.703x OSX PPC: HKL2000_mac_0.692i 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, add this line to your $HOME/.cshrc file after sourcing the SBGrid labcshrc: source /programs/labcshrc setenv HKLPATH /path/to/your/hklint The HKLPATH line will override the defaults for your site. License Type This software is distributed under a Non-Profit license. Static link to the SBGrid HKL2000 page.
HKL2MAP	- a graphical user-interface for macromolecular phasing.	check	check	check	a graphical user-interface for macromolecular phasing. Developers Thomas Schneider Categories X-ray Crystallography Versions Linux 32: 0.2 Linux 64: 0.2 OSX Intel: 0.2 OSX PPC: 0.2 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. License Type This software is distributed under a Non-Profit license.
a graphical user-interface for macromolecular phasing. Developers Thomas Schneider Categories X-ray Crystallography Versions Linux 32: 0.2 Linux 64: 0.2 OSX Intel: 0.2 OSX PPC: 0.2 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. License Type This software is distributed under a Non-Profit license. 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 ...	check	check	check	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 Linux 32: 1.0.6 Linux 64: 1.0.6 OSX Intel: 1.0.6 OSX PPC: 1.0.5 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 License Type This software is distributed under an Open license.
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 Linux 32: 1.0.6 Linux 64: 1.0.6 OSX Intel: 1.0.6 OSX PPC: 1.0.5 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 License Type This software is distributed under an Open license. Static link to the SBGrid iMosflm page.
LABELIT	- an autoindexing program designed to correct three commonly experienced problems: getting the wrong beam center, finding a ...	check		check	an autoindexing program designed to correct three commonly experienced problems: getting the wrong beam center, finding a unit cell that is too large, and improperly identifying the allowed Bravais symmetry. If successful, LABELIT can be operated with minimal user input, and will return its results generally within 30-60 seconds. LABELIT is now included in the PHENIX package. Developers Nicholas Sauter Categories X-ray Crystallography Versions Linux 32: 1.000rc15 OSX Intel: 1.000rc15 OSX PPC: 1.000rc15 Citations Sauter and Poon. Autoindexing with outlier rejection and identification of superimposed lattices. J Appl Crystallogr (2010) vol. 43 (Pt 3) pp. 611-616 Poon et al. Detection and correction of underassigned rotational symmetry prior to structure deposition. Acta Crystallogr D Biol Crystallogr (2010) vol. 66 (Pt 5) pp. 503-13 Sauter and Zwart. Autoindexing the diffraction patterns from crystals with a pseudotranslation. Acta Crystallogr D Biol Crystallogr (2009) vol. 65 (Pt 6) pp. 553-9 License Type This software is distributed under a Non-Profit license.
an autoindexing program designed to correct three commonly experienced problems: getting the wrong beam center, finding a unit cell that is too large, and improperly identifying the allowed Bravais symmetry. If successful, LABELIT can be operated with minimal user input, and will return its results generally within 30-60 seconds. LABELIT is now included in the PHENIX package. Developers Nicholas Sauter Categories X-ray Crystallography Versions Linux 32: 1.000rc15 OSX Intel: 1.000rc15 OSX PPC: 1.000rc15 Citations Sauter and Poon. Autoindexing with outlier rejection and identification of superimposed lattices. J Appl Crystallogr (2010) vol. 43 (Pt 3) pp. 611-616 Poon et al. Detection and correction of underassigned rotational symmetry prior to structure deposition. Acta Crystallogr D Biol Crystallogr (2010) vol. 66 (Pt 5) pp. 503-13 Sauter and Zwart. Autoindexing the diffraction patterns from crystals with a pseudotranslation. Acta Crystallogr D Biol Crystallogr (2009) vol. 65 (Pt 6) pp. 553-9 License Type This software is distributed under a Non-Profit license. Static link to the SBGrid LABELIT page.
LAFIRE	- (Local-correlation-coefficient-based Automatic FItting for REfinement) is an automatic refinement system for protein crystallography. The system starts with ...	check	check	check	(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 Categories X-ray Crystallography Versions Linux 32: 3.5 Linux 64: 3.5 OSX Intel: 3.5 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 License Type This software is distributed under a Non-Profit license.
(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 Categories X-ray Crystallography Versions Linux 32: 3.5 Linux 64: 3.5 OSX Intel: 3.5 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 License Type This software is distributed under a Non-Profit license. Static link to the SBGrid LAFIRE page.
MAIN	- a model building application for X-ray crystallography.	check			a model building application for X-ray crystallography. Developers Dusan Turk Categories X-ray Crystallography Versions Linux 32: 2004 SGI Irix: 2004 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 License Type This software is distributed under a Non-Profit license.
a model building application for X-ray crystallography. Developers Dusan Turk Categories X-ray Crystallography Versions Linux 32: 2004 SGI Irix: 2004 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 License Type This software is distributed under a Non-Profit license. 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 ...	check			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 Linux 32: 8.0 License Type This software is distributed under an Open license.
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 Linux 32: 8.0 License Type This software is distributed under an Open license. 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 ...	check			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 Categories X-ray Crystallography Structure Visualization Versions Linux 32: 8.0 License Type This software is distributed under an Open license.
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 Categories X-ray Crystallography Structure Visualization Versions Linux 32: 8.0 License Type This software is distributed under an Open license. Static link to the SBGrid MIFit page.
MOLREP	- an automated program for molecular replacement using a full-symmetry translation function combined with a packing function.	check		check	an automated program for molecular replacement using a full-symmetry translation function combined with a packing function. Developers Alexei Vagin Categories X-ray Crystallography Versions Linux 32: 10.2.2 OSX Intel: 10.2.2 OSX PPC: 10.2.2 SGI Irix: 7.1 Citations Vagin and Teplyakov. Molecular replacement with MOLREP. Acta crystallographica Section D, Biological crystallography (2010) vol. 66 (Pt 1) pp. 22-5 Lebedev et al. Model preparation in MOLREP and examples of model improvement using X-ray data. Acta crystallographica Section D, Biological crystallography (2008) vol. 64 (Pt 1) pp. 33-9 Vagin and Teplyakov. An approach to multi-copy search in molecular replacement. Acta crystallographica Section D, Biological crystallography (2000) vol. 56 (Pt 12) pp. 1622-4 License Type This software is distributed under a Non-Profit license.
an automated program for molecular replacement using a full-symmetry translation function combined with a packing function. Developers Alexei Vagin Categories X-ray Crystallography Versions Linux 32: 10.2.2 OSX Intel: 10.2.2 OSX PPC: 10.2.2 SGI Irix: 7.1 Citations Vagin and Teplyakov. Molecular replacement with MOLREP. Acta crystallographica Section D, Biological crystallography (2010) vol. 66 (Pt 1) pp. 22-5 Lebedev et al. Model preparation in MOLREP and examples of model improvement using X-ray data. Acta crystallographica Section D, Biological crystallography (2008) vol. 64 (Pt 1) pp. 33-9 Vagin and Teplyakov. An approach to multi-copy search in molecular replacement. Acta crystallographica Section D, Biological crystallography (2000) vol. 56 (Pt 12) pp. 1622-4 License Type This software is distributed under a Non-Profit license. Static link to the SBGrid MOLREP page.
MOSFLM	- a package for processing film and image plate data.	check	check	check	a package for processing film and image plate data. Developers Harry Powell Categories X-ray Crystallography Versions Linux 32: 7.0.8 Linux 64: 7.0.8 OSX Intel: 7.0.8 OSX PPC: 7.0.7 SGI Irix: 6.2.5 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. License Type This software is distributed under an Open license.
a package for processing film and image plate data. Developers Harry Powell Categories X-ray Crystallography Versions Linux 32: 7.0.8 Linux 64: 7.0.8 OSX Intel: 7.0.8 OSX PPC: 7.0.7 SGI Irix: 6.2.5 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. License Type This software is distributed under an Open license. Static link to the SBGrid MOSFLM page.
O	- a model building application for X-ray crystallography.	check	check	check	a model building application for X-ray crystallography. Developers Alwyn Jones Categories X-ray Crystallography Versions Linux 32: 13.0 Linux 64: 13.0 OSX Intel: 13.0 OSX PPC: 13.0 SGI Irix: 10.0.1 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. License Type This software is distributed under an Open license.
a model building application for X-ray crystallography. Developers Alwyn Jones Categories X-ray Crystallography Versions Linux 32: 13.0 Linux 64: 13.0 OSX Intel: 13.0 OSX PPC: 13.0 SGI Irix: 10.0.1 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. License Type This software is distributed under an Open license. Static link to the SBGrid O page.
PHASER	- a program for phasing macromolecular crystal structures with maximum likelihood methods. This program is now included with ...	check		check	a program for phasing macromolecular crystal structures with maximum likelihood methods. This program is now included with the CCP4 installation. Developers Randy Read Categories X-ray Crystallography Versions Linux 32: 2.1.4 OSX Intel: 2.1.4 OSX PPC: 2.1.4 Citations All members should register as separate users though members do not have to install phaser separately. McCoy et al. Phaser crystallographic software. J. Appl. Cryst. (2007). 40, 658-674. Technical Notes How to cite: Acta Cryst. (2005). D61, 458-464. Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve, L. C. Storoni and R. J. Read. License Type This software is distributed under a Non-Profit license.
a program for phasing macromolecular crystal structures with maximum likelihood methods. This program is now included with the CCP4 installation. Developers Randy Read Categories X-ray Crystallography Versions Linux 32: 2.1.4 OSX Intel: 2.1.4 OSX PPC: 2.1.4 Citations All members should register as separate users though members do not have to install phaser separately. McCoy et al. Phaser crystallographic software. J. Appl. Cryst. (2007). 40, 658-674. Technical Notes How to cite: Acta Cryst. (2005). D61, 458-464. Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve, L. C. Storoni and R. J. Read. License Type This software is distributed under a Non-Profit license. Static link to the SBGrid PHASER page.
PHENIX	- (Python-based Hierarchical Environment for INtegrated Xtallography) provides tools for automated structure solution by X-ray crystallography. The PHENIX ...	check	check	check	(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 Linux 32: 1.7.3-928 Linux 64: 1.7.3-928 OSX Intel: 1.7.3-928 OSX PPC: 1.7-650 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) License Type This software is distributed under a Non-Profit license.
(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 Linux 32: 1.7.3-928 Linux 64: 1.7.3-928 OSX Intel: 1.7.3-928 OSX PPC: 1.7-650 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) License Type This software is distributed under a Non-Profit license. Static link to the SBGrid PHENIX page.
PROFphd	- a new package added as part of the pipeline to create fragments for Rosetta.	check		check	a new package added as part of the pipeline to create fragments for Rosetta. Developers Burkhard Rost Categories X-ray Crystallography Versions Linux 32: 20090416 OSX Intel: 20090304 Citations Rost and Sander. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins (1994) vol. 19 (1) pp. 55-72 License Type This software is distributed under a Non-Profit license.
a new package added as part of the pipeline to create fragments for Rosetta. Developers Burkhard Rost Categories X-ray Crystallography Versions Linux 32: 20090416 OSX Intel: 20090304 Citations Rost and Sander. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins (1994) vol. 19 (1) pp. 55-72 License Type This software is distributed under a Non-Profit license. Static link to the SBGrid PROFphd page.
RCrane	- allows for semi-automated building of RNA structure within Coot.	check		check	allows for semi-automated building of RNA structure within Coot. Developers Kevin Keating Categories X-ray Crystallography Nucleic Acids Versions Linux 32: 0.5 OSX Intel: 0.5 OSX PPC: 0.5 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 License Type This software is distributed under an Open license.
allows for semi-automated building of RNA structure within Coot. Developers Kevin Keating Categories X-ray Crystallography Nucleic Acids Versions Linux 32: 0.5 OSX Intel: 0.5 OSX PPC: 0.5 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 License Type This software is distributed under an Open license. 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 ...	check	check	check	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 Linux 32: 3.14.080821 Linux 64: 3.14.080821 OSX Intel: 3.14.080821 OSX PPC: 3.13.080428 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. 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. License Type This software is distributed under an Open license.
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 Linux 32: 3.14.080821 Linux 64: 3.14.080821 OSX Intel: 3.14.080821 OSX PPC: 3.13.080428 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. 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. License Type This software is distributed under an Open license. 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 ...	check	check	check	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 Categories X-ray Crystallography Versions Linux 32: 5.7.0028 Linux 64: 5.7.0028 OSX Intel: 5.7.0028 OSX PPC: 5.4.0066 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. License Type This software is distributed under a Non-Profit license.
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 Categories X-ray Crystallography Versions Linux 32: 5.7.0028 Linux 64: 5.7.0028 OSX Intel: 5.7.0028 OSX PPC: 5.4.0066 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. License Type This software is distributed under a Non-Profit license. 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 ...	check		check	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 Linux 32: 4.1 OSX Intel: 4.1 OSX PPC: 4.1 SGI Irix: 4.1 Citations Tong and Rossmann. Rotation function calculations with GLRF program. Meth Enzymol (1997) vol. 276 pp. 594-611 License Type This software is distributed under a Non-Profit license.
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 Linux 32: 4.1 OSX Intel: 4.1 OSX PPC: 4.1 SGI Irix: 4.1 Citations Tong and Rossmann. Rotation function calculations with GLRF program. Meth Enzymol (1997) vol. 276 pp. 594-611 License Type This software is distributed under a Non-Profit license. Static link to the SBGrid REPLACE (GLRF and TF) page.
Ringer	- a program to detect molecular motions by automatic electron density sampling.	check	check	check	a program to detect molecular motions by automatic electron density sampling. Developers Ringer Licensing Ringer Developer Group Terry Lang Categories X-ray Crystallography Versions Linux 32: 1.0 Linux 64: 1.0 OSX Intel: 1.0 OSX PPC: 1.0 Citations Lang et al. Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Protein Sci (2010) vol. 19 (7) pp. 1420-31 License Type This software is distributed under a Non-Profit license.
a program to detect molecular motions by automatic electron density sampling. Developers Ringer Licensing Ringer Developer Group Terry Lang Categories X-ray Crystallography Versions Linux 32: 1.0 Linux 64: 1.0 OSX Intel: 1.0 OSX PPC: 1.0 Citations Lang et al. Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Protein Sci (2010) vol. 19 (7) pp. 1420-31 License Type This software is distributed under a Non-Profit license. 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 ...	check			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 TNTâ€™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 Linux 32: 200605 Citations Korostelev et al. Simulated-annealing real-space refinement as a tool in model building. Acta Cryst. 2002. D58: 761-767. License Type This software is distributed under a Non-Profit license.
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 TNTâ€™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 Linux 32: 200605 Citations Korostelev et al. Simulated-annealing real-space refinement as a tool in model building. Acta Cryst. 2002. D58: 761-767. License Type This software is distributed under a Non-Profit license. Static link to the SBGrid RSRef2000 page.
SGXPro	- a parallel workflow engine that was designed to automatically manage communication between the different processes and build ...	check			a parallel workflow engine that was designed to automatically manage communication between the different processes and build systematic searches of algorithm/program/parameter space to generate the best possible result for a given data set. The current SGXPro program palette includes 3DSCALE, SHELXD, ISAS, SOLVE/RESOLVE, DM, SOLOMON, DMMULTI, BLAST, AMoRe, EPMR, XTALVIEW, ARP/wARP and MAID. Developers Albert Fu Categories X-ray Crystallography Versions Linux 32: 0.7 Citations Fu et al. SGXPro: a parallel workflow engine enabling optimization of program performance and automation of structure determination. Acta Crystallogr D Biol Crystallogr. 2005. 61(Pt 7):951-9. ---------- Forwarded message ---------- From: Zheng-Qing Fu fuzq@anl.gov Date: Fri, Dec 10, 2010 at 1:10 PM Subject: RE: SBGrid developer update To: sliz@hkl.hms.harvard.edu Dear Piotrek, Thank you for sending me update about the recent development of SBGrid. I'll let you know if there is any major upgrade of SGXPRO, or found some other programs which might be a valuable addition to SBGrid. Keep in touch. Have a nice weekend, Albert Zheng-Qing Fu, Ph.D. (nickname Albert) APS, Argonne National Laboratory 9700 South Cass Avenue Bldg. 436B, Room B004 Argonne, IL 60439-4861 Tel: (630)252-0649 Fax: (630)252-0652 Email: fuzq@anl.gov also Department of Biochemistry & Molecular Biology University of Georgia, Athens, GA 30602 Email: fuzq@uga.edu License Type This software is distributed under a Non-Profit license.
a parallel workflow engine that was designed to automatically manage communication between the different processes and build systematic searches of algorithm/program/parameter space to generate the best possible result for a given data set. The current SGXPro program palette includes 3DSCALE, SHELXD, ISAS, SOLVE/RESOLVE, DM, SOLOMON, DMMULTI, BLAST, AMoRe, EPMR, XTALVIEW, ARP/wARP and MAID. Developers Albert Fu Categories X-ray Crystallography Versions Linux 32: 0.7 Citations Fu et al. SGXPro: a parallel workflow engine enabling optimization of program performance and automation of structure determination. Acta Crystallogr D Biol Crystallogr. 2005. 61(Pt 7):951-9. ---------- Forwarded message ---------- From: Zheng-Qing Fu fuzq@anl.gov Date: Fri, Dec 10, 2010 at 1:10 PM Subject: RE: SBGrid developer update To: sliz@hkl.hms.harvard.edu Dear Piotrek, Thank you for sending me update about the recent development of SBGrid. I'll let you know if there is any major upgrade of SGXPRO, or found some other programs which might be a valuable addition to SBGrid. Keep in touch. Have a nice weekend, Albert Zheng-Qing Fu, Ph.D. (nickname Albert) APS, Argonne National Laboratory 9700 South Cass Avenue Bldg. 436B, Room B004 Argonne, IL 60439-4861 Tel: (630)252-0649 Fax: (630)252-0652 Email: fuzq@anl.gov also Department of Biochemistry & Molecular Biology University of Georgia, Athens, GA 30602 Email: fuzq@uga.edu License Type This software is distributed under a Non-Profit license. Static link to the SBGrid SGXPro page.
SHARP/autoSHARP	- an automated structure solution pipeline built around the heavy-atom refinement and phasing program SHARP, the density modification ...	check	check	check	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 Linux 32: various Linux 64: various OSX Intel: various OSX PPC: various 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 help@sbgrid.org to gain access. License Type This software is distributed under a Non-Profit license.
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 Linux 32: various Linux 64: various OSX Intel: various OSX PPC: various 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 help@sbgrid.org to gain access. License Type This software is distributed under a Non-Profit license. Static link to the SBGrid SHARP/autoSHARP page.
SHELX	- a set of programs for macromolecular phasing. SHELXC is designed to provide a simple and fast way ...	check		check	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 Linux 32: 97-2.20090720 OSX Intel: 97-2.20090720 OSX PPC: 97-2.20090720 SGI Irix: 97-2 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. License Type This software is distributed under a Commercial license.
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 Linux 32: 97-2.20090720 OSX Intel: 97-2.20090720 OSX PPC: 97-2.20090720 SGI Irix: 97-2 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. License Type This software is distributed under a Commercial license. Static link to the SBGrid SHELX page.
SnB	- determination of the anomalously scattering substructures of selenomethionyl-substituted proteins containing as many as 160 Se sites. SnB ...	check		check	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 Linux 32: 2.3 OSX Intel: 2.3 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) License Type This software is distributed under a Non-Profit license.
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 Linux 32: 2.3 OSX Intel: 2.3 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) License Type This software is distributed under a Non-Profit license. 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.	check	check	check	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 Linux 32: 2.13 Linux 64: 2.13 OSX Intel: 2.13 OSX PPC: 2.13 SGI Irix: 2.10 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. License Type This software is distributed under a Non-Profit license.
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 Linux 32: 2.13 Linux 64: 2.13 OSX Intel: 2.13 OSX PPC: 2.13 SGI Irix: 2.10 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. License Type This software is distributed under a Non-Profit license. Static link to the SBGrid SOLVE/RESOLVE page.
SOMoRe	- 6D global search and multi-start optimization molecular replacement package.	check	check	check	6D global search and multi-start optimization molecular replacement package. Developers Diane Jamrog Categories X-ray Crystallography Versions Linux 32: 0.93 Linux 64: 0.93 OSX Intel: 0.93 OSX PPC: 0.93 Citations Jamrog et al. SOMoRe: a multi-dimensional search and optimization approach to molecular replacement. Acta Cryst. 2003. D59: 304-314. License Type This software is distributed under an Open license.
6D global search and multi-start optimization molecular replacement package. Developers Diane Jamrog Categories X-ray Crystallography Versions Linux 32: 0.93 Linux 64: 0.93 OSX Intel: 0.93 OSX PPC: 0.93 Citations Jamrog et al. SOMoRe: a multi-dimensional search and optimization approach to molecular replacement. Acta Cryst. 2003. D59: 304-314. License Type This software is distributed under an Open license. 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. ...	check			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 Linux 32: 0.7 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. License Type This software is distributed under an Open license.
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 Linux 32: 0.7 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. License Type This software is distributed under an Open license. 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, ...	check	check	check	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 Linux 32: 20090203 Linux 64: 20110630 OSX Intel: 20090203 OSX PPC: 20090203 Citations See list of literature references here: http://www.hhmi.swmed.edu/Manuals/gerard/gerard_manuals.html License Type This software is distributed under an Open license.
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 Linux 32: 20090203 Linux 64: 20110630 OSX Intel: 20090203 OSX PPC: 20090203 Citations See list of literature references here: http://www.hhmi.swmed.edu/Manuals/gerard/gerard_manuals.html License Type This software is distributed under an Open license. Static link to the SBGrid USF Gerard Utilities page.
WASP	- searches PDB files for misidentified water molecules that should be modeled as cations.	check	check	check	searches PDB files for misidentified water molecules that should be modeled as cations. Developers Enrico DiCera Categories X-ray Crystallography Structure Analysis Versions Linux 32: 1.0 Linux 64: 1.0 OSX Intel: 1.0 OSX PPC: 1.0 License Type This software is distributed under an Open license.
searches PDB files for misidentified water molecules that should be modeled as cations. Developers Enrico DiCera Categories X-ray Crystallography Structure Analysis Versions Linux 32: 1.0 Linux 64: 1.0 OSX Intel: 1.0 OSX PPC: 1.0 License Type This software is distributed under an Open license. 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 ...	check	check	check	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 Linux 32: 20120315 Linux 64: 20120315 OSX Intel: 20120315 SGI Irix: December-2004 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 License Type This software is distributed under a Non-Profit license.
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 Linux 32: 20120315 Linux 64: 20120315 OSX Intel: 20120315 SGI Irix: December-2004 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 License Type This software is distributed under a Non-Profit license. 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.	check		check	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 Linux 32: 0.6 OSX Intel: 0.6 OSX PPC: 0.6 Citations Kabsch. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 1993. 26: 795-800. License Type This software is distributed under an Open license.
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 Linux 32: 0.6 OSX Intel: 0.6 OSX PPC: 0.6 Citations Kabsch. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 1993. 26: 795-800. License Type This software is distributed under an Open license. 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 ...	check	check		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 Linux 32: 0.92 Linux 64: 0.92 Citations Kursula P. XDSi - a graphical interface for the data processing program XDS. J. Appl. Cryst. 2004. 37: 347-348. License Type This software is distributed under an Academic license.
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 Linux 32: 0.92 Linux 64: 0.92 Citations Kursula P. XDSi - a graphical interface for the data processing program XDS. J. Appl. Cryst. 2004. 37: 347-348. License Type This software is distributed under an Academic license. 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 ...	check		check	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 Linux 32: 20080429 OSX Intel: 20080429 OSX PPC: 20080429 License Type This software is distributed under a Non-Profit license.
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 Linux 32: 20080429 OSX Intel: 20080429 OSX PPC: 20080429 License Type This software is distributed under a Non-Profit license. 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 ...	check	check	check	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 Linux 32: 0.3.4.0 Linux 64: 0.3.4.0 OSX Intel: 0.3.4.0 OSX PPC: 0.3.3.1 License Type This software is distributed under an Open license.
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 Linux 32: 0.3.4.0 Linux 64: 0.3.4.0 OSX Intel: 0.3.4.0 OSX PPC: 0.3.3.1 License Type This software is distributed under an Open license. Static link to the SBGrid XIA2 page.
XTALVIEW	- a complete package for solving a macromolecular crystal structure by isomorphous replacement, including building the molecular model.	check	check		a complete package for solving a macromolecular crystal structure by isomorphous replacement, including building the molecular model. Developers Duncan McRee Categories X-ray Crystallography Versions Linux 32: 4.1 Linux 64: 4.1 SGI Irix: 4.1 Citations McRee DE. XtalView, protein structure solution and protein graphics, a short history. J Struct Biol. 2008. 163(3): 208-13. McRee DE and Israel M. XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density. J Struct Biol. 1999. 125(2-3): 156-65. Technical Notes This software only runs on Red Hat 5. The software is abandoned and will not run on newer versions of Linux including Red Hat 6, Fedora 7+, Ubuntu 10.04+, etc. License Type This software is distributed under a Non-Profit license.
a complete package for solving a macromolecular crystal structure by isomorphous replacement, including building the molecular model. Developers Duncan McRee Categories X-ray Crystallography Versions Linux 32: 4.1 Linux 64: 4.1 SGI Irix: 4.1 Citations McRee DE. XtalView, protein structure solution and protein graphics, a short history. J Struct Biol. 2008. 163(3): 208-13. McRee DE and Israel M. XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density. J Struct Biol. 1999. 125(2-3): 156-65. Technical Notes This software only runs on Red Hat 5. The software is abandoned and will not run on newer versions of Linux including Red Hat 6, Fedora 7+, Ubuntu 10.04+, etc. License Type This software is distributed under a Non-Profit license. Static link to the SBGrid XTALVIEW page.

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