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.
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3DNA |
- a package for analyzing, visualizing and rebuilding 3-dimensional nucleic acid structures. 3DNA was created by Dr. Xiang-Jun ... |
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DevelopersWilma Olson Xiang-Jun Lu CategoriesVersions
CitationsXiang-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. |
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DevelopersWilma Olson Xiang-Jun Lu CategoriesVersions
CitationsXiang-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. |
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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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DevelopersAndy Arvai CategoriesVersions
Technical NotesAdxv will display data from most current detectors:
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DevelopersAndy Arvai CategoriesVersions
Technical NotesAdxv will display data from most current detectors:
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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. DevelopersMartin Raditsch Anastassis Perrakis Victor Lamzin CategoriesVersions
CitationsLanger et al. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc (2008) vol. 3 (7) pp. 1171-9 |
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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. DevelopersMartin Raditsch Anastassis Perrakis Victor Lamzin CategoriesVersions
CitationsLanger et al. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc (2008) vol. 3 (7) pp. 1171-9 |
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BALBES |
- aims to integrate into one system all the components necessary for finding a solution structure by MR. ... |
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DevelopersFei Long Garib Murshudov CategoriesVersions
CitationsLong et al. BALBES: a molecular-replacement pipeline. Acta Crystallogr D Biol Crystallogr (2008) vol. 64 (Pt 1) pp. 125-32 |
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DevelopersFei Long Garib Murshudov CategoriesVersions
CitationsLong et al. BALBES: a molecular-replacement pipeline. Acta Crystallogr D Biol Crystallogr (2008) vol. 64 (Pt 1) pp. 125-32 |
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BEST |
- a program for optimal planning of X-ray data collection from protein crystals. This software is licensed on ... |
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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. DevelopersGleb Bourenkov Alexander Popov Martin Raditsch CategoriesVersions
CitationsBourenkov and Popov. Optimization of data collection taking radiation damage into account. Acta Crystallogr D Biol Crystallogr (2010) vol. 66 (Pt 4) pp. 409-19 |
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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. DevelopersGleb Bourenkov Alexander Popov Martin Raditsch CategoriesVersions
CitationsBourenkov and Popov. Optimization of data collection taking radiation damage into account. Acta Crystallogr D Biol Crystallogr (2010) vol. 66 (Pt 4) pp. 409-19 |
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BnP |
- Buffalo and Pittsburgh) an interface for complete protein phasing suite includes SnB and Phases. |
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DevelopersWilliam Furey Charles Weeks CategoriesVersionsTechnical NotesTest the package with BnP test data (can be downloaded from BnP web page) |
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DevelopersWilliam Furey Charles Weeks CategoriesVersionsTechnical NotesTest the package with BnP test data (can be downloaded from BnP web page) |
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CCP4 |
- (Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries which can ... |
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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. DevelopersRonan Keegan Charles Ballard CategoriesVersions
CitationsCCP4: 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 |
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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. DevelopersRonan Keegan Charles Ballard CategoriesVersions
CitationsCCP4: 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 |
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CNS |
- an X-ray crystallography suite used for refinement, phasing, and molecular replacement |
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DevelopersAxel Brunger CategoriesVersions
CitationsBrunger. 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 |
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DevelopersAxel Brunger CategoriesVersions
CitationsBrunger. 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 |
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Coot |
- (Crystallographic Object-Oriented Toolkit) supports model building and real space refinement. The application interfaces with refmac, Phenix, and ... |
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DevelopersPaul Emsley CategoriesVersions
CitationsEmsley 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 NotesVersions later than 0.3.3 will not work on Fedora Core 3 or older machines due to a change in the GLIBC ABI. |
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DevelopersPaul Emsley CategoriesVersions
CitationsEmsley 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 NotesVersions later than 0.3.3 will not work on Fedora Core 3 or older machines due to a change in the GLIBC ABI. |
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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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CategoriesVersions
CitationsPflugrath. The finer things in X-ray diffraction data collection. Acta Crystallogr D Biol Crystallogr (1999) vol. 55 (Pt 10) pp. 1718-25 Technical NotesWe 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. |
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CategoriesVersions
CitationsPflugrath. The finer things in X-ray diffraction data collection. Acta Crystallogr D Biol Crystallogr (1999) vol. 55 (Pt 10) pp. 1718-25 Technical NotesWe 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. |
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DPS |
- (Data Processing Suite) a suite of programs for processing of single crystal X-ray diffraction data of proteins, ... |
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DevelopersMarian Szebenyi CategoriesVersionsCitationsRossmann and van Beek. Data processing. Acta Crystallogr D Biol Crystallogr (1999) vol. 55 (Pt 10) pp. 1631-40 |
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DevelopersMarian Szebenyi CategoriesVersionsCitationsRossmann and van Beek. Data processing. Acta Crystallogr D Biol Crystallogr (1999) vol. 55 (Pt 10) pp. 1631-40 |
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Eden |
- a crystallographic real-space electron-density refinement and optimization program that produces electron density maps with minimal model bias ... |
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DevelopersHanna Szoke CategoriesVersions
CitationsMurray 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 |
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DevelopersHanna Szoke CategoriesVersions
CitationsMurray 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 |
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Elves |
- automates most of the repetitive and mindless procedures used in solving macromolecular crystal structures, and is capable ... |
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DevelopersTom Alber CategoriesVersions
CitationsHolton 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 |
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DevelopersTom Alber CategoriesVersions
CitationsHolton 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 |
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EPMR |
- a program that finds crystallographic molecular replacement solutions using an evolutionary search algorithm. The program directly optimizes ... |
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DevelopersCharles Kissinger CategoriesVersions
CitationsKissinger et al. Rapid automated molecular replacement by evolutionary search. Acta crystallographica Section D, Biological crystallography (1999) vol. 55 (Pt 2) pp. 484-91 |
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DevelopersCharles Kissinger CategoriesVersions
CitationsKissinger et al. Rapid automated molecular replacement by evolutionary search. Acta crystallographica Section D, Biological crystallography (1999) vol. 55 (Pt 2) pp. 484-91 |
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HKL2000 |
- a data processing suite for X-ray crystallography that provides a sleek interface for devising a data collection ... |
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CategoriesVersions
CitationsMinor 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 NotesOnce 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. |
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CategoriesVersions
CitationsMinor 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 NotesOnce 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. |
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HKL2MAP |
- a graphical user-interface for macromolecular phasing. |
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DevelopersThomas Schneider CategoriesVersions
CitationsThomas Pape & Thomas R. Schneider HKL2MAP: a graphical user interface for phasing with SHELX programs. J. Appl. Cryst. 2004. 37:843-844. Technical NotesTo use HKL2MAP, you need to have licenced versions of SHELXC/D/E and Xfit in the executable path of your computer. |
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DevelopersThomas Schneider CategoriesVersions
CitationsThomas Pape & Thomas R. Schneider HKL2MAP: a graphical user interface for phasing with SHELX programs. J. Appl. Cryst. 2004. 37:843-844. Technical NotesTo use HKL2MAP, you need to have licenced versions of SHELXC/D/E and Xfit in the executable path of your computer. |
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iMosflm |
- a data processing application for macromolecular crystallography. iMosflm (Graphical User Interface) and Mosflm (data processing application) are ... |
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DevelopersHarry Powell CategoriesVersions
CitationsBattye 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 |
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DevelopersHarry Powell CategoriesVersions
CitationsBattye 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 |
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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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DevelopersLafire Developer Group M Yao CategoriesVersions
CitationsYao 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 |
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DevelopersLafire Developer Group M Yao CategoriesVersions
CitationsYao 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 |
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MAIN |
- a model building application for X-ray crystallography. |
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DevelopersDusan Turk CategoriesVersions
CitationsD.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 |
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DevelopersDusan Turk CategoriesVersions
CitationsD.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 |
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MIExpert |
- an expert system for running molecular replacement and refinement applications, and analyzing the data obtained from high-throughput ... |
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DevelopersJohn Badger CategoriesVersions
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DevelopersJohn Badger CategoriesVersions
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MIFit |
- an interactive graphics application for molecular modeling, fitting, and refinement of protein structures from X-ray crystallography developed ... |
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DevelopersBradley Smith John Badger CategoriesVersions |
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DevelopersBradley Smith John Badger CategoriesVersions |
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MOSFLM |
- a package for processing film and image plate data. |
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DevelopersHarry Powell CategoriesVersions
CitationsLeslie. 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 NotesA graphical user interface to MOSFLM is provided by iMosflm. |
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DevelopersHarry Powell CategoriesVersions
CitationsLeslie. 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 NotesA graphical user interface to MOSFLM is provided by iMosflm. |
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O |
- a model building application for X-ray crystallography. |
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DevelopersAlwyn Jones CategoriesVersions
CitationsJones. 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 NotesAs 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.
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. |
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DevelopersAlwyn Jones CategoriesVersions
CitationsJones. 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 NotesAs 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.
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. |
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PHENIX |
- (Python-based Hierarchical Environment for INtegrated Xtallography) provides tools for automated structure solution by X-ray crystallography. The PHENIX ... |
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We also maintain a recent PHENIX nightly build in the software suite. DevelopersPavel Afonine Ralf Grosse-Kunstleve Nat Echols Paul Adams CategoriesVersions
CitationsAdams et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. 2010. D66: 213-221. Technical NotesIf you use PHENIX to solve a structure please cite this publication:
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We also maintain a recent PHENIX nightly build in the software suite. DevelopersPavel Afonine Ralf Grosse-Kunstleve Nat Echols Paul Adams CategoriesVersions
CitationsAdams et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. 2010. D66: 213-221. Technical NotesIf you use PHENIX to solve a structure please cite this publication:
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PROFphd |
- a new package added as part of the pipeline to create fragments for Rosetta. For commercial users, ... |
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DevelopersBurkhard Rost Guy Yachdav CategoriesVersions
CitationsRost and Sander. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins (1994) vol. 19 (1) pp. 55-72 |
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DevelopersBurkhard Rost Guy Yachdav CategoriesVersions
CitationsRost and Sander. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins (1994) vol. 19 (1) pp. 55-72 |
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RCrane |
- allows for semi-automated building of RNA structure within Coot. |
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DevelopersAnna Pyle Kevin Keating CategoriesVersions
CitationsKeating 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 |
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DevelopersAnna Pyle Kevin Keating CategoriesVersions
CitationsKeating 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 |
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Reduce |
- a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in ... |
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DevelopersJane Richardson David Richardson CategoriesVersions
CitationsWord, 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 NotesA 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. |
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DevelopersJane Richardson David Richardson CategoriesVersions
CitationsWord, 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 NotesA 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. |
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REFMAC |
- carries out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular ... |
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DevelopersGarib Murshudov Rob Nicholls CategoriesVersions
CitationsWinn 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 NotesHow to cite: Click here. |
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DevelopersGarib Murshudov Rob Nicholls CategoriesVersions
CitationsWinn 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 NotesHow to cite: Click here. |
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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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DevelopersLiang Tong CategoriesVersions
CitationsTong and Rossmann. Rotation function calculations with GLRF program. Meth Enzymol (1997) vol. 276 pp. 594-611 |
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DevelopersLiang Tong CategoriesVersions
CitationsTong and Rossmann. Rotation function calculations with GLRF program. Meth Enzymol (1997) vol. 276 pp. 594-611 |
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Ringer |
- a program to detect molecular motions by automatic electron density sampling. |
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DevelopersRinger Licensing Ringer Developer Group Terry Lang CategoriesVersions
CitationsLang et al. Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Protein Sci (2010) vol. 19 (7) pp. 1420-31 |
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DevelopersRinger Licensing Ringer Developer Group Terry Lang CategoriesVersions
CitationsLang et al. Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Protein Sci (2010) vol. 19 (7) pp. 1420-31 |
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RSRef2000 |
- supports real-space simulated annealing refinement with X-ray data. RSRef uses an electron density function that is resolution ... |
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DevelopersMichael Chapman RSRef Developer Group CategoriesVersionsCitationsKorostelev et al. Simulated-annealing real-space refinement as a tool in model building. Acta Cryst. 2002. D58: 761-767. |
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DevelopersMichael Chapman RSRef Developer Group CategoriesVersionsCitationsKorostelev et al. Simulated-annealing real-space refinement as a tool in model building. Acta Cryst. 2002. D58: 761-767. |
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SHARP/autoSHARP |
- an automated structure solution pipeline built around the heavy-atom refinement and phasing program SHARP, the density modification ... |
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DevelopersGerard Bricogne Clemens Vonrhein CategoriesVersions
CitationsSHARP: 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 NotesSHARP/autoSHARP is installed on our server at Harvard Medical School. Please email accounts@sbgrid.org to gain access. |
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DevelopersGerard Bricogne Clemens Vonrhein CategoriesVersions
CitationsSHARP: 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 NotesSHARP/autoSHARP is installed on our server at Harvard Medical School. Please email accounts@sbgrid.org to gain access. |
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SHELX-97 |
- a set of programs for macromolecular phasing. SHELXC is designed to provide a simple and fast way ... |
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All users must first obtain license from George Sheldrick, and then request software installation by writing to bugs@sbgrid.org. DevelopersGeorge Sheldrick CategoriesVersions
CitationsSheldrick. A short history of SHELX. Acta Cryst. 2008. A64:112-122. Technical NotesAll users must first obtain license from George Sheldrick, and then request software installation by writing to bugs@sbgrid.org. |
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All users must first obtain license from George Sheldrick, and then request software installation by writing to bugs@sbgrid.org. DevelopersGeorge Sheldrick CategoriesVersions
CitationsSheldrick. A short history of SHELX. Acta Cryst. 2008. A64:112-122. Technical NotesAll users must first obtain license from George Sheldrick, and then request software installation by writing to bugs@sbgrid.org. |
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SnB |
- determination of the anomalously scattering substructures of selenomethionyl-substituted proteins containing as many as 160 Se sites. SnB ... |
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DevelopersSnB Developer Group Russ Miller CategoriesVersions
CitationsVersion 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 NotesRequires the libXp libraries (yum -y install libXp) |
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DevelopersSnB Developer Group Russ Miller CategoriesVersions
CitationsVersion 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 NotesRequires the libXp libraries (yum -y install libXp) |
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SOLVE/RESOLVE |
- a program that can automatically search for heavy atom sites, calculate initial phases and perform density modification. |
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DevelopersTom Terwilliger CategoriesVersions
CitationsSOLVE: 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. |
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DevelopersTom Terwilliger CategoriesVersions
CitationsSOLVE: 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. |
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SOMoRe |
- 6D global search and multi-start optimization molecular replacement package. |
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DevelopersDiane Jamrog CategoriesVersions
CitationsJamrog et al. SOMoRe: a multi-dimensional search and optimization approach to molecular replacement. Acta Cryst. 2003. D59: 304-314. |
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DevelopersDiane Jamrog CategoriesVersions
CitationsJamrog et al. SOMoRe: a multi-dimensional search and optimization approach to molecular replacement. Acta Cryst. 2003. D59: 304-314. |
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Untangle |
- a program designed to separate overlapping diffraction patterns from a set of crystals with slightly different orientations. ... |
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DevelopersLiev Buts CategoriesVersionsCitationsButs et al. Untangle, a tool for filtering overlapping diffraction patterns from multicrystals. Acta. Crystallogr. D. Biol. Crystallogr. 2004. 60(Pt 5):983-4. |
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DevelopersLiev Buts CategoriesVersionsCitationsButs et al. Untangle, a tool for filtering overlapping diffraction patterns from multicrystals. Acta. Crystallogr. D. Biol. Crystallogr. 2004. 60(Pt 5):983-4. |
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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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DevelopersGerard Kleywegt CategoriesVersions
CitationsSee list of literature references here: http://www.hhmi.swmed.edu/Manuals/gerard/gerard_manuals.html |
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DevelopersGerard Kleywegt CategoriesVersions
CitationsSee list of literature references here: http://www.hhmi.swmed.edu/Manuals/gerard/gerard_manuals.html |
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WASP |
- searches PDB files for misidentified water molecules that should be modeled as cations. |
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DevelopersDavid Gohara Enrico DiCera CategoriesVersions
CitationsNayal, M., & Di Cera, E. (1996) J. Mol. Biol. 256: 228-234 |
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DevelopersDavid Gohara Enrico DiCera CategoriesVersions
CitationsNayal, M., & Di Cera, E. (1996) J. Mol. Biol. 256: 228-234 |
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XDS |
- X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method. Written by Wolfgang ... |
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DevelopersWolfgang Kabsch CategoriesVersions
CitationsKabsch. XDS. Acta Cryst. 2010. D66: 125-132. Additional references found at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/references.html |
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DevelopersWolfgang Kabsch CategoriesVersions
CitationsKabsch. XDS. Acta Cryst. 2010. D66: 125-132. Additional references found at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/references.html |
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XDS-Viewer |
- an X-ray diffraction and control image viewing utility for data processed using the XDS program package. |
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DevelopersWolfgang Kabsch CategoriesVersions
CitationsKabsch. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 1993. 26: 795-800. |
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DevelopersWolfgang Kabsch CategoriesVersions
CitationsKabsch. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 1993. 26: 795-800. |
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XDSi |
- allows processing of datasets in a given directory with minimum effort when you supply it with a ... |
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Note that this software requires 'kpdf' to display its output. DevelopersPetri Kursula CategoriesVersions
CitationsKursula P. XDSi - a graphical interface for the data processing program XDS. J. Appl. Cryst. 2004. 37: 347-348. |
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Note that this software requires 'kpdf' to display its output. DevelopersPetri Kursula CategoriesVersions
CitationsKursula P. XDSi - a graphical interface for the data processing program XDS. J. Appl. Cryst. 2004. 37: 347-348. |
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XDSSTAT |
- a home-brewn program that prints various statistics (that are not available from XDS itself) in the form ... |
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DevelopersKay Diederichs CategoriesVersions
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DevelopersKay Diederichs CategoriesVersions
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XIA2 |
- an automated data reduction system designed to work from raw diffraction data and a little metadata, and ... |
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DevelopersGraeme Winter CategoriesVersions
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DevelopersGraeme Winter CategoriesVersions
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