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start [2020/06/10 14:28] – screenshot gui malystart [2024/11/18 09:08] (current) – new address maly
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 //Automatic PAIRed REFinement protocol// //Automatic PAIRed REFinement protocol//
 +
 +<color #00a2e8>**THE WEBSITE HAS BEEN MOVED TO [[https://pairef.structbio.org]]. PLEASE CONTINUE THERE.**</color>
  
 //PAIREF// is a tool for macromolecular crystallographers that performs the //PAIRed REFinement protocol//(([[https://science.sciencemag.org/content/336/6084/1030|P.A. Karplus, K. Diederichs: "Linking crystallographic model and data quality." (2012) Science, 336(6084):1030-3.]] //PAIREF// is a tool for macromolecular crystallographers that performs the //PAIRed REFinement protocol//(([[https://science.sciencemag.org/content/336/6084/1030|P.A. Karplus, K. Diederichs: "Linking crystallographic model and data quality." (2012) Science, 336(6084):1030-3.]]
-)) automatically to estimate the optimal high-resolution cutoff. It is developed in Python 2.7 and can be installed as a module into the [[https://cci.lbl.gov/cctbx_docs/index.html|Computational Crystallography Toolbox]]. It provides graphical and command-line interface that executes all the needed calculations. Parameters of refinement can be specified in detail to put all the calculations under full control of the user. Obtained results are presented as plots and tables in HTML log file. [[http://www.ccp4.ac.uk/html/refmac5.html|REFMAC5]] (part of the [[http://www.ccp4.ac.uk/|CCP4 Software Suite]]) is used for structure model refinement. +)) automatically to estimate the optimal high-resolution cutoff. It is developed in Python and can be installed as a module into the [[https://cci.lbl.gov/cctbx_docs/index.html|Computational Crystallography Toolbox]]. It provides graphical and command-line interface that executes all the needed calculations. Parameters of refinement can be specified in detail to put all the calculations under full control of the user. Obtained results are presented as plots and tables in HTML log file. //PAIREF// supports [[http://www.ccp4.ac.uk/html/refmac5.html|REFMAC5]] (part of the [[http://www.ccp4.ac.uk/|CCP4 Software Suite]]) and [[https://www.phenix-online.org/documentation/reference/refinement.html|phenix.refine]] (part of the [[https://www.phenix-online.org|PHENIX]]) for structure model refinement.
- +
-[[https://pairef.fjfi.cvut.cz/docs|{{sphinx_logo.png?200}}]]**[[https://pairef.fjfi.cvut.cz/docs|DOCUMENTATION]]**        [[https://github.com/MartinMalyMM/pairef|{{github_logo.jpg?200|GitHub}}]] [[https://pypi.org/project/pairef/|{{pypi_logo.png?150|PyPI}}]]+
  
 {{example_gui.gif?320|PAIREF screenshot}} {{example_gui.gif?320|PAIREF screenshot}}
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 ===== Installation and system requirements ===== ===== Installation and system requirements =====
  
-//PAIREF// depends on the [[http://www.ccp4.ac.uk/|CCP4 Software Suite]] (it contains [[https://cci.lbl.gov/cctbx_docs/index.html|Computational Crystallography Toolbox]] with Python 2.7 and [[https://pip.pypa.io/en/stable/|pip]]).+//PAIREF// depends on the installation of the [[http://www.ccp4.ac.uk/|CCP4 Software Suite]] or [[https://www.phenix-online.org/|PHENIX]] (both contain [[https://cci.lbl.gov/cctbx_docs/index.html|Computational Crystallography Toolbox]] with Python.
  
-//PAIREF// can be easily installed running command ''%%cctbx.python -m pip install pairef --user --no-deps%%'' in terminal (GNU/Linux, macOS) or CCP4Console (Windows). More information are available in [[https://pairef.fjfi.cvut.cz/docs/installation.html|documentation]]. Check also the //PAIREF// homepage at https://pairef.fjfi.cvut.cz/ and [[https://pypi.org/project/pairef/|PyPI repository]].+//PAIREF// can be easily installed running the command ''%%cctbx.python -m pip install pairef --user --no-deps%%'' in terminal (GNU/Linux, macOS) or CCP4Console (Windows). More information are available in [[https://pairef.fjfi.cvut.cz/docs/installation.html|documentation]]. Check also the //PAIREF// homepage at https://pairef.fjfi.cvut.cz/ and [[https://pypi.org/project/pairef/|PyPI repository]].
  
-===== Example =====+[[https://pairef.fjfi.cvut.cz/docs|{{sphinx_logo.png?200}}]]**[[https://pairef.fjfi.cvut.cz/docs|DOCUMENTATION]]**        [[https://github.com/MartinMalyMM/pairef|{{github_logo.jpg?200|GitHub}}]] [[https://pypi.org/project/pairef/|{{pypi_logo.png?150|PyPI}}]]
  
-To run paired refinement of a model (previously refined at 1.81 Å) for a series of cutoffs (1.7, 1.6, and 1.5 Å), execute a following command:+===== Examples ===== 
 + 
 +To run paired refinement of a model (previously refined at 1.81 Å) for a series of cutoffs (1.7, 1.6, and 1.5 Å), execute the following command: 
 + 
 +   cctbx.python -m pairef --XYZIN model_1-81A.pdb --HKLIN data_1-5A.mtz --HKLIN_UNMERGED data_1-5A_unmerged.mtz -i 1.81 -r 1.7,1.6,1.5
  
 For detailed information about other program parameters, read the documentation available at http://pairef.fjfi.cvut.cz/docs. For detailed information about other program parameters, read the documentation available at http://pairef.fjfi.cvut.cz/docs.
 +
 +For the explanation of the paired refinement protocol and a short tutorial, check our video from [[webinar_2021-03|PAIREF webinar]].
 +
 +[[https://pairef.fjfi.cvut.cz/docs/pairef_poli_webinar/PAIREF_webinar_23Mar2021_.mp4|{{ ::pairef_webinar_2021-03_video.gif?250 |}}]]
 +
 +
 +===== Example cases =====
 +
 +Example runs presented in our scientific paper [[https://doi.org/10.1107/S2052252520005916|Paired refinement under the control of PAIREF]] (2020) in //IUCrJ// **7** are available online and can be downloaded from [[http://doi.org/10.5281/zenodo.3687267|Zenodo]]:
 +  * simulated data set for lysozyme from //Gallus gallus// (SIM) -- [[https://pairef.fjfi.cvut.cz/docs/publication_examples/3-1_SIM/pairef_1H87_dui/PAIREF_1H87_dui.html|resolution step 0.10 A]]
 +  * measured data set for thermolysin from //Bacillus thermoproteolyticus// (TL) 
 +    * [[https://pairef.fjfi.cvut.cz/docs/publication_examples/3-2_TL/pairef_TL_step0-10A/PAIREF_TL_step0-10A.html|resolution step 0.10 A]], [[https://pairef.fjfi.cvut.cz/docs/publication_examples/3-2_TL/pairef_TL_step0-01A/PAIREF_TL_step0-01A.html|resolution step 0.01 A]]
 +  * measured data set for cysteine-bound complex of cysteine dioxygenase from //Rattus norvegicus// (CDO) 
 +    * [[https://pairef.fjfi.cvut.cz/docs/publication_examples/3-3_CDO/pairef_CDO_step0-10A/PAIREF_CDO_step0-10A.html|resolution step 0.10 A]], [[https://pairef.fjfi.cvut.cz/docs/publication_examples/3-3_CDO/pairef_CDO_complete/PAIREF_CDO_complete.html|20-fold cross-validation with resolution step 0.10 A]], [[https://pairef.fjfi.cvut.cz/docs/publication_examples/3-3_CDO/pairef_CDO_step0-01A/PAIREF_CDO_step0-01A.html|resolution step 0.01 A]]
 +  * measured data set for endothiapepsin from //Cryphonectria parasitica// in complex with fragment B53 (EP)  -- [[https://pairef.fjfi.cvut.cz/docs/publication_examples/3-4_EP/pairef_EP/PAIREF_EP.html|resolution step 0.05 A]]
 +  * measured data set for interferon gamma from //Paralichthys olivaceus// (POLI) -- [[https://pairef.fjfi.cvut.cz/docs/publication_examples/3-5_POLI/pairef_poli67/PAIREF_poli67.html|resolution step 0.10 A]]
 +  * measured data set for bilirubin oxidase from //Myrothecium verrucaria// (BO)
 +    * [[https://pairef.fjfi.cvut.cz/docs/publication_examples/3-6_BO/pairef_BO/PAIREF_BO.html|resolution step 0.10 A from 2.60 A]], [[https://pairef.fjfi.cvut.cz/docs/publication_examples/3-6_BO/pairef_BO_from2-80A/PAIREF_BO_from2-80A.html|resolution step 0.10 A from 2.80 A]]
 +
 +===== Publications =====
 +
 +M. Maly, K. Diederichs, J. Dohnalek, P. Kolenko: [[https://doi.org/10.1107/S2052252520005916|Paired refinement under the control of PAIREF]] (2020) //IUCrJ// **7**, 681-692 [[https://doi.org/10.1107/S2052252520005916]] [[https://pairef.fjfi.cvut.cz/docs/pdf/Maly_2020_Paired_refinement_under_the_control_of_PAIREF.pdf|PDF]]
 +
 +M. Maly, K. Diederichs, J. Dohnalek, P. Kolenko: [[https://doi.org/10.1107/S2053230X21006129|PAIREF: paired refinement also for Phenix users]] (2021) //Acta Cryst F//**77**, 226-229 [[https://doi.org/10.1107/S2053230X21006129]] [[https://pairef.fjfi.cvut.cz/docs/pdf/Maly_2021_PAIREF_paired_refinement_also_for_Phenix_users.pdf|PDF]]
 +
  
 ===== Credits and contact ===== ===== Credits and contact =====
  
-Please reference: M. Maly, K. Diederichs, J. Dohnalek, P. Kolenko: [[https://doi.org/10.1107/S2052252520005916|Paired refinement under the control of PAIREF]] (2020) //IUCrJ// **7**+Please refer: M. Maly, K. Diederichs, J. Dohnalek, P. Kolenko: [[https://doi.org/10.1107/S2052252520005916|Paired refinement under the control of PAIREF]] (2020) //IUCrJ// **7**
  
 //PAIREF// is developed by Martin Malý in collaboration of Czech Technical University, Czech Academy of Sciences, and University of Konstanz. In case of any questions or problems, please do not hesitate and write us: <martin.maly@fjfi.cvut.cz>. //PAIREF// is developed by Martin Malý in collaboration of Czech Technical University, Czech Academy of Sciences, and University of Konstanz. In case of any questions or problems, please do not hesitate and write us: <martin.maly@fjfi.cvut.cz>.