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--- start [2021/03/10 12:51]
maly heading Example cases
+++ start [2022/12/22 09:13]
maly smaller ccp4 image
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 //Automatic PAIRed REFinement protocol//
-//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. //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}}]]
+----
+===== Upcoming event: CCP4 Study Weekend 2023 - Lunchtime Byte about PAIREF =====
+We are pleased to announce a Lunchtime Byte about PAIREF at [[https://ccp4sw.org/|CCP4 Study Weekend 2023]]. This event will be held on 5th January 2023 at 13:00 (UTC - London). We will cover both - theoretical background and a short tutorial.
+**[[lunchtime_byte_2023| Continue to the event page]]** {{ccp4.jpg?124x52 nolink}}
+----
+//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 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.
 {{example_gui.gif?320|PAIREF screenshot}}
@@ Line 14: / Line 22: @@
 ===== 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 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]].
+[[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}}]]
 ===== Examples =====
@@ Line 25: / Line 35: @@
 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 =====
@@ Line 38: / Line 53: @@
   * 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 =====
-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>.

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