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tutorial [2021/03/11 14:53] – Tunning arguments for particular data malytutorial [2021/03/12 10:20] (current) – convergence maly
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 ===== First simple PAIREF run ===== ===== First simple PAIREF run =====
  
-Now we are prepared to examine data at resolution higher than 2.3 Å. Despite poor merging statistics, there can be still a useful signal in the high-resolution data beyond that cutoff. We will divide the high-resolution data in three shells (2.3-2.1O Å, 2.1-2.0 Å and 2.0-1.9 Å) and add the step by step in the refinement process. Open terminal (GNU/Linux, macOS) or CCP4 console (Windows) and go to the folder where your structure model and diffraction data are saved. For example, if you saved those three files to folder ''C:/Users/Lab/PAIREF_tutorial_poli'', write ''cd C:/Users/Lab/PAIREF_tutorial_poli'' into the console and press ''Enter''. Now let's execute //PAIREF// in a minimalistic way - the required arguments are a structure model and merged diffraction data:+Now we are prepared to examine data at resolution higher than 2.3 Å. Despite poor merging statistics, there can be still a useful signal in the high-resolution data beyond that cutoff. We will divide the high-resolution data in three shells (2.3-2.10 Å, 2.1-2.0 Å and 2.0-1.9 Å) and add the step by step in the refinement process. Open terminal (GNU/Linux, macOS) or CCP4 console (Windows) and go to the folder where your structure model and diffraction data are saved. For example, if you saved those three files to folder ''C:/Users/Lab/PAIREF_tutorial_poli'', write ''cd C:/Users/Lab/PAIREF_tutorial_poli'' into the console and press ''Enter''. Now let's execute //PAIREF// in a minimalistic way - the required arguments are a structure model and merged diffraction data:
 <code>cctbx.python -m pairef --XYZIN poli67_edit12_2-3A_refmac1.pdb --HKLIN poli67_1-9A.mtz -r 2.1,2.0,1.9</code> <code>cctbx.python -m pairef --XYZIN poli67_edit12_2-3A_refmac1.pdb --HKLIN poli67_1-9A.mtz -r 2.1,2.0,1.9</code>
  
-Follow the note ''%%------> RESULTS AND THE CURRENT STATUS OF CALCULATIONS ARE LISTED IN A HTML LOG FILE%%'' in the program output and open the stated file in your preferred web browser (//e.g.// Firefox). The running process can be monitored on this HTML page and the results are summarized there as well. You should see a [[page similar to this]].  Calculations take some time but they should be finished in 30 minutes.+Follow the note ''%%------> RESULTS AND THE CURRENT STATUS OF CALCULATIONS ARE LISTED IN A HTML LOG FILE%%'' in the program output and open the stated file in your preferred web browser (//e.g.// Firefox). The running process can be monitored on this HTML page and the results are summarized there as well. You should see a [[https://pairef.fjfi.cvut.cz/docs/tutorial_poli/pairef_project/PAIREF_project.html|page similar to this]].  Calculations take some time but they should be finished in 30 minutes.
  
 However, we can see this warning message: However, we can see this warning message:
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 This indicates that we have to think a bit more about our input structure and data to gain meaningful results. We will have to find out the suitable parameters for this particular case. This indicates that we have to think a bit more about our input structure and data to gain meaningful results. We will have to find out the suitable parameters for this particular case.
  
-===== Tunning arguments for particular data =====+===== Tunning command arguments for particular data =====
 Distant versions of a refinement program such as REFMAC5 can have more or less different behaviour. In this case of structure refined in an older REFMAC version 5.8.0158, it is recommended to refine the structure using the current version at the poorer cutoff (here 2.3 Å) at first. This can be performed with //PAIREF//: we should add the argument ''%%--prerefinement-ncyc 10%%'' so 10 cycles of refinement at 2.3 Å will be carried out before the paired refinement procedure. Distant versions of a refinement program such as REFMAC5 can have more or less different behaviour. In this case of structure refined in an older REFMAC version 5.8.0158, it is recommended to refine the structure using the current version at the poorer cutoff (here 2.3 Å) at first. This can be performed with //PAIREF//: we should add the argument ''%%--prerefinement-ncyc 10%%'' so 10 cycles of refinement at 2.3 Å will be carried out before the paired refinement procedure.
  
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 -p poli -p poli
 </code> </code>
 +
 +If you want to terminate the calculation before it is finished, press ''Ctrl'' + ''C''. Within half an hour, the calculations should be done and you will see the [[https://pairef.fjfi.cvut.cz/docs/tutorial_poli/pairef_poli/PAIREF_poli.html|results]].
 +
 +===== Graphical user interface =====
 +//PAIREF// provides also a [[https://pairef.fjfi.cvut.cz/docs/gui.html|graphical user interface (GUI)]] for intuitive setting of arguments without making up a command. However, it depends on the installation of CCP4 suite. For launching the PAIREF GUI, execute the following command:
 +<code>ccp4-python -m pairef --gui</code>
 +
 +To execute the same procedure as in the previous section, set the form analogously to this screenshot and click on the ''RUN'' button. After a while, a web page with results is available and you can click on the ''Open in browser...'' button.
 +{{ :pairef_tutorial_poli_gui.png?direct |}}
 +
 +
 +===== Interpretation of results - Where to cut? =====
 +//PAIREF// did couple of calculations automatically but the interpretation of[[https://pairef.fjfi.cvut.cz/docs/tutorial_poli/pairef_poli/PAIREF_poli.html|results]] is up to us.
 +
 +The first thing that should be checked is whether the refinements have converged. Scroll at the very bottom of page, here you can see plots of Rwork and Rfree vs. refinement cycle. We can conclude that all the refinements have converged.