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tutorial [2021/03/12 08:48] maly links to results |
tutorial [2021/03/12 10:20] (current) maly convergence |
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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> | ||
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| ===== Interpretation of results - Where to cut? ===== | ===== 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. | //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. | ||
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| + | 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. | ||
