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lunchtime_byte_2023 [2022/12/21 15:21] maly |
lunchtime_byte_2023 [2023/01/05 12:39] (current) maly cc* English |
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| - | ====== PAIREF in CCP4 - lunchtime byte ====== | + | ====== PAIREF in CCP4 - CCP4SW Lunchtime Byte ====== |
| - | 5 Jan 2023 | + | 5th Jan 2023 |
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| + | [[https://pairef.fjfi.cvut.cz/docs/pairef_poli_ccp4sw2023/20230105_ccp4sw_pairef.pdf|{{pdf_icon.png?30x35}}]] [[https://pairef.fjfi.cvut.cz/docs/pairef_poli_ccp4sw2023/20230105_ccp4sw_pairef.pdf|Download presentation in PDF]] | ||
| In this short tutorial, we submit a paired refinement job using the //PAIREF// program, now distributed in the [[http://www.ccp4.ac.uk/|CCP4 suite]]. You can use our example data from interferon gamma from //Paralichthys olivaceus// (POLI) (([[https://www.sciencedirect.com/science/article/pii/S1050464818302651|Zahradnik et al. (2018). Fish Shellfish Immunol. 79:140–152]])), PDB entry [[https://www.rcsb.org/structure/6F1E|6F1E]]. | In this short tutorial, we submit a paired refinement job using the //PAIREF// program, now distributed in the [[http://www.ccp4.ac.uk/|CCP4 suite]]. You can use our example data from interferon gamma from //Paralichthys olivaceus// (POLI) (([[https://www.sciencedirect.com/science/article/pii/S1050464818302651|Zahradnik et al. (2018). Fish Shellfish Immunol. 79:140–152]])), PDB entry [[https://www.rcsb.org/structure/6F1E|6F1E]]. | ||
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| The results should look similar to ours: [[https://pairef.fjfi.cvut.cz/docs/pairef_poli_ccp4sw2023/PAIREF_poli_ccp4sw2023.html]]. | The results should look similar to ours: [[https://pairef.fjfi.cvut.cz/docs/pairef_poli_ccp4sw2023/PAIREF_poli_ccp4sw2023.html]]. | ||
| - | //PAIREF// ran all the calculation and did also an automatic suggestion of an optimal high-resolution cut off. Let's check the table in the top of the HTML log file: | + | //PAIREF// ran all the calculation and did also an automatic suggestion of an optimal high-resolution cut off. Let's check the table on top of the HTML log file: |
| {{ :poli_ccp4sw2023_verdict_table.png?nolink |}} | {{ :poli_ccp4sw2023_verdict_table.png?nolink |}} | ||
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| {{ :poli_ccp4sw2023_rfree.png?nolink |}} | {{ :poli_ccp4sw2023_rfree.png?nolink |}} | ||
| - | CC* a model-independent measure of noise is in the diffraction data. CC* is higher than CCwork in whole resolution range (except the shell 2.0-1.9 Å where CC* is undefined due to negative CC1/2. Thus, the overfitting was not indicated. To access overfitting, it is not needed to test set, so the comparison of CC* with CCwork is much better then with CCfree as CCwork is calculated on more data. | + | CC* is a model-independent measure of noise is in the diffraction data. For this data set, CC* is higher than CCwork in the whole resolution range, except the shell 2.0-1.9 Å where CC* is undefined due to negative CC1/2. That means overfitting was not indicated but the shell 2.0-1.9 Å should be discarded because these data are very noisy. Note that to access overfitting, it is not needed to use test set, so the comparison of CC* with CCwork is much better than with CCfree as CCwork is calculated on more data. |
| {{ :poli_ccp4sw2023_ccwork.png?nolink |}} | {{ :poli_ccp4sw2023_ccwork.png?nolink |}} | ||
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| 07 2.10 2.00 49772 4021 12.38 98.51 0.3 0.1 16.989 17.721 4.963 0.027 0.008 0.2293 | 07 2.10 2.00 49772 4021 12.38 98.51 0.3 0.1 16.989 17.721 4.963 0.027 0.008 0.2293 | ||
| 08 2.00 1.90 35920 4046 8.88 81.18 0.1 0.0 41.435 43.993 14.417 -0.132 -0.016 N/A</code> | 08 2.00 1.90 35920 4046 8.88 81.18 0.1 0.0 41.435 43.993 14.417 -0.132 -0.016 N/A</code> | ||
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| + | ==== Stay tuned, CCP4i2 interface for PAIREF is coming soon! ==== | ||
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| + | {{ :pairef_ccp4i2_dev.png?nolink |}} | ||
| ==== Run PAIREF in command line ==== | ==== Run PAIREF in command line ==== | ||
