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lunchtime_byte_2023 [2022/12/21 15:40] – CCP4i2 interface screenshot malylunchtime_byte_2023 [2023/01/05 12:39] (current) – cc* English maly
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-====== PAIREF in CCP4 - lunchtime byte ======+====== PAIREF in CCP4 - CCP4SW Lunchtime Byte ======
  
-5 Jan 2023+5th Jan 2023 
 + 
 +[[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 |}}