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lunchtime_byte_2023 [2023/01/04 10:48] – pairef-gui malylunchtime_byte_2023 [2023/01/05 12:39] (current) – cc* English maly
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 Now execute the following command for launching the PAIREF GUI: Now execute the following command for launching the PAIREF GUI:
-<code>pairef-gui</code> +<code>ccp4-python -m pairef --gui</code>
- +
-Note: The previous command should work. In case of problems, you can try to use also the following command: ''ccp4-python -m pairef --gui''+
  
 The structure of POLI was originally refined at 2.3 Å resolution. Nevertheless, we will inspect an impact of the reflection beyond this high-resolution cutoff on the model quality, We have data processed up to 1.9 Å resolution. Thus, we will add three high-resolution shells step by step: 2.3-2.1 Å, 2.1-2.0 Å and 2.0-1.9 Å. The structure of POLI was originally refined at 2.3 Å resolution. Nevertheless, we will inspect an impact of the reflection beyond this high-resolution cutoff on the model quality, We have data processed up to 1.9 Å resolution. Thus, we will add three high-resolution shells step by step: 2.3-2.1 Å, 2.1-2.0 Å and 2.0-1.9 Å.
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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 |}}