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lunchtime_byte_2023 [2023/01/04 10:48] maly pairef-gui |
lunchtime_byte_2023 [2023/01/05 12:39] (current) maly cc* English |
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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 |}} | ||
