Differences

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--- webinar_2021-03 [2021/03/16 14:44] – [Graphical user interface] new screenshot of gui maly
+++ webinar_2021-03 [2021/03/24 10:09] (current) – video maly
@@ Line 1: / Line 1: @@
 ====== PAIREF webinar ======
 Mar 2021, 3pm (CET)
-  - Introduction to paired refinement. [[Download the presentation in PDF]].
+=== IMPORTANT: Please install PAIREF and download data before the webinar (instructions below). ===
+  - Introduction to paired refinement. [[https://pairef.fjfi.cvut.cz/docs/pairef_poli_webinar/PAIREF_webinar_2021_kolenko.pdf|Download presentation in PDF]].
   - Installation of //PAIREF// for CCP4 and PHENIX users.
   - Short tutorial. [[https://pairef.fjfi.cvut.cz/docs/pairef_poli_webinar/PAIREF_webinar_poli.zip|Download the archive with the data]].
   - Discussion.
-===== Tutorial =====
+[[https://pairef.fjfi.cvut.cz/docs/pairef_poli_webinar/PAIREF_webinar_2021-03.pdf|Download these webinar instructions in PDF]]
-==== Install PAIREF - before webinar ====
+==== Video recording from the webinar ====
+[[https://pairef.fjfi.cvut.cz/docs/pairef_poli_webinar/PAIREF_webinar_23Mar2021_.mp4|{{ ::pairef_webinar_2021-03_video.gif |}}]]
+===== Tutorial =====
-=== Please install //PAIREF// before the webinar. ===
+==== PAIREF installation: IMPORTANT: Please install PAIREF before the webinar ====
 Althought //PAIREF// has been developed to be installed easily, atypical computer setting can cause problems sometimes. Feel free to contact us via email ([[martin.maly@fjfi.cvut.cz]]) and we will help you.
@@ Line 23: / Line 30: @@
 {{:ccp4console.gif?nolink|}} {{:phenix_command_prompt.gif?nolink|}}
-Now execute the following command that installs PAIREF on your computer:
+Now execute the following commands that install PAIREF into CCP4 environment on your computer:
-<code>cctbx.python -m pip install pairef --no-deps --user</code>
+<code>
+ccp4-python -m ensurepip --user
+ccp4-python -m pip install pairef --no-deps --upgrade --user
+</code>
 If the installation was not successful, please go through the section [[https://pairef.fjfi.cvut.cz/docs/installation.html#troubleshooting|Installation - Troubleshooting]] in our documentation.
+**In the end, please check whether the installation was successful: Try to show the help message executing the following command:**
+<code>ccp4-python -m pairef --help</code>
+If the help message appears, the installation seems to be successful. Please download also the data before the webinar - the instruction follows.
 ==== Download data ====
@@ Line 36: / Line 52: @@
   * Merged diffraction data up to 1.9 Å - //poli67_1-9A.mtz//
   * Unmerged diffraction data up to 1.9 Å - //poli67_XDS_ASCII_1-9A.HKL//
+**If you have installed //PAIREF// and extract the data, you are ready for the webinar.** :-)
 ==== Open console in working directory ====
 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''.
 ==== Run PAIREF in command line ====
-We will add three high-resolution shells step by step: 2.3-2.10 Å, 2.1-2.0 Å and 2.0-1.9 Å. Run //PAIREF//: <code>cctbx.python -m pairef --XYZIN poli67_webinar_2-3A.pdb --HKLIN poli67_1-9A.mtz -u poli67_XDS_ASCII_1-9A.HKL -r 2.1,2.0,1.9 -w 0.06 -p poli_webinar</code>
+We will add three high-resolution shells step by step: 2.3-2.10 Å, 2.1-2.0 Å and 2.0-1.9 Å. Run //PAIREF//: <code>ccp4-python -m pairef --XYZIN poli67_webinar_2-3A.pdb --HKLIN poli67_1-9A.mtz -u poli67_XDS_ASCII_1-9A.HKL -r 2.1,2.0,1.9 -w 0.06 -p poli_webinar</code>
 Note: The structure model was refined using X-ray weight 0.06, we have to keep this setting to gain unbiased results.
@@ Line 57: / Line 73: @@
 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.
-Rfree decreased after the addition of shells 2.3-2.10 Å and 2.1-2.0 Å.
+Rfree decreased after the addition of shells 2.3-2.10 Å and 2.1-2.0 Å:
 {{ :poli_webinar_r-values.png?nolink |}}
-Since a perfect model gives an R value of 0.42 against random data (i.e. pure noise) – assuming non-tNCS (translational non-crystallographic symmetry) data from a non-twinned crystal ((Evans, P. R. & Murshudov, G. N. (2013). Acta Cryst. D69, 1204-1214.)) – a higher R value in the (current) high-resolution shell indicates either the involvement of high-resolution data without information content (the data are even worse than noise), or poor quality of the model, or the presence of tNCS. This is indicated for the shell  2.0-1.9 Å.
+Since a perfect model gives an R-value of 0.42 against random data (i.e. pure noise) – assuming non-tNCS (translational non-crystallographic symmetry) data from a non-twinned crystal ((Evans, P. R. & Murshudov, G. N. (2013). Acta Cryst. D69, 1204-1214.)) – a higher R-value in the (current) high-resolution shell indicates either the involvement of high-resolution data without information content (the data are even worse than noise), or poor quality of the model, or the presence of tNCS. This is indicated for the shell  2.0-1.9 Å.
 {{ :poli_webinar_rfree.png?nolink |}}
-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. No overfitting was indicated.
+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.
 {{ :poli_webinar_ccwork.png?nolink |}}
@@ Line 80: / Line 96: @@
       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
       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>
+===== Contact =====
+In case of any questions or problems, please do not hesitate and write us: [[martin.maly@fjfi.cvut.cz]].
+===== Further reading =====
+  * [[https://doi.org/10.1107/S2052252520005916|Paired refinement under the control of PAIREF. M. Maly, K. Diederichs, J. Dohnalek, P. Kolenko (2020) IUCrJ 7]]
+  * More information about //PAIREF// settings and possibilities are explained in the [[https://pairef.fjfi.cvut.cz/docs/|documentation]].
+  * Linking crystallographic model and data quality. P.A. Karplus & K. Diederichs (2012) Science 336:1030–3
+  * Assessing and maximizing data quality in macromolecular crystallography. P.A. Karplus & K. Diederichs (2015) Cur. Op. in Str. Biology 34:60–68
+  * Better models by discarding data? P.A. Karplus & K. Diederichs (2013) Acta Cryst. D59:1215–1222