Merge branch 'master' into powerfit_tutorial_update

Author: AnnaEngel98

Gemfile.lock

@@ -102,7 +102,7 @@ GEM
     rb-fsevent (0.11.2)
     rb-inotify (0.11.1)
       ffi (~> 1.0)
-    rexml (3.4.1)
+    rexml (3.4.2)
     rouge (4.5.2)
     safe_yaml (1.0.5)
     sass-embedded (1.89.2)

_data/alumni.yml

@@ -405,19 +405,37 @@
 -   name: Daphne van Oosten
     status: student
 
--   name:  Bora Akdari
+-   name: Bora Akdari
     status: student
 
--   name:  Erdem Kertmen
+-   name: Erdem Kertmen
     status: student
 
 -   name: Tineke Kadijk
     status: student
 
--   name:  Joe Zhang
+-   name: Joe Zhang
     status: student
 
--   name:  Miguel Sanchez Marin
+-   name: Miguel Sanchez Marin
     status: student
 
+-   name: Alkis Katsetsiadis
+    status: Student
+
+-   name: Ilaria-Coratella
+    status: Student
+
+-   name: Yara Weldam
+    status: Student
+
+-   name: Lorenzo Possanzini
+    status: Student
+
+-   name: Qingyang Yang
+    status: Student
+
+-   name: Emile Straat
+    status: Student
+  
 

_data/members.yml

@@ -38,6 +38,10 @@
 - name: Danai Kotzampasi
   position: Postdoctoral Researcher
   avatar: /images/people/Danai-Kotzampasi.png
+  
+- name: Shantanu Khatri
+  position: Postdoctoral Researcher
+  avatar: /images/people/Shantanu-Khatri.jpg
 
 - name: Xiaotong Xu
   position: Ph.D Candidate
@@ -55,26 +59,30 @@
   bluesky: https://bsky.app/profile/aengel1.bsky.social
   linkedin: https://www.linkedin.com/in/anna-engel-msc-53266a157/
 
-- name: Alkis Katsetsiadis
-  position: M.Sc Student
-  avatar: /images/people/Alkis-Katsetsiadis.png
-
-- name: Emile Straat
-  position: M.Sc Student
-  avatar: /images/people/Emile-Straat.png
+- name: Andrea Roconli
+  position: External Ph.D Candidate (Roche)
+  avatar: /images/people/Andrea-Roncoli.jpg
 
-- name: Yara Weldam
-  position: M.Sc Student
-  avatar: /images/people/Yara-Weldam.png
+- name: Han Kurt
+  position: Visiting Ph.D Candidate
+  avatar: /images/people/Han-Kurt.png
 
-- name: Ilaria-Coratella
+- name: Luca Gazolla
+  position: Visiting Ph.D Candidate
+  avatar: /images/people/Luca-Gazolla.png
+  
+- name: Jahaciel Villaverde Nogues
   position: M.Sc Student
-  avatar: /images/people/Ilaria-Coratella.png
-
-- name: Lorenzo Possanzini
+  avatar: /images/people/Jahaciel-Villaverde.jpg
+  
+- name: Robert Romijn
   position: M.Sc Student
-  avatar: /images/people/Lorenzo_Possanzini.jpg
+  avatar: /images/people/Robert-Romijn.png
 
-- name: Qingyang Yang
+- name: Felix Maas
+  position: M.Sc Student
+  avatar: /images/people/Felix-Maas.jpg
+
+- name: Viktoria Vodilovska
   position: M.Sc Student
-  avatar: /images/people/Qingyang-Yang.png
+  avatar: /images/people/Viktoria-Vodilovska.jpg

education/HADDOCK/HADDOCK-CASP-CAPRI-T70/index.md

@@ -234,10 +234,10 @@ Let's have a more detailed look at the quality and ranking of the generated mode
 
 In order to perform the more quantitative analysis, download the full run from the results page (provide in a link in the first line of the result page) and unpack it. Alternatively, download the pre-calculated data from the following links:
 
-* T70 tetramer docking - reduced settings: [link](https://surfdrive.surf.nl/files/index.php/s/rGOGKnVwF8wjjU1/download)
-* T70 tetramer docking - full sampling: [link](https://surfdrive.surf.nl/files/index.php/s/T9HOh5lAWgtO3nD/download)
-* T70 dimer docking - reduced settings: [link](https://surfdrive.surf.nl/files/index.php/s/1RSEiHK80uIL30l/download)
-* T70 dimer docking - full sampling: [link](https://surfdrive.surf.nl/files/index.php/s/b7qEcpzOPQfvXif/download)
+* T70 tetramer docking - reduced settings: [link](https://surfdrive.surf.nl/public.php/dav/files/rGOGKnVwF8wjjU1)
+* T70 tetramer docking - full sampling: [link](https://surfdrive.surf.nl/public.php/dav/files/T9HOh5lAWgtO3nD)
+* T70 dimer docking - reduced settings: [link](https://surfdrive.surf.nl/public.php/dav/files/1RSEiHK80uIL30l)
+* T70 dimer docking - full sampling: [link](https://surfdrive.surf.nl/public.php/dav/files/b7qEcpzOPQfvXif)
 
 Then start the quantitative analysis in the directory where you saved and unpacked the run with the following command:
 

education/HADDOCK/XL-MS-oligomer/index.md

@@ -356,9 +356,6 @@ __Note:__ _The blue bars on the server can be folded/unfolded by clicking on the
 
 * **Step2:** Input the first protein PDB file. For this unfold the **First Molecule menu**.
 
-<a class="prompt prompt-info">
-First molecule: where is the structure provided? -> "I am submitting it"
-</a>
 <a class="prompt prompt-info">
 Which chain to be used? -> All (for this particular case)
 </a>
@@ -415,7 +412,7 @@ Center of mass restraints -> Check the box
 Use this type of restraints	 -> Check the box
 </a>
 Unfold the **segment pair menu** and define for N molecules N-1 segment pairs, e.g. for a trimer this would be: A-B and B-C.
-The protein sequence starts at residue 32 and ends at residue 254. Use those numbers to define the various segments.
+The protein sequence starts at residue 32 and ends at residue 254. Use those numbers to define the various segments (a segment is thus defined by range of residues with the first and last residues specified here).
 
 * **Step 6:** Define the symmetry restraints to enforce the symmetry that corresponds to the oligomeric state you choose. For this unfold the **symmetry restraints menu**:
 
@@ -448,10 +445,10 @@ Remember that we have increased the weight of the distance restraints for our ru
 
 <details style="background-color:#DAE4E7"><summary><b>Don't want to wait for your results?</b>
 </summary>
-<li> <a href="https://surfdrive.surf.nl/files/index.php/s/tQuToprVwHZORnb" target="_blank">Download dimer HADDOCK run</a></li>
-<li> <a href="https://surfdrive.surf.nl/files/index.php/s/za9ILYprxF9gDVw" target="_blank">Download trimer HADDOCK run</a></li>
-<li> <a href="https://surfdrive.surf.nl/files/index.php/s/VkiC8cZBosVALBR" target="_blank">Download tetramer HADDOCK run</a></li>
-<li> <a href="https://surfdrive.surf.nl/files/index.php/s/sAh09Cf2bJNykbk" target="_blank">Download pentamer HADDOCK run</a></li>
+<li> <a href="https://surfdrive.surf.nl/public.php/dav/files/tQuToprVwHZORnb" target="_blank">Download dimer HADDOCK run</a></li>
+<li> <a href="https://surfdrive.surf.nl/public.php/dav/files/za9ILYprxF9gDVw" target="_blank">Download trimer HADDOCK run</a></li>
+<li> <a href="https://surfdrive.surf.nl/public.php/dav/files/VkiC8cZBosVALBR" target="_blank">Download tetramer HADDOCK run</a></li>
+<li> <a href="https://surfdrive.surf.nl/public.php/dav/files/sAh09Cf2bJNykbk" target="_blank">Download pentamer HADDOCK run</a></li>
 
 </details>
 <br>

education/HADDOCK24/HADDOCK24-CASP-CAPRI-T70/index.md

@@ -251,10 +251,10 @@ Let's have a more detailed look at the quality and ranking of the generated mode
 
 In order to perform the more quantitative analysis, download the full run from the results page (provide in a link in the first line of the result page) and unpack it. Alternatively, download the pre-calculated data from the following links:
 
-* T70 tetramer docking - reduced settings: [link](https://surfdrive.surf.nl/files/index.php/s/jUjk3gbLRkylPo4/download)
-* T70 tetramer docking - full sampling: [link](https://surfdrive.surf.nl/files/index.php/s/NQe3VPuPF05iFVY/download)
-* T70 dimer docking - reduced settings: [link](https://surfdrive.surf.nl/files/index.php/s/tnT2sZKcpDNmZeP/download)
-* T70 dimer docking - full sampling: [link](https://surfdrive.surf.nl/files/index.php/s/t7wIYpuddJqhlFn/download)
+* T70 tetramer docking - reduced settings: [link](https://surfdrive.surf.nl/public.php/dav/files/jUjk3gbLRkylPo4)
+* T70 tetramer docking - full sampling: [link](https://surfdrive.surf.nl/public.php/dav/files/NQe3VPuPF05iFVY)
+* T70 dimer docking - reduced settings: [link](https://surfdrive.surf.nl/public.php/dav/files/tnT2sZKcpDNmZeP)
+* T70 dimer docking - full sampling: [link](https://surfdrive.surf.nl/public.php/dav/files/t7wIYpuddJqhlFn)
 
 Then start the quantitative analysis in the directory where you saved and unpacked the run with the following command:
 

education/HADDOCK24/HADDOCK24-antibody-antigen-basic/index.md

@@ -857,11 +857,9 @@ Considering the predicted most advantageous mutations, how different are those t
 </a>
 
 
-_Note_: For the purpose of our EMBO course pre-calculated runs are provided:
+_Note_: A pre-calculated run for the 4G6M crystal stucture is provided:
 
-* [_4G6M_matched_](http://proton.tools.ibg.edu.tr:8001/result/dae4ee4df0ec47e9a119fd512fdbfd98){:target="_blank"} (crystal structure)
-* [_cluster5_1_](http://proton.tools.ibg.edu.tr:8001/result/73cdda1fade6457faefa98af9e55b454){:target="_blank"} (top ranked cluster, l-RMSD 7.3Å)
-* [_cluster2_1_](http://proton.tools.ibg.edu.tr:8001/result/5ab290262ad340eaba0e6357b6ef46f2){:target="_blank"} (second best ranked cluster, l-RMSD 2.2Å)
+* [_4G6M_matched_](http://proton.tools.ibg.edu.tr:8001/result/4G6M_matched_chain_A_EvoEF1){:target="_blank"} (crystal structure)
 
 
 <br>

education/HADDOCK24/HADDOCK24-local-tutorial/index.md

@@ -1093,7 +1093,7 @@ There are various steps that can be performed:
 * Performing cluster analysis
 * Rerunning the analysis for a single cluster
 
-In order to work with real data, we have performed full runs on this system. Download and unpack the following [gzipped tar archive](https://surfdrive.surf.nl/files/index.php/s/sf2FUVau1Iasocd){:target="_blank"}.
+In order to work with real data, we have performed full runs on this system. Download and unpack the following [gzipped tar archive](https://surfdrive.surf.nl/public.php/dav/files/sf2FUVau1Iasocd){:target="_blank"}.
 
 <a class="prompt prompt-cmd">
   tar xfz antibody-antigen.tgz