Merge branch 'master' into air-in-web

Author: AnnaKravchenko

_data/members.yml

@@ -42,6 +42,10 @@
 - name: Xiaotong Xu
   position: Ph.D Candidate
   avatar: /images/people/Xiaotong-Xu.jpg
+  github: https://github.com/ntxxt
+  orcid: https://orcid.org/0009-0006-1883-6692
+  linkedin: https://www.linkedin.com/in/xiaotong-xu-91176a184/
+  bluesky: https://bsky.app/profile/xiaotong-xu.bsky.social
 
 - name: Anna Engel
   position: Ph.D Candidate
@@ -70,3 +74,7 @@
 - name: Lorenzo Possanzini
   position: M.Sc Student
   avatar: /images/people/Lorenzo_Possanzini.jpg
+  
+- name: Qingyang Yang
+  position: M.Sc Student
+  avatar: /images/people/Qingyang-Yang.png

education/HADDOCK3/HADDOCK3-antibody-antigen/index.md

@@ -213,85 +213,119 @@ This tutorial was last tested using HADDOCK3 version 2024.10.0b7. The provided p
 
 
 <hr>
-
 ### BioExcel summerschool, Pula, Sardinia June 2025
-
-
-We will be making use of the local computers for this tutorial. 
-The software and data required for this tutorial have been pre-installed.
-
-In order to run the tutorial, go into the HADDOCK3-antibody-antigen directory and activate the HADDOCK3 environment:
-
-<a class="prompt prompt-cmd">
-cd ~/BioExcel_SS_2025/HADDOCK/HADDOCK3-antibody-antigen<br>
-</a>
-
-This directory contains all necessary data and scripts to run this tutorial.
-
-To activate the HADDOCK3 environment type:
-
-<a class="prompt prompt-cmd">
-haddock3env<br>
-</a>
-
-which is alias to `source ~/BioExcel_SS_2025/HADDOCK/haddock3/.venv/bin/activate`
-
-You can then test that `haddock3` is indeed accessible with:
-
-<a class="prompt prompt-cmd">
-haddock3 -h
-</a>
-
-You should see a small help message explaining how to use the software.
-
-<details style="background-color:#DAE4E7">
-  <summary>
-  <i>View output</i><i class="material-icons">expand_more</i>
- </summary>
-<pre>
-(haddock3)$ haddock3 -h
-usage: haddock3 [-h] [--restart RESTART] [--extend-run EXTEND_RUN] [--setup]
-                [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-v]
-                recipe
-
-positional arguments:
-  recipe                The input recipe file path
-
-optional arguments:
-  -h, --help            show this help message and exit
-  --restart RESTART     Restart the run from a given step. Previous folders from the
-                        selected step onward will be deleted.
-  --extend-run EXTEND_RUN
-                        Start a run from a run directory previously prepared with the
-                        `haddock3-copy` CLI. Provide the run directory created with
-                        `haddock3-copy` CLI.
-  --setup               Only setup the run, do not execute
-  --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
-  -v, --version         show version
-</pre>
-</details>
-<br>
+<details>
+  <summary style="font-weight:bold; cursor:pointer;">
+    <i>click to expand</i>
+  </summary>
+    <p>
+      We will be making use of the local computers for this tutorial. 
+      The software and data required for this tutorial have been pre-installed.
+    </p>
+
+    <p>
+      In order to run the tutorial, go into the 
+      <code>HADDOCK3-antibody-antigen</code> directory and activate the HADDOCK3 environment:
+    </p>
+
+    <a class="prompt prompt-cmd">cd ~/BioExcel_SS_2025/HADDOCK/HADDOCK3-antibody-antigen</a>
+
+    <p>
+      This directory contains all necessary data and scripts to run this tutorial.  
+      To activate the HADDOCK3 environment type:
+    </p>
+
+    <a class="prompt prompt-cmd">haddock3env</a>
+
+    <p>
+      which is an alias for:<br>
+      <code>source ~/BioExcel_SS_2025/HADDOCK/haddock3/.venv/bin/activate</code>
+    </p>
+
+    <p>
+      You can then test that <code>haddock3</code> is accessible with:
+    </p>
+
+    <a class="prompt prompt-cmd">haddock3 -h</a>
+  You should see a small help message explaining how to use the software.
+
+    <details style="background-color:#DAE4E7">
+      <summary>
+      <i>View output</i><i class="material-icons">expand_more</i>
+    </summary>
+      <pre>
+      (haddock3)$ haddock3 -h
+      usage: haddock3 [-h] [--restart RESTART] [--extend-run EXTEND_RUN] [--setup]
+                      [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-v]
+                      recipe
+
+      positional arguments:
+        recipe                The input recipe file path
+
+      optional arguments:
+        -h, --help            show this help message and exit
+        --restart RESTART     Restart the run from a given step. Previous folders from the
+                              selected step onward will be deleted.
+        --extend-run EXTEND_RUN
+                              Start a run from a run directory previously prepared with the
+                              `haddock3-copy` CLI. Provide the run directory created with
+                              `haddock3-copy` CLI.
+        --setup               Only setup the run, do not execute
+        --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
+        -v, --version         show version
+      </pre>
+    </details>
+  <br>
+  </details>
 
 <hr>
 
 
 ### Local setup (on your own)
+<details>
+  <summary style="font-weight:bold; cursor:pointer;">
+    <i>click to expand</i>
+  </summary>
+  <br>
+  If you are installing HADDOCK3 on your own system, check the instructions and requirements below.
 
-If you are installing HADDOCK3 on your own system, check the instructions and requirements below.
-
+  <h4> Installing HADDOCK3</h4>
 
-#### Installing HADDOCK3
+  <p>
+    To obtain HADDOCK3, fill the
+    <a href="https://docs.google.com/forms/d/e/1FAIpQLScDcd0rWtuzJ_4nftkDAHoLVwr1IAVwNJGhbaZdTYZ4vWu25w/viewform" target="_blank">
+      registration form
+    </a>,
+    and then follow the
+    <a href="https://www.bonvinlab.org/haddock3-user-manual/install.html" target="_blank">
+      installation instructions
+    </a>.
+  </p>
 
-To obtain HADDOCK3 navigate to [its repository][haddock-repo], fill the
-registration form, and then follow the [installation instructions](https://www.bonvinlab.org/haddock3/INSTALL.html){:target="_blank"}.
+  <p>
+    <strong><em>Note</em></strong> that depending on the system you are installing HADDOCK3 on, 
+    you might have to recompile CNS if the provided executable is not working. 
+    See the 
+    <a href="https://github.com/haddocking/haddock3/blob/main/DEVELOPMENT.md#troubleshooting-the-cns-executable" target="_blank">
+      CNS troubleshooting section
+    </a> 
+    on the HADDOCK3 GitHub repository for instructions.
+  </p>
 
-**_Note_** that depending on the system you are installing HADDOCK3 on, you might have to recompile CNS if the provided executable is not working. See the [CNS troubleshooting section](https://github.com/haddocking/haddock3/blob/main/DEVELOPMENT.md#troubleshooting-the-cns-executable){:target="_blank"} on the HADDOCK3 GitHub repository for instructions.
 
-#### Auxiliary software
+  <h4> Auxiliary software </h4>
 
-[**PyMOL**](https://www.pymol.org/){:target="_blank"}: In this tutorial we will make use of PyMOL for visualization. If not
-already installed on your system, download and install [**PyMOL**](https://www.pymol.org/){:target="_blank"}. Note that you can use your favorite visulation software but instructions are only provided here for PyMOL.
+  <p>
+    <a href="https://www.pymol.org/" target="_blank"><strong>PyMOL</strong></a>: 
+    In this tutorial we will make use of PyMOL for visualization. 
+    If not already installed on your system, download and install 
+    <a href="https://www.pymol.org/" target="_blank"><strong>PyMOL</strong></a>. 
+    Note that you can use your favorite visualization software, 
+    but instructions are only provided here for PyMOL.
+  </p>
 
+  <br>
+  </details>
 
 <hr>
 <hr>
@@ -302,7 +336,7 @@ In this section we will prepare the PDB files of the antibody and antigen for do
 Crystal structures of both the antibody and the antigen in their free forms are available from the
 [PDBe database](https://www.pdbe.org){:target="_blank"}. 
 
-*__Important:__ For a docking run with HADDOCK, each molecule should consist of a single chain with non-overlapping residue numbering within the same chain.
+__Important:__ For a docking run with HADDOCK, each molecule should consist of a single chain with non-overlapping residue numbering within the same chain.
 
 As an antibody consists of two chains (L+H), we will have to prepare it for use in HADDOCK. For this we will be making use of `pdb-tools` from the command line.