Merge pull request #732 from haddocking/install-haddock3

Updated HADDOCK3 installation instructions in tutorials

Author: amjjbonvin

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

@@ -203,8 +203,10 @@ Unziping the file will create the `HADDOCK3-antibody-antigen` directory which sh
 
 In case of a workshop of course, HADDOCK3 will usually have been installed on the system you will be using.
 
-It this is not the case, you will have to install it yourself. To obtain and install HADDOCK3, navigate to [its repository][haddock-repo], fill the
-registration form, and then follow the instructions under the **Local setup (on your own)** section below.
+In case HADDOCK3 is not pre-installed in your system, you will have to install it.
+To obtain HADDOCK3, fill the [registration form](https://docs.google.com/forms/d/e/1FAIpQLScDcd0rWtuzJ_4nftkDAHoLVwr1IAVwNJGhbaZdTYZ4vWu25w/viewform?){:target="_blank"}, and then follow the [installation instructions](https://www.bonvinlab.org/haddock3-user-manual/install.html){:target="_blank"}.
+
+In this tutorial we will use the PyMOL molecular visualisation system. If not already installed, download and install PyMOL from [here](https://pymol.org/){:target="_blank"}. You can use your favourite visualisation software instead, but be aware that instructions in this tutorial are provided only for PyMOL.
 
 This tutorial was last tested using HADDOCK3 version 2024.10.0b7. The provided pre-calculated runs were obtained on a Macbook Pro M2 processors with as OS Sequoia 15.3.1.
 

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

@@ -28,7 +28,7 @@ that binds to a nanobody is called **epitope**. Different from antibodies, nanob
 Another important feature of these molecules is that the highly conserved amino acids that are not part of the CDRs, namely the **framework regions (FRs)**,
 can play a role in the binding to the antigen.
 
-Predicting the structure of a nanobody-antigen complex is very challenging, as the epitope can be located in any part of the antigen molecule. In the last years AlphaFold2-Multimer has been shown to be able to predict the correct structure of the nanobody-antigen complex for a limited number of cases. This is due to the fact that there's no co-evolution between the antibody and antigen sequences, which makes the prediction of the correct conformation extremely difficult. AlphaFold3 is expected to improve the prediction of the nanobody-antigen complex, but still fails for many cases.
+Predicting the structure of a nanobody-antigen complex is very challenging, as the epitope can be located in any part of the antigen molecule. In the last years AlphaFold2-Multimer has been shown to be able to predict the correct structure of the nanobody-antigen complex for a limited number of cases. This is due to the fact that there is no co-evolution between the antibody and antigen sequences, which makes the prediction of the correct conformation extremely difficult. AlphaFold3 is expected to improve the prediction of the nanobody-antigen complex, but still fails for many cases.
 
 This tutorial demonstrates the use of the new modular HADDOCK3 version for predicting
 the structure of a nanobody-antigen complex using different possible information scenarios, ranging
@@ -62,13 +62,11 @@ system. We will also make use of [**PyMOL**][link-pymol]{:target="_blank"} (free
 most operating systems) in order to visualize the input and output data.
 
 We assume that you have a working installation of HADDOCK3 on your system. 
-If not, provided you have a working Python version (3.9 to 3.13), you can install it through
 
-```bash
-pip install haddock3
-```
+In case HADDOCK3 is not pre-installed in your system you will have to install it.
+To obtain HADDOCK3, fill the [registration form](https://docs.google.com/forms/d/e/1FAIpQLScDcd0rWtuzJ_4nftkDAHoLVwr1IAVwNJGhbaZdTYZ4vWu25w/viewform?){:target="_blank"}, and then follow the [installation instructions](https://www.bonvinlab.org/haddock3-user-manual/install.html){:target="_blank"}.
 
-or refer to the [HADDOCK3 installation instructions][installation]{:target="_blank"} for more details.
+In this tutorial we will use the PyMOL molecular visualisation system. If not already installed, download and install PyMOL from [here](https://pymol.org/){:target="_blank"}. You can use your favourite visualisation software instead, but be aware that instructions in this tutorial are provided only for PyMOL.
 
 Further we are providing pre-processed PDB files for docking and analysis (but the
 preprocessing of those files will also be explained in this tutorial). The files have been processed

education/HADDOCK3/HADDOCK3-protein-DNA-basic/index.md

@@ -28,7 +28,7 @@ Computation within this tutorial should take 1.5 hours on 8 CPUs. The tutorial d
 
 In this tutorial, we will work with the phage 434 Cro/OR1 complex (PDB: [3CRO](https://www.rcsb.org/structure/3CRO){:target="_blank"}), formed by bacteriophage 434 Cro repressor proteins and the OR1 operator.
 
-Cro is part of the bacteriophage 434 genetic switch, playing a key role in controlling the switch between the lysogenic and lytic cycles of the bacteriophage. It is a *repressor* protein that works in opposition to the phage's repressor cI protein to control the genetic switch. Both repressors compete to gain control over an operator region containing three operators that determine the state of the lytic/lysogenic genetic switch. If Cro prevails, the late genes of the phage will be expressed, resulting in lysis. Conversely, if the cI repressor prevails, the transcription of Cro genes is blocked, and cI repressor synthesis is maintained, resulting in a state of lysogeny.
+Cro is part of the bacteriophage 434 genetic switch, playing a key role in controlling the switch between the lysogenic and lytic cycles of the bacteriophage. It is a *repressor* protein that works in opposition to the phage repressor cI protein to control the genetic switch. Both repressors compete to gain control over an operator region containing three operators that determine the state of the lytic/lysogenic genetic switch. If Cro prevails, the late genes of the phage will be expressed, resulting in lysis. Conversely, if the cI repressor prevails, the transcription of Cro genes is blocked, and cI repressor synthesis is maintained, resulting in a state of lysogeny.
 
 ### Solved structure of the Cro-OR1 complex
 
@@ -63,8 +63,11 @@ It is always possible that you have questions or run into problems for which you
 
 ## Software and data setup
 
-For a complete setup of the local version of Haddock3, refer to the [online documentation](https://www.bonvinlab.org/haddock3/){:target="_blank"}.
-Please, familiarise yourself with the sections ['**A brief introduction to HADDOCK3**'](https://www.bonvinlab.org/haddock3/intro.html){:target="_blank"} and ['**Installation**'](https://www.bonvinlab.org/haddock3/INSTALL.html).
+In order to follow this tutorial you will need to work in a Linux terminal. 
+We assume that you have a working installation of HADDOCK3 on your system. 
+
+In case HADDOCK3 is not pre-installed in your system you will have to install it.
+To obtain HADDOCK3, fill the [registration form](https://docs.google.com/forms/d/e/1FAIpQLScDcd0rWtuzJ_4nftkDAHoLVwr1IAVwNJGhbaZdTYZ4vWu25w/viewform?){:target="_blank"}, and then follow the [installation instructions](https://www.bonvinlab.org/haddock3-user-manual/install.html){:target="_blank"}.
 
 In this tutorial we will use the PyMOL molecular visualisation system. If not already installed, download and install PyMOL from [here](https://pymol.org/){:target="_blank"}. You can use your favourite visualisation software instead, but be aware that instructions in this tutorial are provided only for PyMOL.
 

education/HADDOCK3/HADDOCK3-protein-glycan/index.md

@@ -59,7 +59,9 @@ We will also make use of [**PyMOL**][link-pymol] (freely available for
 most operating systems) in order to visualize the input and output data. 
 We will provide you links to download the various required software and data. 
 We assume that you have a working installation of HADDOCK3 on your system. 
-If not, please refer to the [HADDOCK3 installation instructions](https://github.com/haddocking/haddock3/blob/main/docs/INSTALL.md){:target="_blank"}.
+
+In case HADDOCK3 is not pre-installed in your system you will have to install it.
+To obtain HADDOCK3, fill the [registration form](https://docs.google.com/forms/d/e/1FAIpQLScDcd0rWtuzJ_4nftkDAHoLVwr1IAVwNJGhbaZdTYZ4vWu25w/viewform?){:target="_blank"}, and then follow the [installation instructions](https://www.bonvinlab.org/haddock3-user-manual/install.html){:target="_blank"}.
 
 Further we are providing pre-processed PDB files for docking and analysis (but the
 preprocessing of those files will also be explained in this tutorial).