Update basic prot-prot server tuto

[AnnaKravchenko]

Issue #772

• Added intro about glucose transport
• Tidied up main text, e.g. the spacing
• Edited main text, e.g. added more question-prompts, harmonized “Steps” in the section about the server, etc.

[VGPReys]

I am only half way.
Will continue later.

[AnnaKravchenko]

I am only half way. Will continue later.

Thank you for the detailed review!

UPD: all commenets incorporated, ready for the second part:)

[amjjbonvin]

Covalently bound to one, and interact with another for the transfer to happen

…

On 16 Mar 2026, at 23:26, Victor Reys ***@***.***> wrote: Interact ? or covalently bound ?

[amjjbonvin]

We don’t distinguish anymore between expert and guru. So elevated is in principle the correct wording.

[AnnaKravchenko]

@amjjbonvin litttle question. I found two saved server runs for the E2A-HPR system described in this tutorial. One result page linked inside the tutorial (https://wenmr.science.uu.nl/haddock2.4/result/4242424242/195967-E2A-HPR) and another one linked in “Example” tab of HADDOCK server (https://wenmr.science.uu.nl/haddock2.4/result/4242424242/0-E2A-HPR)

Wonder if we need to keep both or if it’s fine to keep only one of these result pages permanently available?

[amjjbonvin]

If they are the same, then the second one is a simpler link

[VGPReys]

Not found of the check

Suggested change

	*Hint* : you can select phosphate atoms with the following command and check how many atoms are in this selection:
	*Hint* : you can select phosphate atoms with the following command and read from the log how many atoms are in this selection:

[VGPReys]

What about a list ?

Suggested change

	The file will be written to the current working directory: if PyMOL was launched from a terminal, it will be saved in the directory from which PyMOL was started; if PyMOL was opened manually (e.g., via the graphical interface), it is typically saved in your home directory.
	The file will be written to the current working directory:
	- if PyMOL was launched from a terminal, it will be saved in the directory from which PyMOL was started
	- if PyMOL was opened manually (e.g., via the graphical interface), it is typically saved in your home directory.

[VGPReys]

Suggested change

	In case if limiting number of input conformers is an unreasonable choice, it is possible to increase the number of models generated in the rigid-body docking stage (it0).
	If limiting the number of input conformers is an unreasonable choice, it is possible to increase the number of models generated in the rigid-body docking stage (it0).

[VGPReys]

Before the word cartoon was used, I guess it is better to keep it. Also in line with PyMOL naming

Suggested change

	Now let's display all models of this NMR ensemble simultaneously in ribbon representation.
	Now let's display all models of this NMR ensemble simultaneously as cartoon representation.

[amjjbonvin]

I think we are rather showing the models as ribbon and not cartoon - easier to see the differences between the conformations

[amjjbonvin]

The command below explicitly uses the ribbon representation which is basically a CA trace of the backbone.

[VGPReys]

Suggested change

	It may appear that conformations are fairly conserved across all 30 models, but let us look at the side chains of the active residues:
	At first, it may appear that conformations are fairly conserved across all 30 models, but let us look at the side chains of the active residues:

[VGPReys]

Suggested change

	Some residues clearly adopt a wide variety of conformations, and one of these might lead to much better docking results.
	Some residues clearly adopt a wide variety of conformations, and one of these might resemble the bound conformation, hence leading to much better docking results.

[VGPReys]

Suggested change

	To use a modified amino acid in HADDOCK, it is sufficient to edit the PDB file and change the residue name of the corresponding residue. There is no need to add or delete atoms - HADDOCK will take care of this automatically.
	To use a modified amino acid in HADDOCK, it is sufficient to edit the PDB file and change the residue name of the corresponding residue. There is no need to add or delete atoms - HADDOCK will take care of building the missing atoms automatically while generating the topology of the system.

[VGPReys]

Do we want to specify editors not to use ?
Or typical editors to use

[VGPReys]

Suggested change

	<a class="prompt prompt-info">Find histidine with residue sequence number equal to 90</a>
	<a class="prompt prompt-info">Find the histidine with residue number 90</a>

[VGPReys]

proposing a simpler link

Suggested change

	Remember that residue sequence number is the second integer value in the line starting with "ATOM". Check [this link](https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html){:target="_blank"} for more info.
	Remember that residue sequence number is the second integer value in the coordinate lines (starting with "ATOM" or "HETATM"). Check [this link](https://cupnet.net/pdb-format/){:target="_blank"} for more info.

[amjjbonvin]

Why remove this? It is relevant since we do remove the water for the first molecule

[amjjbonvin]

The command below explicitly uses the ribbon representation which is basically a CA trace of the backbone.

[amjjbonvin]

Be aware that there is a copy of this tutorial we use for teaching purposes in the 2nd year bachelor course. Might need to be updated too, but keeping the questions. Check https://www.bonvinlab.org/education/NMRMolmod/

[VGPReys]

Suggested change

	Locate "[Submit a new job](https://wenmr.science.uu.nl/haddock2.4/submit/1){:target="_blank"}" button. Note that you are now in "Input data" tab.
	Locate and click on the "[Submit a new job](https://wenmr.science.uu.nl/haddock2.4/submit/1){:target="_blank"}" button. Note that you are now in "Input data" tab.

[VGPReys]

Suggested change

	* **Step2:** In the field "Number of molecules", select the number of molecules to dock, in this case 2.
	* **Step2:** In the field "Number of molecules", select the number of molecules to dock, in this case 2, which is the default value.

[VGPReys]

Suggested change

	**_Note_** that you can fold and unfold the "Molecule 1 - input" section by clicking on the ▼ icon. This works for any section and subsection of HADDOCK server.
	**_Note_** that you can fold and unfold the "Molecule 1 - input" section by clicking on the ▼ icon. This works for any section and subsection on the HADDOCK2.4 server.

[VGPReys]

Suggested change

	In this tab, we will define distance restraints by specify active residues for each molecule.
	In this tab, we will define distance restraints by specifying active residues for each molecule.

[VGPReys]

Suggested change

	You do not have to keep this page open, all resent jobs can be accessed via the "[Workspace](https://wenmr.science.uu.nl/haddock2.4/workspace){:target="_blank"}" button in the navigation bar.
	You do not have to keep this page open, all recent jobs can be accessed via the "[Workspace](https://wenmr.science.uu.nl/haddock2.4/workspace){:target="_blank"}" button in the navigation bar.

[VGPReys]

Suggested change

	An example output page for E2A-HPR docking can be found [here](https://wenmr.science.uu.nl/haddock2.4/run/4242424242/195967-E2A-HPR){:target="_blank"} - just in case you don't want to wait for the results of your docking run.
	An example output page for E2A-HPR docking can be found [here](https://wenmr.science.uu.nl/haddock2.4/run/4242424242/195967-E2A-HPR){:target="_blank"} - just in case you don't want to wait for the results of your own docking run.

[VGPReys]

At that stage, do we want to make a description of the different parts available on the page ?

[VGPReys]

what about adding a link to the publication itself ?

Suggested change

	where *E_vdw* is the intermolecular van der Waals energy, *E_elec* is the intermolecular electrostatic energy, *E_desol* represents an empirical desolvation energy term adapted from Fernandez-Recio *et al.* J. Mol. Biol. 2004, and *E_air* is a penalty for violation of the restraints.
	where *E_vdw* is the intermolecular van der Waals energy, *E_elec* is the intermolecular electrostatic energy, *E_desol* represents an empirical desolvation energy term adapted from (Fernandez-Recio *et al.* J. Mol. Biol. 2004)[https://www.sciencedirect.com/science/article/pii/S0022283603013755], and *E_air* is a penalty for violation of the restraints.

[VGPReys]

Suggested change

	HADDOCK server integrates the NGL viewer which allows you to quickly visualize a specific structure among clustered. For that click on the "eye" icon next to a structure.
	HADDOCK server integrates the NGL viewer which allows you to quickly visualize a specific structure among clustered ones. For that click on the "eye" icon next to a structure.

[VGPReys]

Suggested change

	<a class="prompt prompt-question">Based on this analysis, which cluster fits biological information the mos does satisfy best the biological information? Is this cluster also the best ranked one?</a>
	<a class="prompt prompt-question">Based on this analysis, which cluster best satisfies the biological information?>
	<a class="prompt prompt-question">Is this cluster also the best ranked one?</a>

[VGPReys]

Suggested change

	This shift is critical for the RMDS calculation described below!
	This shift is critical for appropriate residue mapping when performing the RMDS calculation described below!