Haddock3 online user manual

[VGPReys]

Pull request related to the haddock3 user manual.

Contribute to the book

The book source code is located in software/haddock3/src/.
From here, consider only relative paths for things to be functional.

Compile the book

This manual is ment to be compiled by mdbook.

To generate it, mdbook must be installed (see how to install mdbook).

Then run the following command, once in the software/haddock3/ directory:

mdbook build haddock3-manual --dest-dir ../manual
# or
/Applications/mdbook build haddock3-manual --dest-dir ../manual

Summary

note: Check when reviewed

• Make it an mdbook
• [x] Manual.md
• [x] Introduction
  • [x] HADDOCK
  • [x] Haddock3 modularity
• [x] Installation
  • [x] GitHub repository
  • [x] CNS
  • [x] Virtual environments (conda / venv)
• [x] Command Line Interfaces (CLI)
  • [x] haddock3
  • [x] haddock3-cfg
  • [x] haddock3-restraints
  • [x] haddock3-score
  • [x] haddock3-analyse
  • [x] haddock3-traceback
  • [x] haddock3-re
  • [x] haddock3-copy
  • [x] haddock3-clean
  • [x] haddock3-unpack
  • [ ] haddock3-mpitask
  • [X] haddock3-dmn # not described, to obscure, useless
  • [x] haddock3-pp
  • [X] haddock3-bm. # not described, obsolete, replaced by haddock-runner
• [x] Preparing input files
  • [x] Haddock3 requirements (chains, no resid duplicates, no altloc, etc...)
  • [x] pdb tools to manipulate input structures
• [x] Generating restraints for HADDOCK
  • [x] General introduction
  • [x] haddock-restraints command line interface
    • [x] calc_accessibility
    • [x] passive_from_active
    • [x] active_passive_to_ambig
    • [x] restrain_bodies
    • [x] z-restraints
  • [X] Symmetry restraints
  • [x] Ab-initio docking mode
  • [x] Flexibility
    • [x] Molecules Segments
    • [x] Semi-flexible
    • [x] Fully-flexible
• [x] Generating a docking protocol
  • [x] Configuration file
  • [x] Global parameters
  • [x] Concept of modules / parameters
• [x] Available modules
  • [x] Topology
  • [x] Sampling
  • [x] Refinement
  • [x] Scoring
  • [x] Analysis
• [x] Docking scenario examples
• [x] Getting support / How to ask for help
  • [x] FAQ
• [x] Tutorials
  • [x] Access to various tutorials
  • [x] Best practice guide
    • [x] Structure preparation
    • [x] Generating restraints
    • [x] Small-molecules / Ligands
    • [x] Glycans
    • [x] Peptides
    • [x] DNA / RNA
    • [x] Proteins
    • [x] Clustering
    • [x] Analysing results
• [x] Online lectures
• [x] haddock3 source code architecture
• [x] Citing haddock3
• [x] Acknowledgement

[amjjbonvin]

It's start! Nice.

[amjjbonvin]

I would also add sections about:

• flexibility options
• ab-initio docking mode (for CM restraints and random airs)
• symmetry restraints

May-be as part of a general section about restraints in HADDOCK3 and this is also where the haddock-restraints part should be residing

[AnnaKravchenko]

Question about flexibility options. It is about explaining how to make molecule/part of molecule flexible/semi-flexible in haddokc3, only practical things, right?
Or would you like to see a more theoretical explanation about flexibility in haddock, i.e. that semi-flexible refinement is happening in torsion angle space etc.?

[VGPReys]

Question about flexibility options. It is about explaining how to make molecule/part of molecule flexible/semi-flexible in haddokc3, only practical things, right? Or would you like to see a more theoretical explanation about flexibility in haddock, i.e. that semi-flexible refinement is happening in torsion angle space etc.?

flexref is a module and will have its own documentation.

In my opinion, it is more about explaining how to make molecules/segments flexible/semi-flexible.
Detailed explanation on the various parameters used to define it, and in which modules they can be used.

[rversin]

Suggested change

	An elegant way how to account for larger conformational changes is ensemble docking of conformations generated by Molecular Dynamics (MD).
	Ensemble docking of conformations generated by molecular dynamics (MD) is an elegant way to account for larger conformational changes.

[rversin]

Suggested change

	* HADDOCK can now handle large complexes containing up to 20 chains. An elegant way how to increase the speed of these calculations is to use coarse graining with [Martini](http://cgmartini.nl).
	* HADDOCK can now handle large complexes containing up to 20 chains. An elegant way to increase the speed of these calculations is to use coarse graining with [Martini](http://cgmartini.nl).

[rversin]

Suggested change

	The clustering of conformations and complexes is a key step in most of the workflows, as it allows us to observe convergence, redundancies, or even remove noise coming from singlotons.
	Clustering of conformations and complexes is a key step in most workflows, as it allows us to observe convergence, redundancies, or even remove noise from singletons.

[rversin]

Suggested change

	Those two modules must be followed by the `[clustrmsd]` module, otherwise, only the pair-wise RMSD matrix will be computed, and clustering not performed.
	Those two modules must be followed by the `[clustrmsd]` module; otherwise, only the pair-wise RMSD matrix will be computed, and clustering will not be performed.

[rversin]

Is this a module created for ligands/small molecules and protein/receptor complex ? If so, I would say that it would be interesting to just add a sentence to introduce a general idea as to which cases it is most appropriate to use.

[rversin]

Should we add a sentence about the most important parameters of clusfcc ? Since the other modules get a quick description, it would make sense to at least describe 'clust_cutoff' imo.

[rversin]

Should we add somewhere here which units are used for the cutoffs/rmsd values outputed ? i know it's Angstrom but not every software uses Angstrom themselves, so it would be nice to have it written in my opinion.

[rversin]

In the parameter column, shoud we add the name of the modules in haddock3 ? (especially for the MD steps, as new users might not know immediatelly which module we refer to)

[rversin]

Suggested change

	#### 1.) Information about the interface is available
	### 1.) Information about the interface is available

[rversin]

I am removing one # because of line 111