Haddock3 protein-protein basic docking tuto

[rversin]

This is a tutorial about the protein-protein docking. The link for the archive is not created yet.

[amjjbonvin]

Hi Raphaelle - a few first comments in random order:

1. I would only show scenarios 1 and 3 (the water refinement one does not make sense - no longer our default).

2. For the generation of restraints, we should rather make use of the haddock-restraints software and get rid of all scripts. Some instructions are provided at: https://www.bonvinlab.org/haddock-restraints/active_passive.html (and the software should thus be downloaded).

3. freesasa is not used in this tutorial, only pdb-tools (those are anyway dependencies of the haddock3 installation)

4. For the analysis, haddock3 does have now the automated analysis that generates html tables and plots. This should be added/changed in the section about "visualising the scores and their components" - point to the report.html file in the analysis/XX_caprieval/ directory automatically generated at the end of a run. There is also a way of running a local web server with python that will give you direct visualisation of the models within the web browser (don't remember the command right now).

5. the summary of available modules should be updated to include new modules

6. don't speak of paratope/epitope anymore - there are for antibody-antigen complexes

[rversin]

Ok, besides the creation of an archive, I think all the correction asked are done !

[rversin]

And conflicts are resolved !

[amjjbonvin]

A messy pull request ... Too many unrelated changes! Please clean things up first - updated to the latest version and only pull the changes related to this tutorial