Victor Reys

I agree that `top_clusters` with an `s` is better than `top_cluster`. But, same as marco, I also do not see the error in the current version

I am not sure of that one. I think we could keep it. We could: - keep the CLI - create bindings to `haddock-restraints` - remove the functions ( in...

> > * create bindings to `haddock-restraints` > > Not sure if that's what you mean The idea was that the `haddock3-restraints` is simply pointing `haddock-restraints`, that comes with the...

To which extend we could also ship the haddock3-ui when installing haddock3, so the `offline = true` would also be functional ?

I see that `plotly` menu is on top of the cluster legend (see screenshot) 

> > To which extend we could also ship the haddock3-ui when installing haddock3, so the `offline = true` would also be functional ? > > Working on offline mode...

> @VGPReys you beat me with #1041, so I will solve the conflicts. Oops... I did not realized that you also worked on it !

To add to @amjjbonvin answer: - You can use [pdb-tools](https://github.com/haddocking/pdb-tools) to easily modify the chain ids. ```bash # to modify your chain to X run pdb_chain -X path/to/pdb_file.pdb > pdb_file_X.pdb...

Dear wangjiawn, I will be addressing this issue in the coming days. sorry for the delay, Thanks for your patience

> In clustrmsd module the value of criterion parameter determines which other module parameters are ignored see > > https://github.com/haddocking/haddock3/blob/a11a7c37a96b12d203717941607daf36bf966eaa/src/haddock/modules/analysis/clustrmsd/defaults.yaml#L50 > . Could we use incompatible parameters there as well?...