local and online arctic3d

[wangjiawen2013]

Hi,

I tried both local and online server of arctic3d. I find the following issues:

1. The local run didn't perform Protein Function clustering, which is optional on the webserver.
2. We cannot see the default parameters values using arctic3d -h.
3. There is a lack of explanation of results generated by local arctic3d. For example, 5j7f_updated.cif, clustered_residues_probs.out Q00987-5j7f-C_cl1.pdb, arctic3d.log , dendrogram_average.png ,clustered_interfaces.out, interface_matrix.txt and so on.
4. What does the "contact probability score" mean ? For example, in https://www.bonvinlab.org/education/HADDOCK3/HADDOCK3-protein-peptide/#bonus-how-to-use-arctic-3d-to-predict-interface-residues, the sum of the "contact probability score" don't equal to 1.0 among all the clusters for a residue.

Hope you can helps!

[VGPReys]

Dear wangjiawn,

I will be addressing this issue in the coming days.

sorry for the delay,
Thanks for your patience

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[rvhonorato]

Indeed the default parameters were not being shown, it has been fixed with #509. For the clustering, this was a "feature drift", something offered in one interface (web) and not on the other (cli) which is not ideal. I have updated the command line with #510 to add a --biological-clustering option.

As for the explanation of the results, I will wait for @VGPReys to have a look at that and once that is done I can make a new release with the changes. Thanks for raising this issue @wangjiawen2013 (:

[github-actions]

This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days.