Pdb order in cluster.out

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab

What order is used to list all the pdb files in each cluster in file cluster.out? It seems that most are displayed by numeric increasing but not the first one. What special about the first pdb in each cluster?


The numbers listed correspond to the rank.

The first number is the cluster centre.

And when using for example the ana_cluster.csh script the models will be selected based on their score

Thanks. :+1:

I finally figured out that the number in “cluster.out” is NOT the pdb filename, but the haddock score rankings, ie, “10” means the tenth lowest haddock score, or the tenth pdb file in “file.nam_haddock-score”.

You are correct! :slight_smile:

Also keep in mind that the first “model-index” is not the best model, but the cluster center:

The output looks like:

Cluster 1 → 8 1 2 3 5 6 7 9 10 11 12 13 14 15 …
Cluster 2 → 23 25 26 29 39 62 66 67 72 74 78 …
Cluster 3 → 153 4 32 43 96 131 147 158 163 …

The numbers correspond to the structure number in the analysis file. For example 8 corresponds to structure number 8 in analysis, i.e, the eigth structure in file.list in it1/water . The first structure of each cluster above corresponds to the cluster center. The remaining structures are sorted according to their index.

Have a look here for more info: HADDOCK2.4 manual - Analysis – Bonvin Lab