Haddock-score vs rmsd graph

1

I am trying to generate Haddock-score vs RMSD graph and following the steps below. Could you please tell me the process is correct?

Once haddock docking is finished
In the /run1/structures/it1/water/ directory run the below command
$HADDOCKTOOLS/ana_clusters.csh -best 4 analysis/cluster.out

This will give two files

  1. cluster_haddock-score.txt_best4 (containing haddock score of the clusters)
  2. cluster_rmsd.txt_best4 (containing rmsd values of the clusters)

Make a graph for haddock-score at y-axis and rmsd values at x-axis.

Thank you for your help,

2

Provided you have profit installed locally, the clusters_haddock-sorted.stat_best4 file should contain all you need, including the HADDOCK score of the clusters and their RMSD to the best model.

And for a structure-based analysis, have a look at the structures_haddock-sorted.stat file (generated by running the ana_structures.csh script)l