Non-clustered structures

HADDOCK
1

Hi everyone,
I was checking the plots in the result page and saw that the structure with the lowest HADDOCK score wasn’t in the given clustered structures (I think due to the clustering parameters were not optimal). So, I decided to find the pdb file of that lowest structure but when I checked the zip file of complete run, the IDs of the structures in the cluster.out file were different than the ones on the plots. Also, in the structure folder, I think I should look into the water folder to find the final structures generated but I am confused about the IDs. So, I would like to ask that what is the reason of this difference in IDs and where can I find the structure that has lowest HADDOCK score given in the plots?

Thank you in advance.

2

If you move your mouse over the best model in one of the plot on the results pages, it will give you a model number.
That’s the number of the model in the structures/it1/water directory.

If you also check in that directory the file.list file you will find the ranking of the models.
The top one is the best.

In the analysis directory, however, the models have been renumbered from 1 (best) to last (worst).

3

Oh okay, thank you for your reply professor.