I ran protein-DNA system on haddock web and on linux and I am able to reproduce same HADDOCK score. However, I am not able to get the iRMSD present in the “CAPRI_analysis” folder.
I have used this command to get the i-rmsd values =>
cd cluster/analysis
./i-rmsd_to_target.csh *.pdb
Could you please direct me the correct way to compute the iRMSD.
These RMSDs are calculated taking as reference the best model (top ranked).
The ana_structures.csh and and_clusters.csh scripts are calling the profit software to calculate those RMSDs.
They have nothing to do with the RMSD to the reference structure. Only in the examples there are script to calculate i-RMSDs from the reference.
I am attempting to generate the HADDOCK score vs. i-RMSD graph on my Linux system and compare it with the one obtained from the web version. I have acquired both RMSD and HADDOCK scores; however, while the i-RMSD is present in the web version (within the downloaded gzipped tar file), it is absent in the Linux version.
My questions are as follows:
1. Does it automatically generate with HADDOCK, or do we need to manually run the script? The i-RMSD values I am obtaining in Linux range between 11.0 and 20.0, whereas the i-RMSD from the HADDOCK web version ranges between 0.0 and 7.0.
2. Additionally, in the downloaded gzipped tar file, all the clusters are located in the home directory. However, in Linux, I do not have access to them. Could you provide a method to obtain all the clusters (such as Cluster 4, Cluster 3, Cluster 1, and Cluster 2)?
Note: The Profit software is installed and running properly.
Thank you so much for your guidance.
The instructions to perform a manual analysis of a local run can be found at:
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Thanks for your response. I was able to run all the commands mentioned on this page. However, on this page the last graph is Haddock score vs RMSD. However, on the web version the clusters are selected based on HADDOCK SCORE vs i-RMSD.
Obviously the (HADDOCK SCORE vs RMSD) and (HADDOCK SCORE vs i-RMSD) clusters are different. Hence, I am asking about the i-RMSD calculation in Linux.
Please guide me through the process.
Best Regards,
Clusters are selected purely on the score
There is no simple way to replicate what the server is doing
