Find NOE violations

Hi,
I see in your tutorial an explanation of how to find the NOE violations using print_noes.inp and ana_noe_viol.csh scripts (from Bonvin Lab). However, I was unable to run these scripts.
Maybe I am running them incorrectly- how should I?
I want to know which violations happen and by what distances.
I am using the local version haddock2.4
Thank you very much!

The simplest way is to run the full analysis in HADDOCK.

Change for that the runana parameter to full in run.cns


{======================= analysis and clustering ==========================}
{* Full or limited analysis of results? *}
{+ choice: "full" "cluster" "none" +}
{===>} runana=“full;

You can empty the analysis directory and restart haddock2.4

And if you want to do that for a specific cluster check the online manual at:

[

HADDOCK2.4 manual - Analysis
bonvinlab.org

](HADDOCK2.4 manual - Analysis – Bonvin Lab)

Thank you
How can I do this if the docking is finished?
If I empty the analysis directory and do haddock2.4 (in directory with run.cns) then it will only fill the analysis directory without starting the docking over?

Yes - it will only perform the analysis

Thank you
I ran the analysis on only cluster 1 and this is how the beginning of the file looks

Rexp= 4.670 Rave= 10.991 Viol= -6.319 #viol= 165 ( A 63 LEU HG) ( B 16 TYR HE1)
Rexp= 4.380 Rave= 9.528 Viol= -5.143 #viol= 157 ( A 63 LEU HD12) ( B 16 TYR HE1)
Rexp= 5.480 Rave= 9.187 Viol= -3.705 #viol= 1 ( A 33 GLU HG2) ( B 13 ARG HH22)
Rexp= 5.080 Rave= 8.729 Viol= -3.649 #viol= 152 ( A 63 LEU HD21) ( B 16 TYR HE2)

How could this be? There aren’t 165 structures in cluster 1. (And when I analyze all structures the first #viol is 519 when I only have 200 structures.)

Thank you

Which file are you looking at?

And how many models are there in cluster 1?

114 structures

Ana_noe_vio_all

Try analysing the ambig and unambig files instead of all

Thank you
I looked and it is still higher

This is how I ran it:
cd /home/qnt/drorimi2/full_analize_40PDB/7pll/HADDOCK/run_flex_6_1/structures/it1/water/
$HADDOCKTOOLS/make_links.csh clust1
cd /home/qnt/drorimi2/full_analize_40PDB/7pll/ADDOCK/run_flex_6_1/
haddock2.4

I also noticed that all the structures are in analysis_clust1

Check how many models are in the file.nam in the water dir.

After running the make_links.csh command it should in principle only contain the clust1 models.

file.nam should be a link to file.nam_clust1

Also important: Did you first run the ana_clusters.csh script in the water directory?

yes I did
attaching is my full script (first time in run.cns was analysed by “clusters”)

#!/bin/tcsh

#Set up environment
cd /home/qnt/drorimi2/software/haddock2.4-2023-01/
source /home/qnt/drorimi2/anaconda3/etc/profile.d/conda.csh
conda activate /home/qnt/drorimi2/anaconda3/envs/haddock2.4
./install.csh config.local
source ./haddock_configure.csh

#Define pdb_name variable
set pdb_name = “7pll”

set filename = ( “run_7pll_HB_flex” )

#Loop through each filename
foreach arg ($filename)
echo 1
echo ${arg}
set haddock_dir = “/home/qnt/drorimi2/full_analize_40PDB/${pdb_name}/HADDOCK/${arg}”

#Navigate to directory
cd ${haddock_dir}/structures/it1/water/


# Clean up analysis directories
rm -f /home/qnt/drorimi2/full_analize_40PDB/${pdb_name}/HADDOCK/${arg}/structures/it1/water/analysis/*
rm -f /home/qnt/drorimi2/full_analize_40PDB/${pdb_name}/HADDOCK/${arg}/structures/it1/analysis/*
cd /home/qnt/drorimi2/full_analize_40PDB/${pdb_name}/HADDOCK/${arg}/structures/it1/water/


#Run full analysis
/home/qnt/drorimi2/full_analize_40PDB/7pll/HADDOCK/analyse_and_make_tbl/change_cns_full_a.sh   #chamge to "full" analyse /home/qnt/drorimi2/full_analize_40PDB/${pdb_name}/HADDOCK/${arg}/run.cns
cd /home/qnt/drorimi2/full_analize_40PDB/${pdb_name}/HADDOCK/${arg}/
haddock2.4 
echo "Full analysis completed"


#Run analysis scripts
cd /home/qnt/drorimi2/full_analize_40PDB/${pdb_name}/HADDOCK/${arg}/structures/it1/water/
$HADDOCKTOOLS/ana_structures.csh
$HADDOCKTOOLS/ana_clusters.csh -best 4 analysis/cluster.out


#Run cluster1 analysis
cd /home/qnt/drorimi2/full_analize_40PDB/${pdb_name}/HADDOCK/${arg}/structures/it1/water/
$HADDOCKTOOLS/make_links.csh clust1
cd /home/qnt/drorimi2/full_analize_40PDB/${pdb_name}/HADDOCK/${arg}/
haddock2.4 
echo "Cluster 1 analysis completed"

cd 

end

the error is

wc: analysis/cluster.out: No such file or directory
foreach: No match.

I also tryed $HADDOCKTOOLS/ana_clusters.csh -best 4 analysis/cluster.out.gz and it didn’t work
it gets stuck on
starting analysis scripts for /home/qnt/drorimi2/full_analize_40PDB/7pll/HADDOCK/run_7pll_HB_flex_6_1/structures/it1/water
calculating average structure and similarity matrices
queue command:
waiting for the average structure…
/bin/tcsh HADDOCK_run_7pll_HB_flex_get_average.job

Thank you!

Do you see in the water dir cluster-specific file.nam_clustX files?

Also for the cluster ana script to work the cluster.out file in the analysis directory must be unzipped (i.e. not cluster.out.gz)

you might therefore add to your script a gunzip cluster.out command

Thank you!
Adding the gunzip command worked:)
Also, I couldn’t find anywhere a file where it says for a specific structure what the NOE violations are there, I only saw for a cluster/all. Is there a way?
Thank you,
Miriam

The info is hidden in the .out files…

You could create clusters files containing only one model and repeat the analysis (a bit cumbersome…)