I have successfully install the profit, when i type which profit,it will print /lustre/grp/gyqlab/zhangcw/HADDOCK/software/bin/profit,but when use the $HADDOCKTOOLS/ana_structures.csh to analyse the docking results,the third column of structures_haddock-sorted.stat didn’t show the i-RMSD but print the name of the .pdb file again, any help?
Profit is always tricky.
Check the content of the i-RMSD.dat file in the directory where you run and_structures.csh.
Does it contain RMSD values or only the PDB filenames.
If the latter, then something goes wrong with the Profit calculations.
Did you also define the profit environment variable in the haddock_configure.csh/sh files? And source those before running the analysis?
The contect of I-RMSD.dat file actually only contains the PDB filenames and i have add the path of profit in the haddock_configure.csh/sh files,like this:
alias haddock2.4=“$(which python2.7) $HADDOCK/Haddock/RunHaddock.py”
export HADDOCK HADDOCKTOOLS PYTHONPATH NACCESS PALES PROFIT TENSOR2
Try to define explicitly the PROFIT variable (i.e. full path)
Also what kind of system are you docking? Protein-protein or something else?
i define explicitly the PROFIT variable as this :
BUt it failed again, i’m docking protein-protein system.
Define the path to the executable including the executable itself.
The scripts are calling directly $PROFIT as executable