From ca36e004c11c97013dbc77583ce78d2b29ddc808 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Thu, 21 May 2020 12:54:10 +0100 Subject: [PATCH] fixing hetatm script --- scripts/pdbtools_commands | 25 ++++++++++++++++++------- 1 file changed, 18 insertions(+), 7 deletions(-) diff --git a/scripts/pdbtools_commands b/scripts/pdbtools_commands index 67f6695..9cf29da 100644 --- a/scripts/pdbtools_commands +++ b/scripts/pdbtools_commands @@ -7,24 +7,35 @@ home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_residue_renumber /home /home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_residue_renumber /home/tanu/git/Data/rifampicin/input/rpob_complex_model.pdb -s 29 -r #====================================================== -# extract seq from structure +# pdb_seq.py: extract seq from structure #====================================================== /home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_seq -a /home/tanu/git/Data/ethambutol/input/3byw.pdb > 3byw_seq.txt #/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_seq -c A -a /home/tanu/git/Data/ethambutol/input/3byw.pdb > 3byw_seq.txt #====================================================== -# mutate residue: FIXME, needs charm +# pdb_mutator.py: mutate residue: FIXME, needs charm #====================================================== /home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_mutator -r 39 -m XXX /home/tanu/git/Data/ethambutol/input/3byw.pdb #====================================================== -# check ligands in pdb +# pdb_ligand.py: list ligands within pdb +# note: works ONLY for pdb containing ligands +# this is because such pdbs contain a field 'HETATM ' #====================================================== -/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand /home/tanu/git/Data/ethambutol/input/3byw.pdb - -/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand /home/tanu/git/Data/cycloserine/input/alr_complex_model.pdb - +/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand /home/tanu/git/Data/ethambutol/input/7bvf_b.pdb +/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand /home/tanu/git/Data/ethambutol/input/7bvf.pdb +#====================================================== +# pdb_ligand_tt.py: list ligands for valid pdbs AND docked complexes (my use case) +#====================================================== +/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand_tt /home/tanu/git/Data/cycloserine/input/alr_complex.pdb +/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand_tt /home/tanu/git/Data/pyrazinamide/input/pnca_complex.pdb +/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand_tt /home/tanu/git/Data/ethambutol/input/7bvf_b.pdb +/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand_tt /home/tanu/git/Data/ethambutol/input/7bvf.pdb +#====================================================== +# get torsion angles +#====================================================== +/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_torsion /home/tanu/git/Data/rifampicin/input/rpob_complex.pdb > /home/tanu/git/Data/rifampicin/input/rpob_torsion.txt #^^^^^^^^^^^^^^^^^^^^^^^^^^^^