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fixing hetatm script

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Tanushree Tunstall 2020-05-21 12:54:10 +01:00
parent 15dea0cbf6
commit ca36e004c1
1 changed files with 18 additions and 7 deletions
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25
scripts/pdbtools_commands
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@ -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 /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 -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 #/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 /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/ethambutol/input/7bvf_b.pdb
/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand /home/tanu/git/Data/ethambutol/input/7bvf.pdb
/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand /home/tanu/git/Data/cycloserine/input/alr_complex_model.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
#^^^^^^^^^^^^^^^^^^^^^^^^^^^^ #^^^^^^^^^^^^^^^^^^^^^^^^^^^^