25 lines
1.5 KiB
Text
25 lines
1.5 KiB
Text
|
|
#======================================================
|
|
# renumber pdb file based on user defined start number
|
|
#======================================================
|
|
home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_residue_renumber /home/tanu/git/Data/cycloserine/input/alr_complex_model.pdb -s 35 -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
|
|
#======================================================
|
|
/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
|
|
#======================================================
|
|
/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
|
|
#======================================================
|
|
/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
|