70 lines
4.1 KiB
Text
70 lines
4.1 KiB
Text
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#======================================================
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# renumber pdb file based on user defined start number
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#======================================================
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home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_residue_renumber /home/tanu/git/Data/cycloserine/input/alr_complex_model.pdb -s 35 -r
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/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_residue_renumber /home/tanu/git/Data/rifampicin/input/rpob_complex_model.pdb -s 29 -r
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#======================================================
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# pdb_seq.py: extract seq from structure
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#======================================================
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/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_seq -a /home/tanu/git/Data/ethambutol/input/3byw.pdb > 3byw_seq.txt
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#/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_seq -c A -a /home/tanu/git/Data/ethambutol/input/3byw.pdb > 3byw_seq.txt
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======
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# gidB
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=======
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/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_seq -a /home/tanu/git/LSHTM_3TB/gid/docking/3g89.pdb > 3g89_seq.txt
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/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_seq -a /home/tanu/git/LSHTM_3TB/gid/docking/gidb_chopin1.pdb > gidb_chopin1_seq.txt
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alignment
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>3g89A_ATOM chain_length:238
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MFGKHPGGLSERGRALLLEGGKALGLDLKPHLEAFSRLYALLQEAGEEEVVVKHFLDSLTLLRLPLWQGPLRVLDLGTGA
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GFPGLPLKIVRPELELVLVDATRKKVAFVERAIEVLGLKGARALWGRAEVLAREAGHREAYARAVARAVAPLCVLSELLL
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PFLEVGGAAVAMKGPRVEEELAPLPPALERLGGRLGEVLALQLPLSGEARHLVVLEKTAPTPPAYPRRPGVPERHPLC
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>gidb_chopin1 _ATOM chain_length:224
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MSPIEPAASAIFGPRLGLARRYAEALAGPGVERGLVGPREVGRLWDRHLLNCAVIGELLERGDRVVDIGSGAGLPGVPLA
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IARPDLQVVLLEPLLRRTESLREMVTDLGVAVEIVRGRAEESWVQDQLGGSDAAVSRAVAALDKLTKWSMPLIRPNGRML
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AIKGERAHDEVREHRRVMIASGAVDVRVVTCGANYLRPPATVVFARRGKQIARGSARMASGGTA
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#======================================================
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# pdb_mutator.py: mutate residue: FIXME, needs charm
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#======================================================
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/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_mutator -r 39 -m XXX /home/tanu/git/Data/ethambutol/input/3byw.pdb
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#======================================================
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# pdb_ligand.py: list ligands within pdb
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# note: works ONLY for pdb containing ligands
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# this is because such pdbs contain a field 'HETATM '
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#======================================================
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/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand /home/tanu/git/Data/ethambutol/input/7bvf_b.pdb
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/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand /home/tanu/git/Data/ethambutol/input/7bvf.pdb
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#======================================================
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# pdb_hetatm.py: list ligands for valid pdbs AND docked complexes (my use case)
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#======================================================
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/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand_tt /home/tanu/git/Data/cycloserine/input/alr_complex.pdb
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/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand_tt /home/tanu/git/Data/pyrazinamide/input/pnca_complex.pdb
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/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand_tt /home/tanu/git/Data/ethambutol/input/7bvf_b.pdb
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/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand_tt /home/tanu/git/Data/ethambutol/input/7bvf.pdb
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/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand_tt /home/tanu/git/Data/rifampicin/input/rpob_complex.pdb
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#======================================================
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# get torsion angles
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#======================================================
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/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
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#^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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# my pdb tools
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#======================================================
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# save specifed chains as individual pdbs
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#======================================================
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./pdb_chain_splitter.py -i /home/tanu/git/Data/ethambutol/input/3byw.pdb -c DF -p /home/tanu/git/Data/ethambutol/input -o 3byw
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#======================================================
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# save specifed chains as one pdb
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#======================================================
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./pdb_chain_extract.py -i /home/tanu/git/Data/ethambutol/input/3byw.pdb -c DF -p /home/tanu/git/Data/ethambutol/input -o 3byw^C
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