43 lines
2.1 KiB
Text
43 lines
2.1 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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# 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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# 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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# check ligands in pdb
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#======================================================
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/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand /home/tanu/git/Data/ethambutol/input/3byw.pdb
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/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand /home/tanu/git/Data/cycloserine/input/alr_complex_model.pdb
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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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