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various debug, doc, and args

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Tanushree Tunstall 2020-05-25 14:27:25 +01:00
parent 3a0ff9b35e
commit b28d0afded
4 changed files with 77 additions and 40 deletions
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17
scripts/pdbtools_commands
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@ -11,6 +11,21 @@ home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_residue_renumber /home
#======================================================
/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
======
# gidB
=======
/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_seq -a /home/tanu/git/LSHTM_3TB/gid/docking/3g89.pdb > 3g89_seq.txt
/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
alignment
>3g89A_ATOM chain_length:238
MFGKHPGGLSERGRALLLEGGKALGLDLKPHLEAFSRLYALLQEAGEEEVVVKHFLDSLTLLRLPLWQGPLRVLDLGTGA
GFPGLPLKIVRPELELVLVDATRKKVAFVERAIEVLGLKGARALWGRAEVLAREAGHREAYARAVARAVAPLCVLSELLL
PFLEVGGAAVAMKGPRVEEELAPLPPALERLGGRLGEVLALQLPLSGEARHLVVLEKTAPTPPAYPRRPGVPERHPLC
>gidb_chopin1 _ATOM chain_length:224
MSPIEPAASAIFGPRLGLARRYAEALAGPGVERGLVGPREVGRLWDRHLLNCAVIGELLERGDRVVDIGSGAGLPGVPLA
IARPDLQVVLLEPLLRRTESLREMVTDLGVAVEIVRGRAEESWVQDQLGGSDAAVSRAVAALDKLTKWSMPLIRPNGRML
AIKGERAHDEVREHRRVMIASGAVDVRVVTCGANYLRPPATVVFARRGKQIARGSARMASGGTA
#======================================================
# pdb_mutator.py: mutate residue: FIXME, needs charm
@ -26,7 +41,7 @@ home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_residue_renumber /home
/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)
# pdb_hetatm.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