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Philippos
Philippos
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I'm beginner in bash scriptiscripts, but I try to delete everything in my pdb file (test.pdbtest.pdb) before REMARK time 20.00REMARK time 20.00 and from REMARK time 30.00REMARK time 30.00 to the end of this file. I'm using to this sedsed command, which is such as:

sed 's/^.*(REMARK time 20.00.REMARK time 30.00).$/\1/' test.pdb > end.pdb

sed 's/^.*\(REMARK time 20.00.*REMARK time 30.00\).*$/\1/' test.pdb > end.pdb

My test.pdbtest.pdb file is as follows: REMARK time 10.00 ENERGY 1.95686E+03 HELIX 1 H1 GLU 131 SER 146 1 15 HELIX 2 H2 GLU 278 SER 293 1 15 HELIX 3 H3 GLU 426 SER 441 1 15 HELIX 4 H4 GLU 574 SER 589 1 15 SHEET 1 B1 2 ALA 32 VAL 34 0 SHEET 2 B1 2 LYS 48 GLU 50 -1 N GLU 50 O ALA 32 SHEET 1 B2 2 ALA 32 LEU 35 0 SHEET 2 B2 2 TRP 123 ASP 126 -1 N ASP 126 O ALA 32 SHEET 1 B3 2 LEU 47 PRO 51 0 SHEET 2 B3 2 VAL 62 PHE 66 -1 N PHE 66 O LEU 47 SHEET 1 B4 2 ASN 58 ASN 68 0 SHEET 2 B4 2 ASP 71 LEU 81 -1 N LEU 81 O ASN 58 SHEET 1 B5 2 TRP 77 ASP 82 0 SHEET 2 B5 2 LYS 85 LEU 90 -1 N LEU 90 O TRP 77 SHEET 1 B6 2 ALA 84 LEU 90 0 SHEET 2 B6 2 LEU 93 VAL 99 -1 N VAL 99 O ALA 84 SHEET 1 B7 2 ASN 96 VAL 99 0 SHEET 2 B7 2 ASP 111 GLU 114 -1 N GLU 114 O ASN 96 SHEET 1 B8 2 HIS 107 VAL 113 0 SHEET 2 B8 2 ASP 119 LEU 125 -1 N LEU 125 O HIS 107 SHEET 1 B9 2 ALA 179 VAL 181 0 SHEET 2 B9 2 LYS 195 GLU 197 -1 N GLU 197 O ALA 179 SHEET 1 B* 2 ALA 179 LEU 182 0 ........ ENDMDL REMARK time 20.00 ENERGY 1.96641E+03 HELIX 1 H1 GLU 131 SER 146 1 15 HELIX 2 H2 GLU 278 SER 293 1 15 HELIX 3 H3 GLU 426 SER 441 1 15 HELIX 4 H4 GLU 574 SER 589 1 15 SHEET 1 B1 2 ALA 32 VAL 34 0 SHEET 2 B1 2 LYS 48 GLU 50 -1 N GLU 50 O ALA 32 SHEET 1 B2 2 ALA 32 LEU 35 0 SHEET 2 B2 2 TRP 123 ASP 126 -1 N ASP 126 O ALA 32 SHEET 1 B3 2 LEU 47 PRO 51 0 SHEET 2 B3 2 VAL 62 PHE 66 -1 N PHE 66 O LEU 47 SHEET 1 B4 2 ASN 58 ASN 68 0 SHEET 2 B4 2 ASP 71 LEU 81 -1 N LEU 81 O ASN 58 SHEET 1 B5 2 TRP 77 ASP 82 0 SHEET 2 B5 2 LYS 85 LEU 90 -1 N LEU 90 O TRP 77 SHEET 1 B6 2 ALA 84 LEU 90 0 SHEET 2 B6 2 LEU 93 VAL 99 -1 N VAL 99 O ALA 84 SHEET 1 B7 2 ASN 96 VAL 99 0 SHEET 2 B7 2 ASP 111 GLU 114 -1 N GLU 114 O ASN 96 SHEET 1 B8 2 HIS 107 VAL 113 0 SHEET 2 B8 2 ASP 119 LEU 125 -1 N LEU 125 O HIS 107 SHEET 1 B9 2 ALA 179 VAL 181 0 SHEET 2 B9 2 LYS 195 GLU 197 -1 N GLU 197 O ALA 179 SHEET 1 B* 2 ALA 179 LEU 182 0 SHEET 2 B* 2 TRP 270 ASP 273 -1 N ASP 273 O ALA 179 SHEET 1 B* 2 LEU 194 GLY 196 0 SHEET 2 B* 2 MET 211 PHE 213 -1 N PHE 213 O LEU 194 SHEET 1 B* 2 ASN 205 ASN 215 0 SHEET 2 B* 2 ASP 218 LEU 228 -1 N LEU 228 O ASN 205 SHEET 1 B* 2 TRP 224 ASP 229 0 .................... ENDMDL REMARK time 100.00 ENERGY 1.95395E+03 HELIX 1 H1 GLU 131 SER 146 1 15 HELIX 2 H2 GLU 278 SER 293 1 15 HELIX 3 H3 GLU 426 SER 441 1 15 HELIX 4 H4 GLU 574 SER 589 1 15 SHEET 1 B1 2 ALA 32 VAL 34 0 SHEET 2 B1 2 LYS 48 GLU 50 -1 N GLU 50 O ALA 32 SHEET 1 B2 2 ALA 32 LEU 35 0 SHEET 2 B2 2 TRP 123 ASP 126 -1 N ASP 126 O ALA 32 SHEET 1 B3 2 LEU 47 PRO 51 0 SHEET 2 B3 2 VAL 62 PHE 66 -1 N PHE 66 O LEU 47 SHEET 1 B4 2 ASN 58 ASN 68 0 SHEET 2 B4 2 ASP 71 LEU 81 -1 N LEU 81 O ASN 58 SHEET 1 B5 2 TRP 77 ASP 82 0 SHEET 2 B5 2 LYS 85 LEU 90 -1 N LEU 90 O TRP 77 SHEET 1 B6 2 ALA 84 LEU 90 0 .......

CONECT 1131 1133 1132 CONECT 1133 1135 1134 CONECT 1135 1137 1136 CONECT 1137 1139 1138 CONECT 1139 1141 1140 CONECT 1141 1143 1142 CONECT 1143 1145 1144 CONECT 1145 1146 ENDMDL

REMARK time   10.00                                       ENERGY     1.95686E+03
HELIX    1 H1  GLU    131  SER    146  1                                      15
HELIX    2 H2  GLU    278  SER    293  1                                      15
HELIX    3 H3  GLU    426  SER    441  1                                      15
HELIX    4 H4  GLU    574  SER    589  1                                      15
SHEET    1 B1  2 ALA    32  VAL    34  0
SHEET    2 B1  2 LYS    48  GLU    50 -1  N  GLU    50   O  ALA    32
SHEET    1 B2  2 ALA    32  LEU    35  0
SHEET    2 B2  2 TRP   123  ASP   126 -1  N  ASP   126   O  ALA    32
SHEET    1 B3  2 LEU    47  PRO    51  0
SHEET    2 B3  2 VAL    62  PHE    66 -1  N  PHE    66   O  LEU    47
SHEET    1 B4  2 ASN    58  ASN    68  0
SHEET    2 B4  2 ASP    71  LEU    81 -1  N  LEU    81   O  ASN    58
SHEET    1 B5  2 TRP    77  ASP    82  0
SHEET    2 B5  2 LYS    85  LEU    90 -1  N  LEU    90   O  TRP    77
SHEET    1 B6  2 ALA    84  LEU    90  0
SHEET    2 B6  2 LEU    93  VAL    99 -1  N  VAL    99   O  ALA    84
SHEET    1 B7  2 ASN    96  VAL    99  0
SHEET    2 B7  2 ASP   111  GLU   114 -1  N  GLU   114   O  ASN    96
SHEET    1 B8  2 HIS   107  VAL   113  0
SHEET    2 B8  2 ASP   119  LEU   125 -1  N  LEU   125   O  HIS   107
SHEET    1 B9  2 ALA   179  VAL   181  0
SHEET    2 B9  2 LYS   195  GLU   197 -1  N  GLU   197   O  ALA   179
SHEET    1 B*  2 ALA   179  LEU   182  0
........
ENDMDL
REMARK time   20.00                                       ENERGY     1.96641E+03
HELIX    1 H1  GLU    131  SER    146  1                                      15
HELIX    2 H2  GLU    278  SER    293  1                                      15
HELIX    3 H3  GLU    426  SER    441  1                                      15
HELIX    4 H4  GLU    574  SER    589  1                                      15
SHEET    1 B1  2 ALA    32  VAL    34  0
SHEET    2 B1  2 LYS    48  GLU    50 -1  N  GLU    50   O  ALA    32
SHEET    1 B2  2 ALA    32  LEU    35  0
SHEET    2 B2  2 TRP   123  ASP   126 -1  N  ASP   126   O  ALA    32
SHEET    1 B3  2 LEU    47  PRO    51  0
SHEET    2 B3  2 VAL    62  PHE    66 -1  N  PHE    66   O  LEU    47
SHEET    1 B4  2 ASN    58  ASN    68  0
SHEET    2 B4  2 ASP    71  LEU    81 -1  N  LEU    81   O  ASN    58
SHEET    1 B5  2 TRP    77  ASP    82  0
SHEET    2 B5  2 LYS    85  LEU    90 -1  N  LEU    90   O  TRP    77
SHEET    1 B6  2 ALA    84  LEU    90  0
SHEET    2 B6  2 LEU    93  VAL    99 -1  N  VAL    99   O  ALA    84
SHEET    1 B7  2 ASN    96  VAL    99  0
SHEET    2 B7  2 ASP   111  GLU   114 -1  N  GLU   114   O  ASN    96
SHEET    1 B8  2 HIS   107  VAL   113  0
SHEET    2 B8  2 ASP   119  LEU   125 -1  N  LEU   125   O  HIS   107
SHEET    1 B9  2 ALA   179  VAL   181  0
SHEET    2 B9  2 LYS   195  GLU   197 -1  N  GLU   197   O  ALA   179
SHEET    1 B*  2 ALA   179  LEU   182  0
SHEET    2 B*  2 TRP   270  ASP   273 -1  N  ASP   273   O  ALA   179
SHEET    1 B*  2 LEU   194  GLY   196  0
SHEET    2 B*  2 MET   211  PHE   213 -1  N  PHE   213   O  LEU   194
SHEET    1 B*  2 ASN   205  ASN   215  0
SHEET    2 B*  2 ASP   218  LEU   228 -1  N  LEU   228   O  ASN   205
SHEET    1 B*  2 TRP   224  ASP   229  0
....................
ENDMDL
REMARK time  100.00                                       ENERGY     1.95395E+03
HELIX    1 H1  GLU    131  SER    146  1                                      15
HELIX    2 H2  GLU    278  SER    293  1                                      15
HELIX    3 H3  GLU    426  SER    441  1                                      15
HELIX    4 H4  GLU    574  SER    589  1                                      15
SHEET    1 B1  2 ALA    32  VAL    34  0
SHEET    2 B1  2 LYS    48  GLU    50 -1  N  GLU    50   O  ALA    32
SHEET    1 B2  2 ALA    32  LEU    35  0
SHEET    2 B2  2 TRP   123  ASP   126 -1  N  ASP   126   O  ALA    32
SHEET    1 B3  2 LEU    47  PRO    51  0
SHEET    2 B3  2 VAL    62  PHE    66 -1  N  PHE    66   O  LEU    47
SHEET    1 B4  2 ASN    58  ASN    68  0
SHEET    2 B4  2 ASP    71  LEU    81 -1  N  LEU    81   O  ASN    58
SHEET    1 B5  2 TRP    77  ASP    82  0
SHEET    2 B5  2 LYS    85  LEU    90 -1  N  LEU    90   O  TRP    77
SHEET    1 B6  2 ALA    84  LEU    90  0
.......

CONECT   1131   1133   1132
CONECT   1133   1135   1134
CONECT   1135   1137   1136
CONECT   1137   1139   1138
CONECT   1139   1141   1140
CONECT   1141   1143   1142
CONECT   1143   1145   1144
CONECT   1145   1146
ENDMDL

Finally I want pull out information about only REMARK time 20.00REMARK time 20.00 such as: REMARK time 20.00 ENERGY 1.96641E+03 HELIX 1 H1 GLU 131 SER 146 1 15 HELIX 2 H2 GLU 278 SER 293 1 15 HELIX 3 H3 GLU 426 SER 441 1 15 HELIX 4 H4 GLU 574 SER 589 1 15 SHEET 1 B1 2 ALA 32 VAL 34 0 SHEET 2 B1 2 LYS 48 GLU 50 -1 N GLU 50 O ALA 32 SHEET 1 B2 2 ALA 32 LEU 35 0 SHEET 2 B2 2 TRP 123 ASP 126 -1 N ASP 126 O ALA 32 SHEET 1 B3 2 LEU 47 PRO 51 0 SHEET 2 B3 2 VAL 62 PHE 66 -1 N PHE 66 O LEU 47 SHEET 1 B4 2 ASN 58 ASN 68 0 SHEET 2 B4 2 ASP 71 LEU 81 -1 N LEU 81 O ASN 58 SHEET 1 B5 2 TRP 77 ASP 82 0 SHEET 2 B5 2 LYS 85 LEU 90 -1 N LEU 90 O TRP 77 SHEET 1 B6 2 ALA 84 LEU 90 0 SHEET 2 B6 2 LEU 93 VAL 99 -1 N VAL 99 O ALA 84 SHEET 1 B7 2 ASN 96 VAL 99 0 SHEET 2 B7 2 ASP 111 GLU 114 -1 N GLU 114 O ASN 96 SHEET 1 B8 2 HIS 107 VAL 113 0 SHEET 2 B8 2 ASP 119 LEU 125 -1 N LEU 125 O HIS 107 SHEET 1 B9 2 ALA 179 VAL 181 0 SHEET 2 B9 2 LYS 195 GLU 197 -1 N GLU 197 O ALA 179 SHEET 1 B* 2 ALA 179 LEU 182 0 SHEET 2 B* 2 TRP 270 ASP 273 -1 N ASP 273 O ALA 179 SHEET 1 B* 2 LEU 194 GLY 196 0 SHEET 2 B* 2 MET 211 PHE 213 -1 N PHE 213 O LEU 194 SHEET 1 B* 2 ASN 205 ASN 215 0 SHEET 2 B* 2 ASP 218 LEU 228 -1 N LEU 228 O ASN 205 SHEET 1 B* 2 TRP 224 ASP 229 0 SHEET 2 B* 2 LYS 232 LEU 237 -1 N LEU 237 O TRP 224 ...... CONECT 1141 1143 1142 CONECT 1143 1145 1144 CONECT 1145 1146 ENDMDL

REMARK time   20.00                                       ENERGY     1.96641E+03

HELIX    1 H1  GLU    131  SER    146  1                                      15
HELIX    2 H2  GLU    278  SER    293  1                                      15
HELIX    3 H3  GLU    426  SER    441  1                                      15
HELIX    4 H4  GLU    574  SER    589  1                                      15
SHEET    1 B1  2 ALA    32  VAL    34  0
SHEET    2 B1  2 LYS    48  GLU    50 -1  N  GLU    50   O  ALA    32
SHEET    1 B2  2 ALA    32  LEU    35  0
SHEET    2 B2  2 TRP   123  ASP   126 -1  N  ASP   126   O  ALA    32
SHEET    1 B3  2 LEU    47  PRO    51  0
SHEET    2 B3  2 VAL    62  PHE    66 -1  N  PHE    66   O  LEU    47
SHEET    1 B4  2 ASN    58  ASN    68  0
SHEET    2 B4  2 ASP    71  LEU    81 -1  N  LEU    81   O  ASN    58
SHEET    1 B5  2 TRP    77  ASP    82  0
SHEET    2 B5  2 LYS    85  LEU    90 -1  N  LEU    90   O  TRP    77
SHEET    1 B6  2 ALA    84  LEU    90  0
SHEET    2 B6  2 LEU    93  VAL    99 -1  N  VAL    99   O  ALA    84
SHEET    1 B7  2 ASN    96  VAL    99  0
SHEET    2 B7  2 ASP   111  GLU   114 -1  N  GLU   114   O  ASN    96
SHEET    1 B8  2 HIS   107  VAL   113  0
SHEET    2 B8  2 ASP   119  LEU   125 -1  N  LEU   125   O  HIS   107
SHEET    1 B9  2 ALA   179  VAL   181  0
SHEET    2 B9  2 LYS   195  GLU   197 -1  N  GLU   197   O  ALA   179
SHEET    1 B*  2 ALA   179  LEU   182  0
SHEET    2 B*  2 TRP   270  ASP   273 -1  N  ASP   273   O  ALA   179
SHEET    1 B*  2 LEU   194  GLY   196  0
SHEET    2 B*  2 MET   211  PHE   213 -1  N  PHE   213   O  LEU   194
SHEET    1 B*  2 ASN   205  ASN   215  0
SHEET    2 B*  2 ASP   218  LEU   228 -1  N  LEU   228   O  ASN   205
SHEET    1 B*  2 TRP   224  ASP   229  0
SHEET    2 B*  2 LYS   232  LEU   237 -1  N  LEU   237   O  TRP   224
......
CONECT   1141   1143   1142
CONECT   1143   1145   1144
CONECT   1145   1146
ENDMDL

I'm beginner in bash scripti, but I try delete everything in my pdb file (test.pdb) before REMARK time 20.00 and from REMARK time 30.00 to the end of this file. I'm using to this sed command, which is such as:

sed 's/^.*(REMARK time 20.00.REMARK time 30.00).$/\1/' test.pdb > end.pdb

My test.pdb file is as follows: REMARK time 10.00 ENERGY 1.95686E+03 HELIX 1 H1 GLU 131 SER 146 1 15 HELIX 2 H2 GLU 278 SER 293 1 15 HELIX 3 H3 GLU 426 SER 441 1 15 HELIX 4 H4 GLU 574 SER 589 1 15 SHEET 1 B1 2 ALA 32 VAL 34 0 SHEET 2 B1 2 LYS 48 GLU 50 -1 N GLU 50 O ALA 32 SHEET 1 B2 2 ALA 32 LEU 35 0 SHEET 2 B2 2 TRP 123 ASP 126 -1 N ASP 126 O ALA 32 SHEET 1 B3 2 LEU 47 PRO 51 0 SHEET 2 B3 2 VAL 62 PHE 66 -1 N PHE 66 O LEU 47 SHEET 1 B4 2 ASN 58 ASN 68 0 SHEET 2 B4 2 ASP 71 LEU 81 -1 N LEU 81 O ASN 58 SHEET 1 B5 2 TRP 77 ASP 82 0 SHEET 2 B5 2 LYS 85 LEU 90 -1 N LEU 90 O TRP 77 SHEET 1 B6 2 ALA 84 LEU 90 0 SHEET 2 B6 2 LEU 93 VAL 99 -1 N VAL 99 O ALA 84 SHEET 1 B7 2 ASN 96 VAL 99 0 SHEET 2 B7 2 ASP 111 GLU 114 -1 N GLU 114 O ASN 96 SHEET 1 B8 2 HIS 107 VAL 113 0 SHEET 2 B8 2 ASP 119 LEU 125 -1 N LEU 125 O HIS 107 SHEET 1 B9 2 ALA 179 VAL 181 0 SHEET 2 B9 2 LYS 195 GLU 197 -1 N GLU 197 O ALA 179 SHEET 1 B* 2 ALA 179 LEU 182 0 ........ ENDMDL REMARK time 20.00 ENERGY 1.96641E+03 HELIX 1 H1 GLU 131 SER 146 1 15 HELIX 2 H2 GLU 278 SER 293 1 15 HELIX 3 H3 GLU 426 SER 441 1 15 HELIX 4 H4 GLU 574 SER 589 1 15 SHEET 1 B1 2 ALA 32 VAL 34 0 SHEET 2 B1 2 LYS 48 GLU 50 -1 N GLU 50 O ALA 32 SHEET 1 B2 2 ALA 32 LEU 35 0 SHEET 2 B2 2 TRP 123 ASP 126 -1 N ASP 126 O ALA 32 SHEET 1 B3 2 LEU 47 PRO 51 0 SHEET 2 B3 2 VAL 62 PHE 66 -1 N PHE 66 O LEU 47 SHEET 1 B4 2 ASN 58 ASN 68 0 SHEET 2 B4 2 ASP 71 LEU 81 -1 N LEU 81 O ASN 58 SHEET 1 B5 2 TRP 77 ASP 82 0 SHEET 2 B5 2 LYS 85 LEU 90 -1 N LEU 90 O TRP 77 SHEET 1 B6 2 ALA 84 LEU 90 0 SHEET 2 B6 2 LEU 93 VAL 99 -1 N VAL 99 O ALA 84 SHEET 1 B7 2 ASN 96 VAL 99 0 SHEET 2 B7 2 ASP 111 GLU 114 -1 N GLU 114 O ASN 96 SHEET 1 B8 2 HIS 107 VAL 113 0 SHEET 2 B8 2 ASP 119 LEU 125 -1 N LEU 125 O HIS 107 SHEET 1 B9 2 ALA 179 VAL 181 0 SHEET 2 B9 2 LYS 195 GLU 197 -1 N GLU 197 O ALA 179 SHEET 1 B* 2 ALA 179 LEU 182 0 SHEET 2 B* 2 TRP 270 ASP 273 -1 N ASP 273 O ALA 179 SHEET 1 B* 2 LEU 194 GLY 196 0 SHEET 2 B* 2 MET 211 PHE 213 -1 N PHE 213 O LEU 194 SHEET 1 B* 2 ASN 205 ASN 215 0 SHEET 2 B* 2 ASP 218 LEU 228 -1 N LEU 228 O ASN 205 SHEET 1 B* 2 TRP 224 ASP 229 0 .................... ENDMDL REMARK time 100.00 ENERGY 1.95395E+03 HELIX 1 H1 GLU 131 SER 146 1 15 HELIX 2 H2 GLU 278 SER 293 1 15 HELIX 3 H3 GLU 426 SER 441 1 15 HELIX 4 H4 GLU 574 SER 589 1 15 SHEET 1 B1 2 ALA 32 VAL 34 0 SHEET 2 B1 2 LYS 48 GLU 50 -1 N GLU 50 O ALA 32 SHEET 1 B2 2 ALA 32 LEU 35 0 SHEET 2 B2 2 TRP 123 ASP 126 -1 N ASP 126 O ALA 32 SHEET 1 B3 2 LEU 47 PRO 51 0 SHEET 2 B3 2 VAL 62 PHE 66 -1 N PHE 66 O LEU 47 SHEET 1 B4 2 ASN 58 ASN 68 0 SHEET 2 B4 2 ASP 71 LEU 81 -1 N LEU 81 O ASN 58 SHEET 1 B5 2 TRP 77 ASP 82 0 SHEET 2 B5 2 LYS 85 LEU 90 -1 N LEU 90 O TRP 77 SHEET 1 B6 2 ALA 84 LEU 90 0 .......

CONECT 1131 1133 1132 CONECT 1133 1135 1134 CONECT 1135 1137 1136 CONECT 1137 1139 1138 CONECT 1139 1141 1140 CONECT 1141 1143 1142 CONECT 1143 1145 1144 CONECT 1145 1146 ENDMDL

Finally I want pull out information about only REMARK time 20.00 such as: REMARK time 20.00 ENERGY 1.96641E+03 HELIX 1 H1 GLU 131 SER 146 1 15 HELIX 2 H2 GLU 278 SER 293 1 15 HELIX 3 H3 GLU 426 SER 441 1 15 HELIX 4 H4 GLU 574 SER 589 1 15 SHEET 1 B1 2 ALA 32 VAL 34 0 SHEET 2 B1 2 LYS 48 GLU 50 -1 N GLU 50 O ALA 32 SHEET 1 B2 2 ALA 32 LEU 35 0 SHEET 2 B2 2 TRP 123 ASP 126 -1 N ASP 126 O ALA 32 SHEET 1 B3 2 LEU 47 PRO 51 0 SHEET 2 B3 2 VAL 62 PHE 66 -1 N PHE 66 O LEU 47 SHEET 1 B4 2 ASN 58 ASN 68 0 SHEET 2 B4 2 ASP 71 LEU 81 -1 N LEU 81 O ASN 58 SHEET 1 B5 2 TRP 77 ASP 82 0 SHEET 2 B5 2 LYS 85 LEU 90 -1 N LEU 90 O TRP 77 SHEET 1 B6 2 ALA 84 LEU 90 0 SHEET 2 B6 2 LEU 93 VAL 99 -1 N VAL 99 O ALA 84 SHEET 1 B7 2 ASN 96 VAL 99 0 SHEET 2 B7 2 ASP 111 GLU 114 -1 N GLU 114 O ASN 96 SHEET 1 B8 2 HIS 107 VAL 113 0 SHEET 2 B8 2 ASP 119 LEU 125 -1 N LEU 125 O HIS 107 SHEET 1 B9 2 ALA 179 VAL 181 0 SHEET 2 B9 2 LYS 195 GLU 197 -1 N GLU 197 O ALA 179 SHEET 1 B* 2 ALA 179 LEU 182 0 SHEET 2 B* 2 TRP 270 ASP 273 -1 N ASP 273 O ALA 179 SHEET 1 B* 2 LEU 194 GLY 196 0 SHEET 2 B* 2 MET 211 PHE 213 -1 N PHE 213 O LEU 194 SHEET 1 B* 2 ASN 205 ASN 215 0 SHEET 2 B* 2 ASP 218 LEU 228 -1 N LEU 228 O ASN 205 SHEET 1 B* 2 TRP 224 ASP 229 0 SHEET 2 B* 2 LYS 232 LEU 237 -1 N LEU 237 O TRP 224 ...... CONECT 1141 1143 1142 CONECT 1143 1145 1144 CONECT 1145 1146 ENDMDL

I'm beginner in bash scripts, but I try to delete everything in my pdb file (test.pdb) before REMARK time 20.00 and from REMARK time 30.00 to the end of this file. I'm using to this sed command, which is such as:

sed 's/^.*\(REMARK time 20.00.*REMARK time 30.00\).*$/\1/' test.pdb > end.pdb

My test.pdb file is as follows:

REMARK time   10.00                                       ENERGY     1.95686E+03
HELIX    1 H1  GLU    131  SER    146  1                                      15
HELIX    2 H2  GLU    278  SER    293  1                                      15
HELIX    3 H3  GLU    426  SER    441  1                                      15
HELIX    4 H4  GLU    574  SER    589  1                                      15
SHEET    1 B1  2 ALA    32  VAL    34  0
SHEET    2 B1  2 LYS    48  GLU    50 -1  N  GLU    50   O  ALA    32
SHEET    1 B2  2 ALA    32  LEU    35  0
SHEET    2 B2  2 TRP   123  ASP   126 -1  N  ASP   126   O  ALA    32
SHEET    1 B3  2 LEU    47  PRO    51  0
SHEET    2 B3  2 VAL    62  PHE    66 -1  N  PHE    66   O  LEU    47
SHEET    1 B4  2 ASN    58  ASN    68  0
SHEET    2 B4  2 ASP    71  LEU    81 -1  N  LEU    81   O  ASN    58
SHEET    1 B5  2 TRP    77  ASP    82  0
SHEET    2 B5  2 LYS    85  LEU    90 -1  N  LEU    90   O  TRP    77
SHEET    1 B6  2 ALA    84  LEU    90  0
SHEET    2 B6  2 LEU    93  VAL    99 -1  N  VAL    99   O  ALA    84
SHEET    1 B7  2 ASN    96  VAL    99  0
SHEET    2 B7  2 ASP   111  GLU   114 -1  N  GLU   114   O  ASN    96
SHEET    1 B8  2 HIS   107  VAL   113  0
SHEET    2 B8  2 ASP   119  LEU   125 -1  N  LEU   125   O  HIS   107
SHEET    1 B9  2 ALA   179  VAL   181  0
SHEET    2 B9  2 LYS   195  GLU   197 -1  N  GLU   197   O  ALA   179
SHEET    1 B*  2 ALA   179  LEU   182  0
........
ENDMDL
REMARK time   20.00                                       ENERGY     1.96641E+03
HELIX    1 H1  GLU    131  SER    146  1                                      15
HELIX    2 H2  GLU    278  SER    293  1                                      15
HELIX    3 H3  GLU    426  SER    441  1                                      15
HELIX    4 H4  GLU    574  SER    589  1                                      15
SHEET    1 B1  2 ALA    32  VAL    34  0
SHEET    2 B1  2 LYS    48  GLU    50 -1  N  GLU    50   O  ALA    32
SHEET    1 B2  2 ALA    32  LEU    35  0
SHEET    2 B2  2 TRP   123  ASP   126 -1  N  ASP   126   O  ALA    32
SHEET    1 B3  2 LEU    47  PRO    51  0
SHEET    2 B3  2 VAL    62  PHE    66 -1  N  PHE    66   O  LEU    47
SHEET    1 B4  2 ASN    58  ASN    68  0
SHEET    2 B4  2 ASP    71  LEU    81 -1  N  LEU    81   O  ASN    58
SHEET    1 B5  2 TRP    77  ASP    82  0
SHEET    2 B5  2 LYS    85  LEU    90 -1  N  LEU    90   O  TRP    77
SHEET    1 B6  2 ALA    84  LEU    90  0
SHEET    2 B6  2 LEU    93  VAL    99 -1  N  VAL    99   O  ALA    84
SHEET    1 B7  2 ASN    96  VAL    99  0
SHEET    2 B7  2 ASP   111  GLU   114 -1  N  GLU   114   O  ASN    96
SHEET    1 B8  2 HIS   107  VAL   113  0
SHEET    2 B8  2 ASP   119  LEU   125 -1  N  LEU   125   O  HIS   107
SHEET    1 B9  2 ALA   179  VAL   181  0
SHEET    2 B9  2 LYS   195  GLU   197 -1  N  GLU   197   O  ALA   179
SHEET    1 B*  2 ALA   179  LEU   182  0
SHEET    2 B*  2 TRP   270  ASP   273 -1  N  ASP   273   O  ALA   179
SHEET    1 B*  2 LEU   194  GLY   196  0
SHEET    2 B*  2 MET   211  PHE   213 -1  N  PHE   213   O  LEU   194
SHEET    1 B*  2 ASN   205  ASN   215  0
SHEET    2 B*  2 ASP   218  LEU   228 -1  N  LEU   228   O  ASN   205
SHEET    1 B*  2 TRP   224  ASP   229  0
....................
ENDMDL
REMARK time  100.00                                       ENERGY     1.95395E+03
HELIX    1 H1  GLU    131  SER    146  1                                      15
HELIX    2 H2  GLU    278  SER    293  1                                      15
HELIX    3 H3  GLU    426  SER    441  1                                      15
HELIX    4 H4  GLU    574  SER    589  1                                      15
SHEET    1 B1  2 ALA    32  VAL    34  0
SHEET    2 B1  2 LYS    48  GLU    50 -1  N  GLU    50   O  ALA    32
SHEET    1 B2  2 ALA    32  LEU    35  0
SHEET    2 B2  2 TRP   123  ASP   126 -1  N  ASP   126   O  ALA    32
SHEET    1 B3  2 LEU    47  PRO    51  0
SHEET    2 B3  2 VAL    62  PHE    66 -1  N  PHE    66   O  LEU    47
SHEET    1 B4  2 ASN    58  ASN    68  0
SHEET    2 B4  2 ASP    71  LEU    81 -1  N  LEU    81   O  ASN    58
SHEET    1 B5  2 TRP    77  ASP    82  0
SHEET    2 B5  2 LYS    85  LEU    90 -1  N  LEU    90   O  TRP    77
SHEET    1 B6  2 ALA    84  LEU    90  0
.......

CONECT   1131   1133   1132
CONECT   1133   1135   1134
CONECT   1135   1137   1136
CONECT   1137   1139   1138
CONECT   1139   1141   1140
CONECT   1141   1143   1142
CONECT   1143   1145   1144
CONECT   1145   1146
ENDMDL

Finally I want pull out information about only REMARK time 20.00 such as:

REMARK time   20.00                                       ENERGY     1.96641E+03

HELIX    1 H1  GLU    131  SER    146  1                                      15
HELIX    2 H2  GLU    278  SER    293  1                                      15
HELIX    3 H3  GLU    426  SER    441  1                                      15
HELIX    4 H4  GLU    574  SER    589  1                                      15
SHEET    1 B1  2 ALA    32  VAL    34  0
SHEET    2 B1  2 LYS    48  GLU    50 -1  N  GLU    50   O  ALA    32
SHEET    1 B2  2 ALA    32  LEU    35  0
SHEET    2 B2  2 TRP   123  ASP   126 -1  N  ASP   126   O  ALA    32
SHEET    1 B3  2 LEU    47  PRO    51  0
SHEET    2 B3  2 VAL    62  PHE    66 -1  N  PHE    66   O  LEU    47
SHEET    1 B4  2 ASN    58  ASN    68  0
SHEET    2 B4  2 ASP    71  LEU    81 -1  N  LEU    81   O  ASN    58
SHEET    1 B5  2 TRP    77  ASP    82  0
SHEET    2 B5  2 LYS    85  LEU    90 -1  N  LEU    90   O  TRP    77
SHEET    1 B6  2 ALA    84  LEU    90  0
SHEET    2 B6  2 LEU    93  VAL    99 -1  N  VAL    99   O  ALA    84
SHEET    1 B7  2 ASN    96  VAL    99  0
SHEET    2 B7  2 ASP   111  GLU   114 -1  N  GLU   114   O  ASN    96
SHEET    1 B8  2 HIS   107  VAL   113  0
SHEET    2 B8  2 ASP   119  LEU   125 -1  N  LEU   125   O  HIS   107
SHEET    1 B9  2 ALA   179  VAL   181  0
SHEET    2 B9  2 LYS   195  GLU   197 -1  N  GLU   197   O  ALA   179
SHEET    1 B*  2 ALA   179  LEU   182  0
SHEET    2 B*  2 TRP   270  ASP   273 -1  N  ASP   273   O  ALA   179
SHEET    1 B*  2 LEU   194  GLY   196  0
SHEET    2 B*  2 MET   211  PHE   213 -1  N  PHE   213   O  LEU   194
SHEET    1 B*  2 ASN   205  ASN   215  0
SHEET    2 B*  2 ASP   218  LEU   228 -1  N  LEU   228   O  ASN   205
SHEET    1 B*  2 TRP   224  ASP   229  0
SHEET    2 B*  2 LYS   232  LEU   237 -1  N  LEU   237   O  TRP   224
......
CONECT   1141   1143   1142
CONECT   1143   1145   1144
CONECT   1145   1146
ENDMDL
added 2052 characters in body; edited title
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skywalker
skywalker
  • 11
  • 2

How can I delete everything from match patternbefore and everything after anotherafrer match pattern from a linepdb file?

Finally I want pull out information about only REMARK time 20.00 such as: REMARK time 20.00 ENERGY 1.96641E+03 HELIX 1 H1 GLU 131 SER 146 1 15 HELIX 2 H2 GLU 278 SER 293 1 15 HELIX 3 H3 GLU 426 SER 441 1 15 HELIX 4 H4 GLU 574 SER 589 1 15 SHEET 1 B1 2 ALA 32 VAL 34 0 SHEET 2 B1 2 LYS 48 GLU 50 -1 N GLU 50 O ALA 32 SHEET 1 B2 2 ALA 32 LEU 35 0 SHEET 2 B2 2 TRP 123 ASP 126 -1 N ASP 126 O ALA 32 SHEET 1 B3 2 LEU 47 PRO 51 0 SHEET 2 B3 2 VAL 62 PHE 66 -1 N PHE 66 O LEU 47 SHEET 1 B4 2 ASN 58 ASN 68 0 SHEET 2 B4 2 ASP 71 LEU 81 -1 N LEU 81 O ASN 58 SHEET 1 B5 2 TRP 77 ASP 82 0 SHEET 2 B5 2 LYS 85 LEU 90 -1 N LEU 90 O TRP 77 SHEET 1 B6 2 ALA 84 LEU 90 0 SHEET 2 B6 2 LEU 93 VAL 99 -1 N VAL 99 O ALA 84 SHEET 1 B7 2 ASN 96 VAL 99 0 SHEET 2 B7 2 ASP 111 GLU 114 -1 N GLU 114 O ASN 96 SHEET 1 B8 2 HIS 107 VAL 113 0 SHEET 2 B8 2 ASP 119 LEU 125 -1 N LEU 125 O HIS 107 SHEET 1 B9 2 ALA 179 VAL 181 0 SHEET 2 B9 2 LYS 195 GLU 197 -1 N GLU 197 O ALA 179 SHEET 1 B* 2 ALA 179 LEU 182 0 SHEET 2 B* 2 TRP 270 ASP 273 -1 N ASP 273 O ALA 179 SHEET 1 B* 2 LEU 194 GLY 196 0 SHEET 2 B* 2 MET 211 PHE 213 -1 N PHE 213 O LEU 194 SHEET 1 B* 2 ASN 205 ASN 215 0 SHEET 2 B* 2 ASP 218 LEU 228 -1 N LEU 228 O ASN 205 SHEET 1 B* 2 TRP 224 ASP 229 0 SHEET 2 B* 2 LYS 232 LEU 237 -1 N LEU 237 O TRP 224 ...... CONECT 1141 1143 1142 CONECT 1143 1145 1144 CONECT 1145 1146 ENDMDL

How can I delete everything from match pattern and everything after another pattern from a line?

How can I delete everything before and afrer match pattern from pdb file?

Finally I want pull out information about only REMARK time 20.00 such as: REMARK time 20.00 ENERGY 1.96641E+03 HELIX 1 H1 GLU 131 SER 146 1 15 HELIX 2 H2 GLU 278 SER 293 1 15 HELIX 3 H3 GLU 426 SER 441 1 15 HELIX 4 H4 GLU 574 SER 589 1 15 SHEET 1 B1 2 ALA 32 VAL 34 0 SHEET 2 B1 2 LYS 48 GLU 50 -1 N GLU 50 O ALA 32 SHEET 1 B2 2 ALA 32 LEU 35 0 SHEET 2 B2 2 TRP 123 ASP 126 -1 N ASP 126 O ALA 32 SHEET 1 B3 2 LEU 47 PRO 51 0 SHEET 2 B3 2 VAL 62 PHE 66 -1 N PHE 66 O LEU 47 SHEET 1 B4 2 ASN 58 ASN 68 0 SHEET 2 B4 2 ASP 71 LEU 81 -1 N LEU 81 O ASN 58 SHEET 1 B5 2 TRP 77 ASP 82 0 SHEET 2 B5 2 LYS 85 LEU 90 -1 N LEU 90 O TRP 77 SHEET 1 B6 2 ALA 84 LEU 90 0 SHEET 2 B6 2 LEU 93 VAL 99 -1 N VAL 99 O ALA 84 SHEET 1 B7 2 ASN 96 VAL 99 0 SHEET 2 B7 2 ASP 111 GLU 114 -1 N GLU 114 O ASN 96 SHEET 1 B8 2 HIS 107 VAL 113 0 SHEET 2 B8 2 ASP 119 LEU 125 -1 N LEU 125 O HIS 107 SHEET 1 B9 2 ALA 179 VAL 181 0 SHEET 2 B9 2 LYS 195 GLU 197 -1 N GLU 197 O ALA 179 SHEET 1 B* 2 ALA 179 LEU 182 0 SHEET 2 B* 2 TRP 270 ASP 273 -1 N ASP 273 O ALA 179 SHEET 1 B* 2 LEU 194 GLY 196 0 SHEET 2 B* 2 MET 211 PHE 213 -1 N PHE 213 O LEU 194 SHEET 1 B* 2 ASN 205 ASN 215 0 SHEET 2 B* 2 ASP 218 LEU 228 -1 N LEU 228 O ASN 205 SHEET 1 B* 2 TRP 224 ASP 229 0 SHEET 2 B* 2 LYS 232 LEU 237 -1 N LEU 237 O TRP 224 ...... CONECT 1141 1143 1142 CONECT 1143 1145 1144 CONECT 1145 1146 ENDMDL

Source Link
skywalker
skywalker
  • 11
  • 2

How can I delete everything from match pattern and everything after another pattern from a line?

I'm beginner in bash scripti, but I try delete everything in my pdb file (test.pdb) before REMARK time 20.00 and from REMARK time 30.00 to the end of this file. I'm using to this sed command, which is such as:

sed 's/^.*(REMARK time 20.00.REMARK time 30.00).$/\1/' test.pdb > end.pdb

Unfortunately, above command generate end.pdb file, which is totally empty. Can you help me with solve this problem ?

My test.pdb file is as follows: REMARK time 10.00 ENERGY 1.95686E+03 HELIX 1 H1 GLU 131 SER 146 1 15 HELIX 2 H2 GLU 278 SER 293 1 15 HELIX 3 H3 GLU 426 SER 441 1 15 HELIX 4 H4 GLU 574 SER 589 1 15 SHEET 1 B1 2 ALA 32 VAL 34 0 SHEET 2 B1 2 LYS 48 GLU 50 -1 N GLU 50 O ALA 32 SHEET 1 B2 2 ALA 32 LEU 35 0 SHEET 2 B2 2 TRP 123 ASP 126 -1 N ASP 126 O ALA 32 SHEET 1 B3 2 LEU 47 PRO 51 0 SHEET 2 B3 2 VAL 62 PHE 66 -1 N PHE 66 O LEU 47 SHEET 1 B4 2 ASN 58 ASN 68 0 SHEET 2 B4 2 ASP 71 LEU 81 -1 N LEU 81 O ASN 58 SHEET 1 B5 2 TRP 77 ASP 82 0 SHEET 2 B5 2 LYS 85 LEU 90 -1 N LEU 90 O TRP 77 SHEET 1 B6 2 ALA 84 LEU 90 0 SHEET 2 B6 2 LEU 93 VAL 99 -1 N VAL 99 O ALA 84 SHEET 1 B7 2 ASN 96 VAL 99 0 SHEET 2 B7 2 ASP 111 GLU 114 -1 N GLU 114 O ASN 96 SHEET 1 B8 2 HIS 107 VAL 113 0 SHEET 2 B8 2 ASP 119 LEU 125 -1 N LEU 125 O HIS 107 SHEET 1 B9 2 ALA 179 VAL 181 0 SHEET 2 B9 2 LYS 195 GLU 197 -1 N GLU 197 O ALA 179 SHEET 1 B* 2 ALA 179 LEU 182 0 ........ ENDMDL REMARK time 20.00 ENERGY 1.96641E+03 HELIX 1 H1 GLU 131 SER 146 1 15 HELIX 2 H2 GLU 278 SER 293 1 15 HELIX 3 H3 GLU 426 SER 441 1 15 HELIX 4 H4 GLU 574 SER 589 1 15 SHEET 1 B1 2 ALA 32 VAL 34 0 SHEET 2 B1 2 LYS 48 GLU 50 -1 N GLU 50 O ALA 32 SHEET 1 B2 2 ALA 32 LEU 35 0 SHEET 2 B2 2 TRP 123 ASP 126 -1 N ASP 126 O ALA 32 SHEET 1 B3 2 LEU 47 PRO 51 0 SHEET 2 B3 2 VAL 62 PHE 66 -1 N PHE 66 O LEU 47 SHEET 1 B4 2 ASN 58 ASN 68 0 SHEET 2 B4 2 ASP 71 LEU 81 -1 N LEU 81 O ASN 58 SHEET 1 B5 2 TRP 77 ASP 82 0 SHEET 2 B5 2 LYS 85 LEU 90 -1 N LEU 90 O TRP 77 SHEET 1 B6 2 ALA 84 LEU 90 0 SHEET 2 B6 2 LEU 93 VAL 99 -1 N VAL 99 O ALA 84 SHEET 1 B7 2 ASN 96 VAL 99 0 SHEET 2 B7 2 ASP 111 GLU 114 -1 N GLU 114 O ASN 96 SHEET 1 B8 2 HIS 107 VAL 113 0 SHEET 2 B8 2 ASP 119 LEU 125 -1 N LEU 125 O HIS 107 SHEET 1 B9 2 ALA 179 VAL 181 0 SHEET 2 B9 2 LYS 195 GLU 197 -1 N GLU 197 O ALA 179 SHEET 1 B* 2 ALA 179 LEU 182 0 SHEET 2 B* 2 TRP 270 ASP 273 -1 N ASP 273 O ALA 179 SHEET 1 B* 2 LEU 194 GLY 196 0 SHEET 2 B* 2 MET 211 PHE 213 -1 N PHE 213 O LEU 194 SHEET 1 B* 2 ASN 205 ASN 215 0 SHEET 2 B* 2 ASP 218 LEU 228 -1 N LEU 228 O ASN 205 SHEET 1 B* 2 TRP 224 ASP 229 0 .................... ENDMDL REMARK time 100.00 ENERGY 1.95395E+03 HELIX 1 H1 GLU 131 SER 146 1 15 HELIX 2 H2 GLU 278 SER 293 1 15 HELIX 3 H3 GLU 426 SER 441 1 15 HELIX 4 H4 GLU 574 SER 589 1 15 SHEET 1 B1 2 ALA 32 VAL 34 0 SHEET 2 B1 2 LYS 48 GLU 50 -1 N GLU 50 O ALA 32 SHEET 1 B2 2 ALA 32 LEU 35 0 SHEET 2 B2 2 TRP 123 ASP 126 -1 N ASP 126 O ALA 32 SHEET 1 B3 2 LEU 47 PRO 51 0 SHEET 2 B3 2 VAL 62 PHE 66 -1 N PHE 66 O LEU 47 SHEET 1 B4 2 ASN 58 ASN 68 0 SHEET 2 B4 2 ASP 71 LEU 81 -1 N LEU 81 O ASN 58 SHEET 1 B5 2 TRP 77 ASP 82 0 SHEET 2 B5 2 LYS 85 LEU 90 -1 N LEU 90 O TRP 77 SHEET 1 B6 2 ALA 84 LEU 90 0 .......

CONECT 1131 1133 1132 CONECT 1133 1135 1134 CONECT 1135 1137 1136 CONECT 1137 1139 1138 CONECT 1139 1141 1140 CONECT 1141 1143 1142 CONECT 1143 1145 1144 CONECT 1145 1146 ENDMDL