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How to extract the particular residues from PDB files

by Payal (Initiate)
on Apr 24, 2012 at 12:17 UTC ( [id://966813]=perlquestion: print w/replies, xml ) Need Help??

Payal has asked for the wisdom of the Perl Monks concerning the following question:

Dear Monks,

Please tell me how to extract the residues left after ignoring the first 3 and last 3 residue of my interest from a PDB file. For e.g. The PDB files looks like as follows

Where the 6th column represents the residue number. so, i need to extract only the residues from 119-121.

This is an example i have multiple files like this, so could anyone suggest me any program to extract the residues ignoring the first and last 3 residues from the various PDB files and the residue numbers may vary for each file

please help! 

ATOM   2279  P     G 0 116      82.059 150.340  28.009  1.00 31.85    
+       P  
ATOM   2280  OP1   G 0 116      81.476 151.290  27.052  1.00 34.42    
+       O  
ATOM   2281  OP2   G 0 116      82.278 148.940  27.598  1.00 33.86    
+       O  
ATOM   2282  O5'   G 0 116      83.444 150.926  28.532  1.00 30.55    
+       O  
ATOM   2283  C5'   G 0 116      84.687 150.466  27.992  1.00 29.38    
+       C  
ATOM   2284  C4'   G 0 116      85.826 151.264  28.568  1.00 28.39    
+       C  
ATOM   2285  O4'   G 0 116      85.628 152.659  28.245  1.00 27.32    
+       O  
ATOM   2286  C3'   G 0 116      85.947 151.219  30.082  1.00 28.22    
+       C  
ATOM   2287  O3'   G 0 116      86.748 150.108  30.466  1.00 27.76    
+       O  
ATOM   2288  C2'   G 0 116      86.627 152.542  30.399  1.00 27.78    
+       C  
ATOM   2289  O2'   G 0 116      88.022 152.453  30.209  1.00 28.00    
+       O  
ATOM   2290  C1'   G 0 116      86.039 153.463  29.328  1.00 26.71    
+       C  
ATOM   2291  N9    G 0 116      84.884 154.242  29.764  1.00 26.55    
+       N  
ATOM   2292  C8    G 0 116      83.566 154.016  29.448  1.00 26.21    
+       C  
ATOM   2293  N7    G 0 116      82.758 154.904  29.958  1.00 25.33    
+       N  
ATOM   2294  C5    G 0 116      83.590 155.763  30.658  1.00 25.18    
+       C  
ATOM   2295  C6    G 0 116      83.286 156.917  31.405  1.00 24.41    
+       C  
ATOM   2296  O6    G 0 116      82.185 157.436  31.603  1.00 25.14    
+       O  
ATOM   2297  N1    G 0 116      84.427 157.482  31.955  1.00 24.22    
+       N  
ATOM   2298  C2    G 0 116      85.700 156.997  31.802  1.00 25.05    
+       C  
ATOM   2299  N2    G 0 116      86.676 157.673  32.422  1.00 26.78    
+       N  
ATOM   2300  N3    G 0 116      85.999 155.928  31.099  1.00 25.66    
+       N  
ATOM   2301  C4    G 0 116      84.904 155.362  30.557  1.00 26.46    
+       C  
ATOM   2302  P     A 0 117      86.659 149.533  31.961  1.00 26.52    
+       P  
ATOM   2303  OP1   A 0 117      87.699 148.487  32.051  1.00 26.42    
+       O  
ATOM   2304  OP2   A 0 117      85.262 149.206  32.295  1.00 28.33    
+       O  
ATOM   2305  O5'   A 0 117      87.092 150.756  32.874  1.00 27.56    
+       O  
ATOM   2306  C5'   A 0 117      88.476 151.098  33.043  1.00 26.15    
+       C  
ATOM   2307  C4'   A 0 117      88.604 152.215  34.039  1.00 25.69    
+       C  
ATOM   2308  O4'   A 0 117      87.956 153.394  33.506  1.00 25.31    
+       O  
ATOM   2309  C3'   A 0 117      87.898 151.981  35.360  1.00 26.48    
+       C  
ATOM   2310  O3'   A 0 117      88.662 151.204  36.264  1.00 28.07    
+       O  
ATOM   2311  C2'   A 0 117      87.641 153.392  35.861  1.00 25.82    
+       C  
ATOM   2312  O2'   A 0 117      88.767 153.953  36.493  1.00 27.16    
+       O  
ATOM   2313  C1'   A 0 117      87.363 154.134  34.557  1.00 24.60    
+       C  
ATOM   2314  N9    A 0 117      85.935 154.263  34.287  1.00 22.06    
+       N  
ATOM   2315  C8    A 0 117      85.132 153.456  33.524  1.00 21.81    
+       C  
ATOM   2316  N7    A 0 117      83.880 153.839  33.489  1.00 20.36    
+       N  
ATOM   2317  C5    A 0 117      83.858 154.976  34.280  1.00 19.91    
+       C  
ATOM   2318  C6    A 0 117      82.829 155.852  34.643  1.00 18.69    
+       C  
ATOM   2319  N6    A 0 117      81.570 155.729  34.230  1.00 19.04    
+       N  
ATOM   2320  N1    A 0 117      83.141 156.881  35.452  1.00 19.35    
+       N  
ATOM   2321  C2    A 0 117      84.403 157.016  35.861  1.00 20.19    
+       C  
ATOM   2322  N3    A 0 117      85.460 156.265  35.584  1.00 22.83    
+       N  
ATOM   2323  C4    A 0 117      85.116 155.247  34.778  1.00 22.17    
+       C  
ATOM   2324  P     G 0 118      87.902 150.250  37.307  1.00 28.29    
+       P  
ATOM   2325  OP1   G 0 118      88.940 149.427  37.950  1.00 29.52    
+       O  
ATOM   2326  OP2   G 0 118      86.775 149.594  36.622  1.00 28.46    
+       O  
ATOM   2327  O5'   G 0 118      87.302 151.265  38.380  1.00 27.94    
+       O  
ATOM   2328  C5'   G 0 118      88.169 151.888  39.333  1.00 27.42    
+       C  
ATOM   2329  C4'   G 0 118      87.490 153.048  40.024  1.00 25.87    
+       C  
ATOM   2330  O4'   G 0 118      87.004 154.008  39.052  1.00 26.86    
+       O  
ATOM   2331  C3'   G 0 118      86.265 152.778  40.870  1.00 25.76    
+       C  
ATOM   2332  O3'   G 0 118      86.556 152.253  42.141  1.00 25.76    
+       O  
ATOM   2333  C2'   G 0 118      85.660 154.166  40.996  1.00 26.49    
+       C  
ATOM   2334  O2'   G 0 118      86.309 154.965  41.971  1.00 26.41    
+       O  
ATOM   2335  C1'   G 0 118      85.913 154.731  39.604  1.00 25.05    
+       C  
ATOM   2336  N9    G 0 118      84.720 154.532  38.784  1.00 24.09    
+       N  
ATOM   2337  C8    G 0 118      84.515 153.623  37.775  1.00 23.45    
+       C  
ATOM   2338  N7    G 0 118      83.308 153.676  37.279  1.00 23.59    
+       N  
ATOM   2339  C5    G 0 118      82.688 154.689  37.997  1.00 22.64    
+       C  
ATOM   2340  C6    G 0 118      81.368 155.203  37.920  1.00 21.82    
+       C  
ATOM   2341  O6    G 0 118      80.448 154.858  37.183  1.00 22.56    
+       O  
ATOM   2342  N1    G 0 118      81.165 156.224  38.837  1.00 24.13    
+       N  
ATOM   2343  C2    G 0 118      82.106 156.691  39.719  1.00 24.15    
+       C  
ATOM   2344  N2    G 0 118      81.728 157.689  40.530  1.00 22.10    
+       N  
ATOM   2345  N3    G 0 118      83.329 156.218  39.802  1.00 23.59    
+       N  
ATOM   2346  C4    G 0 118      83.550 155.229  38.919  1.00 22.57    
+       C  
ATOM   2347  P     A 0 119      85.451 151.374  42.883  1.00 24.74    
+       P  
ATOM   2348  OP1   A 0 119      86.044 150.927  44.159  1.00 26.05    
+       O  
ATOM   2349  OP2   A 0 119      84.948 150.367  41.917  1.00 25.66    
+       O  
ATOM   2350  O5'   A 0 119      84.274 152.399  43.184  1.00 23.08    
+       O  
ATOM   2351  C5'   A 0 119      84.425 153.413  44.181  1.00 21.80    
+       C  
ATOM   2352  C4'   A 0 119      83.165 154.231  44.297  1.00 21.62    
+       C  
ATOM   2353  O4'   A 0 119      82.848 154.800  43.000  1.00 21.28    
+       O  
ATOM   2354  C3'   A 0 119      81.893 153.504  44.712  1.00 21.73    
+       C  
ATOM   2355  O3'   A 0 119      81.789 153.355  46.128  1.00 22.94    
+       O  
ATOM   2356  C2'   A 0 119      80.808 154.419  44.158  1.00 21.68    
+       C  
ATOM   2357  O2'   A 0 119      80.555 155.534  44.998  1.00 21.44    
+       O  
ATOM   2358  C1'   A 0 119      81.443 154.902  42.853  1.00 20.53    
+       C  
ATOM   2359  N9    A 0 119      81.038 154.093  41.701  1.00 18.91    
+       N  
ATOM   2360  C8    A 0 119      81.773 153.156  41.019  1.00 17.60    
+       C  
ATOM   2361  N7    A 0 119      81.122 152.587  40.040  1.00 15.41    
+       N  
ATOM   2362  C5    A 0 119      79.876 153.191  40.075  1.00 15.59    
+       C  
ATOM   2363  C6    A 0 119      78.726 153.022  39.296  1.00 15.99    
+       C  
ATOM   2364  N6    A 0 119      78.644 152.170  38.276  1.00 17.57    
+       N  
ATOM   2365  N1    A 0 119      77.648 153.769  39.600  1.00 14.95    
+       N  
ATOM   2366  C2    A 0 119      77.735 154.630  40.610  1.00 13.99    
+       C  
ATOM   2367  N3    A 0 119      78.759 154.887  41.408  1.00 16.31    
+       N  
ATOM   2368  C4    A 0 119      79.812 154.122  41.088  1.00 15.76    
+       C  
ATOM   2369  P     A 0 120      80.796 152.244  46.748  1.00 21.32    
+       P  
ATOM   2370  OP1   A 0 120      81.143 152.046  48.169  1.00 23.79    
+       O  
ATOM   2371  OP2   A 0 120      80.804 151.091  45.844  1.00 20.80    
+       O  
ATOM   2372  O5'   A 0 120      79.374 152.967  46.734  1.00 22.75    
+       O  
ATOM   2373  C5'   A 0 120      78.358 152.592  45.803  1.00 22.09    
+       C  
ATOM   2374  C4'   A 0 120      76.997 152.623  46.462  1.00 22.55    
+       C  
ATOM   2375  O4'   A 0 120      77.077 151.946  47.744  1.00 22.12    
+       O  
ATOM   2376  C3'   A 0 120      76.371 153.971  46.789  1.00 21.85    
+       C  
ATOM   2377  O3'   A 0 120      75.672 154.526  45.670  1.00 23.27    
+       O  
ATOM   2378  C2'   A 0 120      75.383 153.593  47.883  1.00 21.38    
+       C  
ATOM   2379  O2'   A 0 120      74.231 152.983  47.340  1.00 21.97    
+       O  
ATOM   2380  C1'   A 0 120      76.158 152.526  48.649  1.00 21.08    
+       C  
ATOM   2381  N9    A 0 120      76.904 153.069  49.790  1.00 19.68    
+       N  
ATOM   2382  C8    A 0 120      78.199 152.806  50.146  1.00 19.52    
+       C  
ATOM   2383  N7    A 0 120      78.590 153.443  51.216  1.00 20.27    
+       N  
ATOM   2384  C5    A 0 120      77.479 154.180  51.593  1.00 19.90    
+       C  
ATOM   2385  C6    A 0 120      77.245 155.068  52.658  1.00 20.06    
+       C  
ATOM   2386  N6    A 0 120      78.159 155.385  53.573  1.00 20.97    
+       N  
ATOM   2387  N1    A 0 120      76.024 155.626  52.753  1.00 19.71    
+       N  
ATOM   2388  C2    A 0 120      75.108 155.310  51.840  1.00 20.35    
+       C  
ATOM   2389  N3    A 0 120      75.205 154.497  50.796  1.00 21.62    
+       N  
ATOM   2390  C4    A 0 120      76.434 153.958  50.726  1.00 19.27    
+       C  
ATOM   2391  P     U 0 121      75.228 156.066  45.692  1.00 18.62    
+       P  
ATOM   2392  OP1   U 0 121      76.432 156.854  45.413  1.00 24.06    
+       O  
ATOM   2393  OP2   U 0 121      74.464 156.320  46.914  1.00 22.04    
+       O  
ATOM   2394  O5'   U 0 121      74.239 156.216  44.458  1.00 23.38    
+       O  
ATOM   2395  C5'   U 0 121      74.735 156.392  43.120  1.00 23.14    
+       C  
ATOM   2396  C4'   U 0 121      73.669 156.018  42.123  1.00 23.88    
+       C  
ATOM   2397  O4'   U 0 121      73.283 154.645  42.328  1.00 24.01    
+       O  
ATOM   2398  C3'   U 0 121      72.376 156.805  42.242  1.00 25.26    
+       C  
ATOM   2399  O3'   U 0 121      72.475 157.976  41.445  1.00 26.37    
+       O  
ATOM   2400  C2'   U 0 121      71.326 155.856  41.676  1.00 25.26    
+       C  
ATOM   2401  O2'   U 0 121      71.155 155.990  40.284  1.00 26.72    
+       O  
ATOM   2402  C1'   U 0 121      71.924 154.482  41.987  1.00 25.28    
+       C  
ATOM   2403  N1    U 0 121      71.243 153.724  43.047  1.00 26.48    
+       N  
ATOM   2404  C2    U 0 121      70.174 152.931  42.675  1.00 26.92    
+       C  
ATOM   2405  O2    U 0 121      69.789 152.838  41.528  1.00 27.89    
+       O  
ATOM   2406  N3    U 0 121      69.569 152.251  43.700  1.00 27.64    
+       N  
ATOM   2407  C4    U 0 121      69.916 152.278  45.030  1.00 26.45    
+       C  
ATOM   2408  O4    U 0 121      69.276 151.602  45.833  1.00 28.11    
+       O  
ATOM   2409  C5    U 0 121      71.029 153.118  45.339  1.00 27.38    
+       C  
ATOM   2410  C6    U 0 121      71.642 153.794  44.363  1.00 26.84    
+       C  
ATOM   2411  P     C 0 122      71.647 159.283  41.839  1.00 27.15    
+       P  
ATOM   2412  OP1   C 0 122      70.813 158.950  43.014  1.00 29.65    
+       O  
ATOM   2413  OP2   C 0 122      71.003 159.827  40.616  1.00 27.43    
+       O  
ATOM   2414  O5'   C 0 122      72.774 160.295  42.310  1.00 27.51    
+       O  
ATOM   2415  C5'   C 0 122      73.693 160.863  41.373  1.00 27.29    
+       C  
ATOM   2416  C4'   C 0 122      75.078 160.844  41.952  1.00 27.42    
+       C  
ATOM   2417  O4'   C 0 122      75.511 159.466  42.081  1.00 28.02    
+       O  
ATOM   2418  C3'   C 0 122      76.149 161.492  41.103  1.00 27.54    
+       C  
ATOM   2419  O3'   C 0 122      76.203 162.895  41.296  1.00 29.00    
+       O  
ATOM   2420  C2'   C 0 122      77.406 160.790  41.583  1.00 27.18    
+       C  
ATOM   2421  O2'   C 0 122      77.850 161.309  42.821  1.00 27.23    
+       O  
ATOM   2422  C1'   C 0 122      76.895 159.367  41.795  1.00 26.41    
+       C  
ATOM   2423  N1    C 0 122      77.077 158.516  40.596  1.00 25.03    
+       N  
ATOM   2424  C2    C 0 122      78.371 158.091  40.254  1.00 24.32    
+       C  
ATOM   2425  O2    C 0 122      79.322 158.435  40.962  1.00 25.65    
+       O  
ATOM   2426  N3    C 0 122      78.549 157.322  39.156  1.00 21.66    
+       N  
ATOM   2427  C4    C 0 122      77.504 156.979  38.407  1.00 21.19    
+       C  
ATOM   2428  N4    C 0 122      77.729 156.225  37.333  1.00 19.39    
+       N  
ATOM   2429  C5    C 0 122      76.180 157.394  38.725  1.00 23.28    
+       C  
ATOM   2430  C6    C 0 122      76.011 158.151  39.820  1.00 25.06    
+       C  
ATOM   2431  P     U 0 123      76.635 163.839  40.073  1.00 29.47    
+       P  
ATOM   2432  OP1   U 0 123      76.680 165.225  40.595  1.00 29.58    
+       O  
ATOM   2433  OP2   U 0 123      75.749 163.514  38.922  1.00 30.88    
+       O  
ATOM   2434  O5'   U 0 123      78.119 163.364  39.727  1.00 29.53    
+       O  
ATOM   2435  C5'   U 0 123      79.159 163.520  40.696  1.00 31.30    
+       C  
ATOM   2436  C4'   U 0 123      80.450 162.859  40.250  1.00 31.85    
+       C  
ATOM   2437  O4'   U 0 123      80.252 161.446  40.010  1.00 30.68    
+       O  
ATOM   2438  C3'   U 0 123      81.180 163.328  38.998  1.00 32.03    
+       C  
ATOM   2439  O3'   U 0 123      81.930 164.516  39.238  1.00 34.85    
+       O  
ATOM   2440  C2'   U 0 123      82.143 162.168  38.759  1.00 31.57    
+       C  
ATOM   2441  O2'   U 0 123      83.282 162.261  39.597  1.00 31.84    
+       O  
ATOM   2442  C1'   U 0 123      81.321 160.963  39.216  1.00 29.73    
+       C  
ATOM   2443  N1    U 0 123      80.795 160.154  38.105  1.00 27.66    
+       N  
ATOM   2444  C2    U 0 123      81.680 159.301  37.468  1.00 26.05    
+       C  
ATOM   2445  O2    U 0 123      82.850 159.207  37.784  1.00 26.21    
+       O  
ATOM   2446  N3    U 0 123      81.144 158.566  36.445  1.00 24.39    
+       N  
ATOM   2447  C4    U 0 123      79.845 158.593  35.999  1.00 26.20    
+       C  
ATOM   2448  O4    U 0 123      79.501 157.828  35.094  1.00 28.05    
+       O  
ATOM   2449  C5    U 0 123      78.991 159.504  36.698  1.00 24.43    
+       C  
ATOM   2450  C6    U 0 123      79.481 160.233  37.702  1.00 26.73    
+       C  
ATOM   2451  P     C 0 124      82.536 165.364  37.998  1.00 36.32    
+       P  
ATOM   2452  OP1   C 0 124      83.145 166.573  38.636  1.00 36.04    
+       O  
ATOM   2453  OP2   C 0 124      81.510 165.527  36.930  1.00 32.60    
+       O  
ATOM   2454  O5'   C 0 124      83.732 164.471  37.438  1.00 36.15    
+       O  
ATOM   2455  C5'   C 0 124      84.949 164.323  38.191  1.00 37.98    
+       C  
ATOM   2456  C4'   C 0 124      85.914 163.412  37.468  1.00 40.39    
+       C  
ATOM   2457  O4'   C 0 124      85.345 162.079  37.356  1.00 39.92    
+       O  
ATOM   2458  C3'   C 0 124      86.268 163.782  36.035  1.00 42.18    
+       C  
ATOM   2459  O3'   C 0 124      87.302 164.754  35.958  1.00 45.00    
+       O  
ATOM   2460  C2'   C 0 124      86.726 162.449  35.462  1.00 41.48    
+       C  
ATOM   2461  O2'   C 0 124      88.045 162.135  35.873  1.00 42.55    
+       O  
ATOM   2462  C1'   C 0 124      85.766 161.479  36.146  1.00 39.16    
+       C  
ATOM   2463  N1    C 0 124      84.577 161.186  35.326  1.00 36.21    
+       N  
ATOM   2464  C2    C 0 124      84.640 160.142  34.394  1.00 34.43    
+       C  
ATOM   2465  O2    C 0 124      85.715 159.534  34.240  1.00 31.04    
+       O  
ATOM   2466  N3    C 0 124      83.533 159.828  33.680  1.00 33.71    
+       N  
ATOM   2467  C4    C 0 124      82.403 160.520  33.862  1.00 33.51    
+       C  
ATOM   2468  N4    C 0 124      81.322 160.154  33.166  1.00 31.93    
+       N  
ATOM   2469  C5    C 0 124      82.326 161.611  34.772  1.00 33.67    
+       C  
ATOM   2470  C6    C 0 124      83.424 161.906  35.476  1.00 35.09    
+       C

[download]

I tried writing the program, which looks like this , could anyone please tell me whats the bug in the program? 

<p>
open(FH,"C:\Users\Payal\Desktop\Project bogola\loop.pdb");

print"Enter the first residue\n";
$b=<>;

print"Enter the second residue\n";
$c=<>;

$d =chomp($b);
$e =chomp($c);

while($a=<FH>)
{
if($a=~/^ATOM/)
{

$residue=substr($d..$e,23,1..3);

if($residue >=$d and $residue <=$e)
{
print FH1 $a;

open(FH1,">>ichain.pdb")

}


}}

[download]

Replies are listed 'Best First'.
Re: How to extract the particular residues from PDB files
by MidLifeXis (Monsignor) on Apr 24, 2012 at 12:55 UTC

    It sounds to me like you want a program that does the following:

    • Read each line of your data file: see perlintro (see "Files and I/O" and "Conditional and looping constructs")
    • Split your line into tokens: see split, perlre
    • Compare the sixth element to see if it is what you want to use: see perlop
    • Emit the output you want using the data you are interested in: see print

    If you don't know what the last residue number is, you will also need to check that three more values exist in your file prior to emitting the output. Update: A FIFO (push data on the front end of an array during your reads, shift it off the back end of the array during your print) would be one structure that could fit this function.

    A note on perlmonks: you will find that you will often get a better discussion on your problem if you present code that you have tried and are getting stuck on. What you have provided is a work request ("Write my code for me for free"). There are many monks that will contract for work, given agreeable terms, but also monks that respond poorly to this no-effort-shown type of request.

    --MidLifeXis

[reply]
[reply]
Re: How to extract the particular residues from PDB files
by Sinistral (Monsignor) on Apr 24, 2012 at 12:53 UTC

    It didn't help that you didn't define what a "PDB file" is. A little Googling led me to RCSB PDB Protein Data Bank. There are actually tools on that site, including a structure comparison tool. Perhaps there is information on this seemingly rich site to help? I also looked at the BioPerl site, but the only hit was a link to Wikipedia's reference for Protein Data Bank, which has a further link back to the RCSB site listing many tools to use.

    You'll find help here for your specific problem, but it's not clear what your asking. Are you literally wanting the 1st three lines of the file and the last three lines of the file removed and then have a resulting file that's 6 lines shorter? If so, then you can use the head and tail utilities to remove the lines. I think you're actually asking for some processing of the data fields, though, and thus think that the RCSB site would be the best place to look

[reply]
Re: How to extract the particular residues from PDB files
by Marshall (Canon) on Apr 24, 2012 at 12:46 UTC
    lines 119-121 are: 
    ATOM   2397  O4'   U 0 121      73.283 154.645  42.328  1.00 24.01    
+       O  
ATOM   2398  C3'   U 0 121      72.376 156.805  42.242  1.00 25.26    
+       C  
ATOM   2399  O3'   U 0 121      72.475 157.976  41.445  1.00 26.37    
+       O

    [download]
    How are those lines different than the other lines?
[reply]
[d/l]

      no difference, i just one to ignore first and last three residues

[reply]

      LOL!

      Values of the 6th column, values in the range 119-121.

       perl -lane " if( $. > 3 ){ push @residues,$_ if $F[5] >= 119 and $F[5] <= 121; } END { pop @residues for 1..3; print for @residues " file

[reply]
[d/l]

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