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
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") } }}
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