How to fetch PDB from local (PC) and apply the pdb-tools on them?

HADDOCK
1

I have come to realize that everyone seems to fetch their pdb from rcsb via script, and so the tutorial was catered in such a way.

But for those who wanted to run their homology models in haddock, and couldn’t due to error like ‘inconsistent data / double occupancy’, we need the pdb-tools to run it.

can anyone provide a step by step tutorial based on the pre-screening of a local based pdb file?
Like this 1 right here http://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-local-tutorial/

thank you

2

A detailed documentation of pdb-tools is available in its website: http://www.bonvinlab.org/pdb-tools/

3

yea, this tutorial is about fetching/download PDB from rcsb website on the terminal. What about fetching it from local (desktop/pc)?

For eg, my pdb file in pc = ABCD, when i tried to fetch it “pdb_fetch ABCD > ABCD.pdb” it displays error.

Needless to say, i cant apply the pdb-tools script on my homology models that’s stored in local pc

4

The pdb_fetch tool is specifically for downloading a structure from the PDB. If you already have the structure stored on your computer, you can use it directly as input for pdb-tools such as pdb_selaltloc.

5

ok thanks a lot, i got the file input sorted.

But when i run pdb_selaltloc, it only displays the list of atoms of my pdb model. how do i know whether they have sorted the inconsistent/double occupancy issues?

"ATOM 2999 O VAL B 334 25.647 28.621 101.304 1.00 53.03 O
ATOM 3000 CB VAL B 334 24.064 30.776 100.482 1.00 50.28 C
ATOM 3001 CG1 VAL B 334 24.478 31.389 101.823 1.00 50.31 C
ATOM 3002 CG2 VAL B 334 23.244 31.767 99.670 1.00 50.16 C
ATOM 3003 N PRO B 335 27.477 29.326 100.152 1.00 54.91 N
ATOM 3004 CA PRO B 335 28.231 28.247 100.794 1.00 56.39 C
ATOM 3005 C PRO B 335 28.505 28.600 102.236 1.00 58.43 C
ATOM 3006 O PRO B 335 29.298 29.482 102.567 1.00 58.82 O
ATOM 3007 CB PRO B 335 29.508 28.137 99.953 1.00 55.71 C
ATOM 3008 CG PRO B 335 29.615 29.447 99.192 1.00 55.40 C
ATOM 3009 CD PRO B 335 28.372 30.281 99.477 1.00 55.19 C
ATOM 3010 N ARG B 336 27.730 27.917 103.065 1.00 59.95 N
ATOM 3011 CA ARG B 336 27.782 27.796 104.501 1.00 61.76 C
ATOM 3012 C ARG B 336 29.077 27.144 105.023 1.00 60.43 C
ATOM 3013 O ARG B 336 29.867 26.669 104.228 1.00 60.36 O
ATOM 3014 CB ARG B 336 26.562 26.957 104.829 1.00 64.60 C
ATOM 3015 CG ARG B 336 26.392 26.305 106.149 1.00 66.62 C
ATOM 3016 CD ARG B 336 24.922 26.250 106.395 1.00 67.30 C
ATOM 3017 NE ARG B 336 24.353 27.502 105.915 1.00 66.52 N
ATOM 3018 CZ ARG B 336 24.431 28.636 106.607 1.00 64.93 C
ATOM 3019 NH1 ARG B 336 25.047 28.642 107.794 1.00 64.28 N
ATOM 3020 NH2 ARG B 336 23.908 29.755 106.114 1.00 64.05 N
ATOM 3021 N SER B 337 29.299 27.108 106.342 1.00 58.90 N
ATOM 3022 CA SER B 337 30.300 26.203 106.913 1.00 57.18 C
ATOM 3023 C SER B 337 29.670 24.835 107.136 1.00 55.81 C
ATOM 3024 O SER B 337 28.510 24.741 107.523 1.00 55.91 O
ATOM 3025 CB SER B 337 30.864 26.737 108.238 1.00 57.08 C
ATOM 3026 OG SER B 337 31.545 27.969 108.066 1.00 57.02 O
ATOM 3027 N GLY B 338 30.428 23.770 106.915 1.00 54.30 N
ATOM 3028 CA GLY B 338 29.874 22.442 107.093 1.00 53.30 C
ATOM 3029 C GLY B 338 29.278 21.884 105.808 1.00 52.20 C
ATOM 3030 O GLY B 338 29.005 20.693 105.705 1.00 53.09 O
ATOM 3031 N GLU B 339 29.075 22.729 104.814 1.00 49.96 N
ATOM 3032 CA GLU B 339 28.508 22.219 103.556 1.00 47.69 C
ATOM 3033 C GLU B 339 29.526 21.473 102.708 1.00 44.06 C
ATOM 3034 O GLU B 339 30.704 21.810 102.674 1.00 43.41 O
ATOM 3035 CB GLU B 339 27.931 23.343 102.721 1.00 49.52 C
ATOM 3036 CG GLU B 339 26.961 24.187 103.456 1.00 51.35 C
ATOM 3037 CD GLU B 339 25.642 24.344 102.751 1.00 52.84 C
ATOM 3038 OE1 GLU B 339 25.424 25.435 102.181 1.00 53.19 O
ATOM 3039 OE2 GLU B 339 24.814 23.399 102.794 1.00 53.75 O
ATOM 3040 N VAL B 340 29.023 20.475 101.996 1.00 40.93 N
ATOM 3041 CA VAL B 340 29.836 19.682 101.096 1.00 38.57 C
ATOM 3042 C VAL B 340 29.105 19.563 99.762 1.00 35.71 C
ATOM 3043 O VAL B 340 27.970 19.060 99.690 1.00 35.83 O
ATOM 3044 CB VAL B 340 30.102 18.291 101.670 1.00 39.20 C
ATOM 3045 CG1 VAL B 340 30.784 17.411 100.654 1.00 39.34 C
ATOM 3046 CG2 VAL B 340 30.883 18.397 102.989 1.00 39.02 C
ATOM 3047 N TYR B 341 29.758 20.048 98.714 1.00 31.15 N
ATOM 3048 CA TYR B 341 29.181 20.008 97.373 1.00 28.46 C
ATOM 3049 C TYR B 341 29.851 18.934 96.517 1.00 27.21 C
ATOM 3050 O TYR B 341 31.064 18.712 96.614 1.00 28.18 O
ATOM 3051 CB TYR B 341 29.332 21.384 96.759 1.00 28.19 C
ATOM 3052 CG TYR B 341 28.536 22.482 97.435 1.00 29.85 C
ATOM 3053 CD1 TYR B 341 27.284 22.828 96.951 1.00 31.08 C
ATOM 3054 CD2 TYR B 341 29.040 23.190 98.530 1.00 31.84 C
ATOM 3055 CE1 TYR B 341 26.529 23.819 97.522 1.00 32.16 C
ATOM 3056 CE2 TYR B 341 28.279 24.204 99.108 1.00 32.44 C
ATOM 3057 CZ TYR B 341 27.024 24.510 98.572 1.00 32.85 C
ATOM 3058 OH TYR B 341 26.238 25.501 99.119 1.00 34.26 O
ATOM 3059 N THR B 342 29.080 18.274 95.669 1.00 24.44 N
ATOM 3060 CA THR B 342 29.686 17.292 94.789 1.00 23.52 C
ATOM 3061 C THR B 342 29.242 17.552 93.357 1.00 20.82 C
ATOM 3062 O THR B 342 28.050 17.752 93.110 1.00 20.48 O
ATOM 3063 CB THR B 342 29.306 15.855 95.182 1.00 25.50 C
ATOM 3064 OG1 THR B 342 29.687 15.610 96.546 1.00 28.05 O
ATOM 3065 CG2 THR B 342 30.024 14.852 94.301 1.00 26.39 C
ATOM 3066 N CYS B 343 30.201 17.574 92.423 1.00 19.08 N
ATOM 3067 CA CYS B 343 29.917 17.571 91.000 1.00 18.04 C
ATOM 3068 C CYS B 343 30.050 16.134 90.509 1.00 17.78 C
ATOM 3069 O CYS B 343 31.087 15.487 90.713 1.00 19.45 O
ATOM 3070 CB CYS B 343 30.861 18.500 90.220 1.00 18.14 C
ATOM 3071 SG CYS B 343 30.405 18.503 88.465 1.00 17.67 S
ATOM 3072 N GLN B 344 28.998 15.626 89.868 1.00 16.21 N
ATOM 3073 CA GLN B 344 28.958 14.240 89.368 1.00 17.40 C
ATOM 3074 C GLN B 344 28.837 14.230 87.876 1.00 16.48 C
ATOM 3075 O GLN B 344 27.990 14.935 87.321 1.00 17.34 O
ATOM 3076 CB GLN B 344 27.753 13.515 89.967 1.00 20.65 C
ATOM 3077 CG GLN B 344 27.599 12.070 89.489 1.00 24.23 C
ATOM 3078 CD GLN B 344 26.311 11.451 89.949 1.00 27.28 C
ATOM 3079 OE1 GLN B 344 26.233 10.910 91.070 1.00 28.98 O
ATOM 3080 NE2 GLN B 344 25.273 11.525 89.090 1.00 28.52 N
ATOM 3081 N VAL B 345 29.651 13.411 87.235 1.00 16.33 N
ATOM 3082 CA VAL B 345 29.710 13.368 85.764 1.00 15.63 C
ATOM 3083 C VAL B 345 29.483 11.948 85.281 1.00 17.58 C
ATOM 3084 O VAL B 345 30.149 10.997 85.776 1.00 19.94 O
ATOM 3085 CB VAL B 345 31.063 13.915 85.254 1.00 15.85 C
ATOM 3086 CG1 VAL B 345 31.158 13.750 83.745 1.00 16.82 C
ATOM 3087 CG2 VAL B 345 31.254 15.394 85.667 1.00 17.13 C
ATOM 3088 N GLU B 346 28.521 11.772 84.374 1.00 16.74 N
ATOM 3089 CA GLU B 346 28.355 10.479 83.680 1.00 17.88 C
ATOM 3090 C GLU B 346 28.608 10.674 82.195 1.00 16.61 C
ATOM 3091 O GLU B 346 28.228 11.713 81.638 1.00 16.77 O
ATOM 3092 CB GLU B 346 26.960 9.928 83.931 1.00 21.34 C
ATOM 3093 CG GLU B 346 26.712 9.639 85.446 1.00 24.27 C
ATOM 3094 CD GLU B 346 25.525 8.763 85.717 1.00 27.95 C
ATOM 3095 OE1 GLU B 346 24.376 9.264 85.633 1.00 29.28 O
ATOM 3096 OE2 GLU B 346 25.736 7.558 86.036 1.00 30.67 O
ATOM 3097 N HIS B 347 29.307 9.722 81.578 1.00 16.78 N
ATOM 3098 CA HIS B 347 29.838 9.860 80.234 1.00 16.26 C
ATOM 3099 C HIS B 347 30.101 8.443 79.735 1.00 17.24 C
ATOM 3100 O HIS B 347 30.456 7.586 80.529 1.00 17.90 O
ATOM 3101 CB HIS B 347 31.149 10.675 80.260 1.00 15.19 C
ATOM 3102 CG HIS B 347 31.725 10.914 78.909 1.00 14.38 C
ATOM 3103 ND1 HIS B 347 32.734 10.122 78.390 1.00 14.70 N
ATOM 3104 CD2 HIS B 347 31.419 11.833 77.953 1.00 15.03 C
ATOM 3105 CE1 HIS B 347 33.033 10.552 77.175 1.00 14.98 C
ATOM 3106 NE2 HIS B 347 32.224 11.559 76.872 1.00 14.77 N
ATOM 3107 N PRO B 348 29.989 8.185 78.421 1.00 18.95 N
ATOM 3108 CA PRO B 348 30.132 6.787 77.981 1.00 20.48 C
ATOM 3109 C PRO B 348 31.521 6.193 78.233 1.00 19.88 C
ATOM 3110 O PRO B 348 31.661 4.973 78.189 1.00 22.05 O
ATOM 3111 CB PRO B 348 29.826 6.863 76.474 1.00 22.00 C
ATOM 3112 CG PRO B 348 28.956 8.102 76.325 1.00 22.43 C
ATOM 3113 CD PRO B 348 29.494 9.084 77.357 1.00 21.13 C
ATOM 3114 N SER B 349 32.539 7.027 78.460 1.00 19.41 N
ATOM 3115 CA SER B 349 33.893 6.525 78.723 1.00 19.83 C
ATOM 3116 C SER B 349 34.058 5.886 80.108 1.00 21.09 C
ATOM 3117 O SER B 349 35.078 5.245 80.371 1.00 22.60 O
ATOM 3118 CB SER B 349 34.927 7.649 78.565 1.00 19.06 C
ATOM 3119 OG SER B 349 34.703 8.629 79.568 1.00 18.12 O
ATOM 3120 N VAL B 350 33.073 6.043 80.994 1.00 22.06 N
ATOM 3121 CA VAL B 350 33.129 5.452 82.342 1.00 24.44 C
ATOM 3122 C VAL B 350 31.827 4.720 82.683 1.00 25.38 C
ATOM 3123 O VAL B 350 30.743 5.054 82.203 1.00 24.45 O
ATOM 3124 CB VAL B 350 33.431 6.521 83.434 1.00 24.92 C
ATOM 3125 CG1 VAL B 350 34.763 7.175 83.174 1.00 25.70 C
ATOM 3126 CG2 VAL B 350 32.339 7.574 83.519 1.00 25.22 C
ATOM 3127 N THR B 351 31.925 3.655 83.470 1.00 27.73 N
ATOM 3128 CA THR B 351 30.714 2.879 83.813 1.00 30.49 C
ATOM 3129 C THR B 351 30.147 3.247 85.182 1.00 32.97 C
ATOM 3130 O THR B 351 29.102 2.708 85.611 1.00 35.40 O
ATOM 3131 CB THR B 351 31.017 1.387 83.766 1.00 32.56 C
ATOM 3132 OG1 THR B 351 32.123 1.150 84.639 1.00 32.77 O
ATOM 3133 CG2 THR B 351 31.403 0.991 82.340 1.00 33.15 C
ATOM 3134 N SER B 352 30.892 4.069 85.902 1.00 33.31 N
ATOM 3135 CA SER B 352 30.463 4.613 87.168 1.00 35.35 C
ATOM 3136 C SER B 352 30.743 6.116 87.203 1.00 33.51 C
ATOM 3137 O SER B 352 31.764 6.535 86.676 1.00 33.06 O
ATOM 3138 CB SER B 352 31.185 3.914 88.314 1.00 38.93 C
ATOM 3139 OG SER B 352 30.692 4.367 89.546 1.00 42.58 O
ATOM 3140 N PRO B 353 29.866 6.909 87.848 1.00 31.72 N
ATOM 3141 CA PRO B 353 30.054 8.369 87.805 1.00 30.74 C
ATOM 3142 C PRO B 353 31.407 8.835 88.331 1.00 29.21 C
ATOM 3143 O PRO B 353 31.894 8.292 89.323 1.00 30.23 O
ATOM 3144 CB PRO B 353 28.916 8.902 88.715 1.00 31.28 C
ATOM 3145 CG PRO B 353 27.877 7.816 88.698 1.00 31.88 C
ATOM 3146 CD PRO B 353 28.657 6.529 88.616 1.00 32.29 C
ATOM 3147 N LEU B 354 31.966 9.853 87.692 1.00 27.96 N
ATOM 3148 CA LEU B 354 33.106 10.574 88.216 1.00 27.08 C
ATOM 3149 C LEU B 354 32.567 11.584 89.195 1.00 25.85 C
ATOM 3150 O LEU B 354 31.621 12.305 88.880 1.00 26.37 O
ATOM 3151 CB LEU B 354 33.877 11.295 87.121 1.00 28.09 C
ATOM 3152 CG LEU B 354 34.594 10.378 86.194 1.00 29.75 C
ATOM 3153 CD1 LEU B 354 35.180 11.229 85.099 1.00 30.03 C
ATOM 3154 CD2 LEU B 354 35.706 9.594 86.926 1.00 30.77 C
ATOM 3155 N THR B 355 33.150 11.649 90.380 1.00 25.85 N
ATOM 3156 CA THR B 355 32.718 12.676 91.320 1.00 26.19 C
ATOM 3157 C THR B 355 33.870 13.517 91.831 1.00 25.68 C
ATOM 3158 O THR B 355 34.979 12.993 92.066 1.00 28.21 O
ATOM 3159 CB THR B 355 31.968 12.057 92.551 1.00 27.83 C
ATOM 3160 OG1 THR B 355 32.829 11.129 93.247 1.00 30.07 O
ATOM 3161 CG2 THR B 355 30.705 11.342 92.089 1.00 27.49 C
ATOM 3162 N VAL B 356 33.597 14.797 92.070 1.00 23.84 N
ATOM 3163 CA VAL B 356 34.566 15.692 92.688 1.00 24.43 C
ATOM 3164 C VAL B 356 33.854 16.436 93.785 1.00 24.88 C
ATOM 3165 O VAL B 356 32.807 17.047 93.561 1.00 23.93 O
ATOM 3166 CB VAL B 356 35.184 16.706 91.676 1.00 24.57 C
ATOM 3167 CG1 VAL B 356 36.069 17.717 92.443 1.00 25.97 C
ATOM 3168 CG2 VAL B 356 36.035 15.972 90.602 1.00 25.03 C
ATOM 3170 N GLU B 357 34.399 16.352 94.994 0.54 25.64 N
ATOM 3172 CA GLU B 357 33.822 17.028 96.159 0.54 27.37 C
ATOM 3174 C GLU B 357 34.531 18.363 96.407 0.54 27.21 C
ATOM 3176 O GLU B 357 35.746 18.494 96.190 0.54 27.85 O
ATOM 3178 CB GLU B 357 33.913 16.131 97.415 0.54 29.52 C
ATOM 3180 CG GLU B 357 33.197 14.769 97.312 0.54 32.12 C
ATOM 3182 CD GLU B 357 33.006 14.114 98.675 0.54 35.14 C
ATOM 3184 OE1 GLU B 357 33.187 14.837 99.666 0.54 36.69 O
ATOM 3186 OE2 GLU B 357 32.661 12.913 98.767 0.54 35.81 O
ATOM 3187 N TRP B 358 33.773 19.353 96.860 1.00 27.78 N
ATOM 3188 CA TRP B 358 34.336 20.635 97.284 1.00 29.43 C
ATOM 3189 C TRP B 358 33.706 21.002 98.622 1.00 30.51 C
ATOM 3190 O TRP B 358 32.502 20.965 98.762 1.00 30.45 O
ATOM 3191 CB TRP B 358 34.050 21.710 96.219 1.00 31.33 C
ATOM 3192 CG TRP B 358 34.714 23.016 96.457 1.00 34.08 C
ATOM 3193 CD1 TRP B 358 35.895 23.452 95.912 1.00 35.51 C
ATOM 3194 CD2 TRP B 358 34.241 24.073 97.291 1.00 35.74 C
ATOM 3195 NE1 TRP B 358 36.188 24.722 96.372 1.00 36.31 N
ATOM 3196 CE2 TRP B 358 35.191 25.126 97.218 1.00 36.58 C
ATOM 3197 CE3 TRP B 358 33.104 24.243 98.081 1.00 36.04 C
ATOM 3198 CZ2 TRP B 358 35.041 26.322 97.925 1.00 36.84 C
ATOM 3199 CZ3 TRP B 358 32.953 25.439 98.783 1.00 36.73 C
ATOM 3200 CH2 TRP B 358 33.918 26.459 98.701 1.00 36.50 C
ATOM 3201 N ARG B 359 34.524 21.342 99.613 1.00 32.58 N
ATOM 3202 CA ARG B 359 33.976 21.671 100.930 1.00 36.51 C
ATOM 3203 C ARG B 359 34.211 23.112 101.308 1.00 38.00 C
ATOM 3204 O ARG B 359 35.290 23.643 101.109 1.00 38.32 O
ATOM 3205 CB ARG B 359 34.581 20.772 101.992 1.00 39.49 C
ATOM 3206 CG ARG B 359 34.320 19.313 101.753 1.00 43.23 C
ATOM 3207 CD ARG B 359 34.531 18.525 103.047 1.00 47.19 C
ATOM 3208 NE ARG B 359 34.982 17.166 102.767 1.00 50.93 N
ATOM 3209 CZ ARG B 359 34.994 16.187 103.665 1.00 53.84 C
ATOM 3210 NH1 ARG B 359 34.557 16.408 104.897 1.00 54.96 N
ATOM 3211 NH2 ARG B 359 35.432 14.978 103.322 1.00 55.02 N
ATOM 3212 N ALA B 360 33.210 23.753 101.881 1.00 40.40 N
ATOM 3213 CA ALA B 360 33.468 25.034 102.515 1.00 42.92 C
ATOM 3214 C ALA B 360 34.331 24.855 103.776 1.00 44.69 C
ATOM 3215 O ALA B 360 34.551 23.740 104.235 1.00 43.16 O
ATOM 3216 CB ALA B 360 32.191 25.713 102.853 1.00 42.97 C
ATOM 3217 N ARG B 361 34.843 25.960 104.295 1.00 47.74 N
ATOM 3218 CA ARG B 361 35.641 25.931 105.514 1.00 50.77 C
ATOM 3219 C ARG B 361 34.844 25.255 106.638 1.00 50.90 C
ATOM 3220 O ARG B 361 33.619 25.382 106.679 1.00 50.38 O
ATOM 3221 CB ARG B 361 36.054 27.363 105.879 1.00 53.56 C
ATOM 3222 CG ARG B 361 36.012 27.730 107.355 1.00 56.25 C
ATOM 3223 CD ARG B 361 35.816 29.241 107.535 1.00 58.48 C
ATOM 3224 NE ARG B 361 35.992 29.712 108.915 1.00 60.16 N
ATOM 3225 CZ ARG B 361 37.160 30.099 109.441 1.00 61.31 C
ATOM 3226 NH1 ARG B 361 38.279 30.061 108.720 1.00 61.47 N
ATOM 3227 NH2 ARG B 361 37.215 30.541 110.690 1.00 61.76 N
ATOM 3228 N SER B 362 35.528 24.486 107.494 1.00 51.53 N
ATOM 3229 CA SER B 362 34.922 23.983 108.733 1.00 52.36 C
ATOM 3230 C SER B 362 34.711 25.169 109.676 1.00 53.69 C
ATOM 3231 O SER B 362 35.614 25.995 109.813 1.00 54.26 O
ATOM 3232 CB SER B 362 35.814 22.951 109.466 1.00 51.88 C
ATOM 3233 OG SER B 362 36.238 21.821 108.721 1.00 51.69 O
ATOM 3234 N GLU B 363 33.564 25.262 110.346 1.00 54.23 N
ATOM 3235 CA GLU B 363 33.471 26.200 111.475 1.00 54.83 C
ATOM 3236 C GLU B 363 33.868 25.493 112.781 1.00 51.86 C
ATOM 3237 O GLU B 363 34.955 25.727 113.303 1.00 52.68 O
ATOM 3238 CB GLU B 363 32.076 26.824 111.593 1.00 58.20 C
ATOM 3239 CG GLU B 363 32.107 28.361 111.666 1.00 61.35 C
ATOM 3240 CD GLU B 363 30.918 29.025 110.969 1.00 64.17 C
ATOM 3241 OE1 GLU B 363 29.844 29.162 111.605 1.00 65.05 O
ATOM 3242 OE2 GLU B 363 31.058 29.427 109.789 1.00 65.30 O
ATOM 3243 N SER B 364 33.016 24.615 113.298 1.00 47.73 N
ATOM 3244 CA SER B 364 33.372 23.872 114.502 1.00 44.43 C
ATOM 3245 C SER B 364 33.260 22.383 114.209 1.00 40.48 C
ATOM 3246 O SER B 364 32.369 21.960 113.467 1.00 40.03 O
ATOM 3247 CB SER B 364 32.469 24.279 115.670 1.00 45.16 C
ATOM 3248 OG SER B 364 32.958 23.735 116.869 1.00 46.17 O
ATOM 3249 N ALA B 365 34.195 21.600 114.725 1.00 36.78 N
ATOM 3250 CA ALA B 365 34.207 20.157 114.544 1.00 34.46 C
ATOM 3251 C ALA B 365 34.329 19.499 115.915 1.00 33.84 C
ATOM 3252 O ALA B 365 35.028 20.022 116.744 1.00 29.47 O
ATOM 3253 CB ALA B 365 35.354 19.748 113.654 1.00 34.08 C
ATOM 3254 N GLN B 366 33.670 18.363 116.135 1.00 36.81 N
ATOM 3255 CA GLN B 366 33.651 17.732 117.461 1.00 41.28 C
ATOM 3256 C GLN B 366 33.889 16.221 117.389 1.00 41.49 C
ATOM 3257 O GLN B 366 33.642 15.585 116.353 1.00 41.08 O
ATOM 3258 CB GLN B 366 32.309 18.023 118.138 1.00 45.82 C
ATOM 3259 CG GLN B 366 31.230 18.292 117.090 1.00 50.13 C
ATOM 3260 CD GLN B 366 29.955 18.865 117.683 1.00 53.86 C
ATOM 3261 OE1 GLN B 366 29.632 18.597 118.846 1.00 55.19 O
ATOM 3262 NE2 GLN B 366 29.213 19.637 116.881 1.00 55.09 N
ATOM 3263 N SER B 367 34.380 15.651 118.485 1.00 41.87 N
ATOM 3264 CA SER B 367 34.486 14.206 118.617 1.00 43.38 C
ATOM 3265 C SER B 367 33.059 13.648 118.773 1.00 48.07 C
ATOM 3266 O SER B 367 32.109 14.401 119.061 1.00 47.95 O
ATOM 3267 CB SER B 367 35.394 13.818 119.814 1.00 40.73 C
ATOM 3268 OG SER B 367 34.880 14.253 121.081 1.00 36.71 O
ATOM 3269 N LYS B 368 32.891 12.349 118.557 1.00 51.85 N
ATOM 3270 CA LYS B 368 31.657 11.716 119.008 1.00 55.43 C
ATOM 3271 C LYS B 368 31.937 10.282 119.438 1.00 56.99 C
ATOM 3272 O LYS B 368 32.476 10.065 120.530 1.00 58.01 O
ATOM 3273 CB LYS B 368 30.570 11.773 117.927 1.00 57.18 C
ATOM 3274 CG LYS B 368 29.178 11.342 118.446 1.00 58.40 C
ATOM 3275 CD LYS B 368 28.959 11.746 119.941 1.00 59.12 C
ATOM 3276 CE LYS B 368 27.473 11.793 120.328 1.00 59.65 C
ATOM 3277 NZ LYS B 368 27.014 10.541 121.014 1.00 59.97 N
CONECT 927 926 1451
CONECT 1451 927 1450
CONECT 1764 1763 2361
CONECT 2361 1764 2360
CONECT 2606 2605 3071
CONECT 3071 2606 3070
END

*i tried to submit to haddock again, and the same issues still persists.

There was an inconsistency in your data

Error message

First pdb file contains multiple forms of the same residue. This is not supported in the current form. If you would like to supply multiple conformations, please create an ensemble
ATOM 400 N AGLU A 47 47.517 10.252 64.654 0.50 23.39 N
Directory of the run: http://alcazar.science.uu.nl/serviceresults/HADDOCK2.2/6851440797/Test_Run

6

You need to redirect the output to a new (.pdb) file. Please refer to the documentation mentioned above for some examples.

7

thanks for the guidance.
output like this one down below??

python pdb_selaltloc.py 4x5w_renumbered.pdb > 4x5w_refined.pdb

8

Yes, redirect with >

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