the output file data format not same as orignal

[JackYang825]

Hello,
rna json data:
[
{
"sequences": [
{
"rnaSequence": {
"sequence": "CUC",
"count": 1
}
}
],
"name": "rep0__J3_1VQ6_007_CU"
}

the original rna data format(pdb):
ATOM 1 O5' C A 1 130.495 111.016 36.330 1.00 0.00 O
ATOM 2 HO5' C A 1 131.180 111.140 36.991 1.00 0.00 H
ATOM 3 C5' C A 1 131.117 110.888 35.057 1.00 0.00 C
ATOM 4 H5' C A 1 131.684 111.792 34.833 1.00 0.00 H
ATOM 5 H5'' C A 1 131.809 110.046 35.072 1.00 0.00 H
ATOM 6 C4' C A 1 130.090 110.659 33.942 1.00 0.00 C
ATOM 7 H4' C A 1 130.630 110.480 33.012 1.00 0.00 H
ATOM 8 O4' C A 1 129.284 109.525 34.238 1.00 0.00 O
ATOM 9 C3' C A 1 129.107 111.808 33.715 1.00 0.00 C
ATOM 10 H3' C A 1 128.733 112.155 34.678 1.00 0.00 H
ATOM 11 O3' C A 1 129.689 112.868 32.957 1.00 0.00 O
ATOM 12 C2' C A 1 128.000 111.052 32.961 1.00 0.00 C
ATOM 13 H2' C A 1 127.021 111.513 33.091 1.00 0.00 H
ATOM 14 O2' C A 1 128.280 110.882 31.581 1.00 0.00 O
ATOM 15 HO2' C A 1 129.224 111.004 31.449 1.00 0.00 H
ATOM 16 C1' C A 1 128.026 109.656 33.586 1.00 0.00 C
ATOM 17 H1' C A 1 127.951 108.921 32.785 1.00 0.00 H
ATOM 18 N1 C A 1 126.889 109.429 34.525 1.00 0.00 N
ATOM 19 C2 C A 1 125.639 109.093 33.986 1.00 0.00 C
ATOM 20 O2 C A 1 125.457 109.056 32.766 1.00 0.00 O
ATOM 21 N3 C A 1 124.598 108.781 34.801 1.00 0.00 N
ATOM 22 C4 C A 1 124.788 108.803 36.109 1.00 0.00 C
ATOM 23 N4 C A 1 123.765 108.483 36.852 1.00 0.00 N
ATOM 24 H41 C A 1 123.850 108.511 37.858 1.00 0.00 H
ATOM 25 H42 C A 1 122.889 108.295 36.386 1.00 0.00 H
ATOM 26 C5 C A 1 126.035 109.123 36.712 1.00 0.00 C
ATOM 27 H5 C A 1 126.177 109.123 37.782 1.00 0.00 H
ATOM 28 C6 C A 1 127.065 109.432 35.888 1.00 0.00 C
ATOM 29 H6 C A 1 128.032 109.679 36.302 1.00 0.00 H
ATOM 30 P U A 2 129.029 114.320 32.931 1.00 0.00 P
ATOM 31 OP1 U A 2 129.895 115.227 32.149 1.00 0.00 O
ATOM 32 OP2 U A 2 128.680 114.684 34.319 1.00 0.00 O
ATOM 33 O5' U A 2 127.681 114.124 32.117 1.00 0.00 O
ATOM 34 C5' U A 2 127.677 113.856 30.721 1.00 0.00 C
ATOM 35 H5' U A 2 128.207 112.934 30.482 1.00 0.00 H
ATOM 36 H5'' U A 2 128.201 114.658 30.200 1.00 0.00 H
ATOM 37 C4' U A 2 126.248 113.782 30.169 1.00 0.00 C
ATOM 38 H4' U A 2 126.300 113.465 29.127 1.00 0.00 H
ATOM 39 O4' U A 2 125.454 112.863 30.921 1.00 0.00 O
ATOM 40 C3' U A 2 125.553 115.148 30.245 1.00 0.00 C
ATOM 41 H3' U A 2 126.280 115.960 30.249 1.00 0.00 H
ATOM 42 O3' U A 2 124.672 115.248 29.135 1.00 0.00 O
ATOM 43 C2' U A 2 124.802 115.043 31.578 1.00 0.00 C
ATOM 44 H2' U A 2 125.502 115.223 32.394 1.00 0.00 H
ATOM 45 O2' U A 2 123.677 115.898 31.716 1.00 0.00 O
ATOM 46 HO2' U A 2 123.737 116.572 31.036 1.00 0.00 H
ATOM 47 C1' U A 2 124.389 113.574 31.541 1.00 0.00 C
ATOM 48 H1' U A 2 123.506 113.496 30.906 1.00 0.00 H
ATOM 49 N1 U A 2 124.103 113.032 32.891 1.00 0.00 N
ATOM 50 C2 U A 2 122.785 112.690 33.205 1.00 0.00 C
ATOM 51 O2 U A 2 121.839 112.822 32.421 1.00 0.00 O
ATOM 52 N3 U A 2 122.566 112.193 34.473 1.00 0.00 N
ATOM 53 H3 U A 2 121.616 111.956 34.722 1.00 0.00 H
ATOM 54 C4 U A 2 123.523 112.012 35.446 1.00 0.00 C
ATOM 55 O4 U A 2 123.202 111.597 36.555 1.00 0.00 O
ATOM 56 C5 U A 2 124.859 112.389 35.056 1.00 0.00 C
ATOM 57 H5 U A 2 125.654 112.296 35.781 1.00 0.00 H
ATOM 58 C6 U A 2 125.104 112.903 33.826 1.00 0.00 C
ATOM 59 H6 U A 2 126.098 113.247 33.582 1.00 0.00 H
ATOM 60 P C A 3 124.193 116.660 28.588 1.00 0.00 P
ATOM 61 OP1 C A 3 125.149 117.104 27.558 1.00 0.00 O
ATOM 62 OP2 C A 3 123.893 117.540 29.735 1.00 0.00 O
ATOM 63 O5' C A 3 122.821 116.264 27.892 1.00 0.00 O
ATOM 64 C5' C A 3 121.807 117.217 27.600 1.00 0.00 C
ATOM 65 H5' C A 3 122.017 118.172 28.082 1.00 0.00 H
ATOM 66 H5'' C A 3 121.772 117.385 26.524 1.00 0.00 H
ATOM 67 C4' C A 3 120.431 116.720 28.078 1.00 0.00 C
ATOM 68 H4' C A 3 119.667 117.388 27.681 1.00 0.00 H
ATOM 69 O4' C A 3 120.219 115.388 27.602 1.00 0.00 O
ATOM 70 C3' C A 3 120.300 116.656 29.608 1.00 0.00 C
ATOM 71 H3' C A 3 120.965 117.360 30.108 1.00 0.00 H
ATOM 72 O3' C A 3 118.942 116.864 29.984 1.00 0.00 O
ATOM 73 HO3' C A 3 118.832 116.345 30.783 1.00 0.00 H
ATOM 74 C2' C A 3 120.680 115.208 29.912 1.00 0.00 C
ATOM 75 H2' C A 3 121.764 115.095 29.871 1.00 0.00 H
ATOM 76 O2' C A 3 120.164 114.751 31.159 1.00 0.00 O
ATOM 77 HO2' C A 3 120.734 114.056 31.497 1.00 0.00 H
ATOM 78 C1' C A 3 120.010 114.532 28.719 1.00 0.00 C
ATOM 79 H1' C A 3 118.941 114.494 28.927 1.00 0.00 H
ATOM 80 N1 C A 3 120.524 113.166 28.452 1.00 0.00 N
ATOM 81 C2 C A 3 119.661 112.077 28.621 1.00 0.00 C
ATOM 82 O2 C A 3 118.490 112.231 28.989 1.00 0.00 O
ATOM 83 N3 C A 3 120.095 110.814 28.372 1.00 0.00 N
ATOM 84 C4 C A 3 121.346 110.643 27.975 1.00 0.00 C
ATOM 85 N4 C A 3 121.720 109.413 27.751 1.00 0.00 N
ATOM 86 H41 C A 3 121.035 108.683 27.885 1.00 0.00 H
ATOM 87 H42 C A 3 122.668 109.226 27.458 1.00 0.00 H
ATOM 88 C5 C A 3 122.263 111.711 27.788 1.00 0.00 C
ATOM 89 H5 C A 3 123.281 111.552 27.465 1.00 0.00 H
ATOM 90 C6 C A 3 121.815 112.965 28.036 1.00 0.00 C
ATOM 91 H6 C A 3 122.470 113.814 27.908 1.00 0.00 H
TER 92 C A 3
END

use protenix predicted data format(pdb):
ATOM 1 OP3 C A 1 -1.975 0.516 -6.397 1.00 0.00 O
ATOM 2 P C A 1 -2.315 1.875 -6.051 1.00 0.00 P
ATOM 3 OP1 C A 1 -2.902 1.881 -4.767 1.00 0.00 O
ATOM 4 OP2 C A 1 -3.054 2.359 -7.141 1.00 0.00 O
ATOM 5 O5' C A 1 -0.953 2.638 -5.912 1.00 0.00 O
ATOM 6 C5' C A 1 -0.138 3.068 -6.990 1.00 0.00 C
ATOM 7 C4' C A 1 0.615 4.258 -6.477 1.00 0.00 C
ATOM 8 O4' C A 1 -0.332 5.183 -5.913 1.00 0.00 O
ATOM 9 C3' C A 1 1.542 3.956 -5.349 1.00 0.00 C
ATOM 10 O3' C A 1 2.798 3.455 -5.816 1.00 0.00 O
ATOM 11 C2' C A 1 1.642 5.289 -4.651 1.00 0.00 C
ATOM 12 O2' C A 1 2.543 6.162 -5.308 1.00 0.00 O
ATOM 13 C1' C A 1 0.197 5.800 -4.795 1.00 0.00 C
ATOM 14 N1 C A 1 -0.625 5.499 -3.608 1.00 0.00 N
ATOM 15 C2 C A 1 -0.380 6.157 -2.451 1.00 0.00 C
ATOM 16 O2 C A 1 0.526 6.999 -2.412 1.00 0.00 O
ATOM 17 N3 C A 1 -1.116 5.882 -1.374 1.00 0.00 N
ATOM 18 C4 C A 1 -2.081 4.971 -1.446 1.00 0.00 C
ATOM 19 N4 C A 1 -2.794 4.721 -0.343 1.00 0.00 N
ATOM 20 C5 C A 1 -2.358 4.292 -2.621 1.00 0.00 C
ATOM 21 C6 C A 1 -1.608 4.579 -3.678 1.00 0.00 C
ATOM 22 P U A 2 3.452 2.187 -5.077 1.00 0.00 P
ATOM 23 OP1 U A 2 2.595 1.002 -5.270 1.00 0.00 O
ATOM 24 OP2 U A 2 4.826 2.137 -5.593 1.00 0.00 O
ATOM 25 O5' U A 2 3.516 2.510 -3.520 1.00 0.00 O
ATOM 26 C5' U A 2 4.329 3.536 -2.984 1.00 0.00 C
ATOM 27 C4' U A 2 3.967 3.725 -1.524 1.00 0.00 C
ATOM 28 O4' U A 2 2.567 4.072 -1.459 1.00 0.00 O
ATOM 29 C3' U A 2 4.088 2.467 -0.695 1.00 0.00 C
ATOM 30 O3' U A 2 5.413 2.317 -0.165 1.00 0.00 O
ATOM 31 C2' U A 2 3.046 2.671 0.384 1.00 0.00 C
ATOM 32 O2' U A 2 3.550 3.465 1.459 1.00 0.00 O
ATOM 33 C1' U A 2 1.957 3.440 -0.364 1.00 0.00 C
ATOM 34 N1 U A 2 0.842 2.619 -0.861 1.00 0.00 N
ATOM 35 C2 U A 2 -0.052 2.128 0.040 1.00 0.00 C
ATOM 36 O2 U A 2 0.052 2.334 1.233 1.00 0.00 O
ATOM 37 N3 U A 2 -1.075 1.392 -0.472 1.00 0.00 N
ATOM 38 C4 U A 2 -1.279 1.100 -1.789 1.00 0.00 C
ATOM 39 O4 U A 2 -2.243 0.425 -2.122 1.00 0.00 O
ATOM 40 C5 U A 2 -0.325 1.628 -2.674 1.00 0.00 C
ATOM 41 C6 U A 2 0.689 2.357 -2.186 1.00 0.00 C
ATOM 42 P C A 3 5.982 0.905 0.254 1.00 0.00 P
ATOM 43 OP1 C A 3 5.632 -0.019 -0.836 1.00 0.00 O
ATOM 44 OP2 C A 3 7.424 1.128 0.524 1.00 0.00 O
ATOM 45 O5' C A 3 5.283 0.372 1.550 1.00 0.00 O
ATOM 46 C5' C A 3 5.837 0.730 2.754 1.00 0.00 C
ATOM 47 C4' C A 3 5.053 0.106 3.853 1.00 0.00 C
ATOM 48 O4' C A 3 3.703 0.595 3.760 1.00 0.00 O
ATOM 49 C3' C A 3 4.915 -1.397 3.769 1.00 0.00 C
ATOM 50 O3' C A 3 6.010 -2.101 4.322 1.00 0.00 O
ATOM 51 C2' C A 3 3.664 -1.623 4.581 1.00 0.00 C
ATOM 52 O2' C A 3 3.921 -1.589 5.969 1.00 0.00 O
ATOM 53 C1' C A 3 2.839 -0.426 4.169 1.00 0.00 C
ATOM 54 N1 C A 3 1.939 -0.722 3.065 1.00 0.00 N
ATOM 55 C2 C A 3 0.631 -0.984 3.386 1.00 0.00 C
ATOM 56 O2 C A 3 0.297 -0.939 4.567 1.00 0.00 O
ATOM 57 N3 C A 3 -0.237 -1.276 2.417 1.00 0.00 N
ATOM 58 C4 C A 3 0.183 -1.317 1.161 1.00 0.00 C
ATOM 59 N4 C A 3 -0.704 -1.612 0.232 1.00 0.00 N
ATOM 60 C5 C A 3 1.509 -1.065 0.795 1.00 0.00 C
ATOM 61 C6 C A 3 2.352 -0.773 1.773 1.00 0.00 C
How can I change the Protenix predicted data format to the original format? There may be missing some atoms. How to fix it?

Sincerely,
Jack

[cloverzizi]

Hi @JackYang825 ，
The structure output by Protenix does not include hydrogen atoms, so it contains fewer atoms compared to the PDB reference you are using. If you need to align the two PDB files, you can remove the hydrogens from the original PDB and then match atoms based on the residue index and atom name.