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🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online
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missing /rna_tools/tools/clarna_play/ClaRNAlib/* #126

Closed pengzhangzhi closed 2 years ago

pengzhangzhi commented 2 years ago

Hi. I use rna_calc_inf.py -t native_1fir.pdb pred_1fir.pdb -m 1 and the output inf.csv shows such error..

target,fn,inf_all,inf_stack,inf_WC,inf_nWC,sns_WC,ppv_WC,sns_nWC,ppv_nWC
sv:,"['library',","'/user/pengzhangzhi/anaconda3/envs/torch/lib/python3.8/site-packages/rna_tools/tools/clarna_play/ClaRNAlib/lib/classifier.bp.json.gz',","'does',","'not',",'exists'],,,,

native_1fir.pdb and pred_1fir.pdb are identical. I receive no errors computing the RMSD.

I use pip install rna-tools to install this wrapper.

For the reproducibility, I open source the two file as follows.

native_1fir.pdb

ATOM 1 C1' G 1 -23.549 28.964 36.523 0.00 0.00
ATOM 1 C4' G 1 -24.956 30.055 34.985 0.00 0.00
ATOM 1 O5' G 1 -24.311 29.438 32.723 0.00 0.00
ATOM 1 N91 G 1 -22.489 28.185 35.905 0.00 0.00
ATOM 1 C1' C 2 -19.493 32.172 37.630 0.00 0.00
ATOM 1 C4' C 2 -20.899 33.946 37.030 0.00 0.00
ATOM 1 O5' C 2 -21.598 33.400 34.816 0.00 0.00
ATOM 1 N91 C 2 -18.966 31.180 36.686 0.00 0.00
ATOM 1 C1' C 3 -14.078 33.717 37.492 0.00 0.00
ATOM 1 C4' C 3 -15.095 35.763 37.921 0.00 0.00
ATOM 1 O5' C 3 -16.792 36.062 36.330 0.00 0.00
ATOM 1 N91 C 3 -14.379 32.859 36.345 0.00 0.00
ATOM 1 C1' C 4 -9.126 34.553 34.891 0.00 0.00
ATOM 1 C4' C 4 -9.462 36.677 35.788 0.00 0.00
ATOM 1 O5' C 4 -11.641 37.526 35.316 0.00 0.00
ATOM 1 N91 C 4 -10.131 33.959 34.009 0.00 0.00
ATOM 1 C1' G 5 -5.883 34.251 30.414 0.00 0.00
ATOM 1 C4' G 5 -5.284 36.423 31.091 0.00 0.00
ATOM 1 O5' G 5 -7.307 37.523 31.808 0.00 0.00
ATOM 1 N91 G 5 -7.285 33.933 30.184 0.00 0.00
ATOM 1 C1' A 7 -8.248 34.277 19.722 0.00 0.00
ATOM 1 C4' A 7 -5.954 34.043 19.281 0.00 0.00
ATOM 1 O5' A 7 -5.424 35.838 20.859 0.00 0.00
ATOM 1 N91 A 7 -9.063 34.553 20.895 0.00 0.00
ATOM 1 C1' U 8 -3.703 39.232 14.558 0.00 0.00
ATOM 1 C4' U 8 -5.272 37.605 13.999 0.00 0.00
ATOM 1 O5' U 8 -5.130 35.996 15.727 0.00 0.00
ATOM 1 N91 U 8 -2.743 39.059 15.644 0.00 0.00
ATOM 1 C1' A 9 -0.198 35.752 8.006 0.00 0.00
ATOM 1 C4' A 9 -2.521 35.683 8.035 0.00 0.00
ATOM 1 O5' A 9 -2.394 35.820 10.426 0.00 0.00
ATOM 1 N91 A 9 0.900 36.524 8.533 0.00 0.00
ATOM 1 C1' C 11 1.560 28.445 12.612 0.00 0.00
ATOM 1 C4' C 11 -0.489 27.767 13.455 0.00 0.00
ATOM 1 O5' C 11 -2.155 28.122 11.831 0.00 0.00
ATOM 1 N91 C 11 1.864 29.687 11.922 0.00 0.00
ATOM 1 C1' U 12 3.925 31.283 17.216 0.00 0.00
ATOM 1 C4' U 12 2.542 29.841 18.423 0.00 0.00
ATOM 1 O5' U 12 0.353 30.064 17.479 0.00 0.00
ATOM 1 N91 U 12 3.336 32.153 16.188 0.00 0.00
ATOM 1 C1' C 13 4.263 36.245 18.463 0.00 0.00
ATOM 1 C4' C 13 3.305 35.606 20.505 0.00 0.00
ATOM 1 O5' C 13 2.562 33.409 21.186 0.00 0.00
ATOM 1 N91 C 13 3.269 36.412 17.410 0.00 0.00
ATOM 1 C1' A 14 4.799 42.247 17.810 0.00 0.00
ATOM 1 C4' A 14 4.929 41.629 20.059 0.00 0.00
ATOM 1 O5' A 14 3.105 40.228 20.846 0.00 0.00
ATOM 1 N91 A 14 3.638 41.880 17.017 0.00 0.00
ATOM 1 C1' G 15 1.428 45.927 16.785 0.00 0.00
ATOM 1 C4' G 15 2.540 46.817 18.636 0.00 0.00
ATOM 1 O5' G 15 2.298 45.209 20.400 0.00 0.00
ATOM 1 N91 G 15 0.575 44.756 16.887 0.00 0.00
ATOM 1 C1' C 17 -2.893 55.762 26.063 0.00 0.00
ATOM 1 C4' C 17 -3.835 53.910 25.091 0.00 0.00
ATOM 1 O5' C 17 -2.170 52.210 25.141 0.00 0.00
ATOM 1 N91 C 17 -1.972 56.068 27.183 0.00 0.00
ATOM 1 C1' G 18 -7.291 54.773 18.302 0.00 0.00
ATOM 1 C4' G 18 -5.437 54.139 19.531 0.00 0.00
ATOM 1 O5' G 18 -6.045 54.956 21.648 0.00 0.00
ATOM 1 N91 G 18 -8.448 55.588 18.636 0.00 0.00
ATOM 1 C1' G 19 -4.037 57.229 12.650 0.00 0.00
ATOM 1 C4' G 19 -2.998 55.144 12.961 0.00 0.00
ATOM 1 O5' G 19 -3.430 54.126 15.126 0.00 0.00
ATOM 1 N91 G 19 -4.511 58.147 13.679 0.00 0.00
ATOM 1 C1' A 21 0.016 45.725 10.926 0.00 0.00
ATOM 1 C4' A 21 0.691 47.816 10.133 0.00 0.00
ATOM 1 O5' A 21 -0.667 48.508 8.282 0.00 0.00
ATOM 1 N91 A 21 -1.131 45.098 10.290 0.00 0.00
ATOM 1 C1' G 22 4.965 43.353 10.774 0.00 0.00
ATOM 1 C4' G 22 5.527 44.279 8.700 0.00 0.00
ATOM 1 O5' G 22 3.550 45.152 7.649 0.00 0.00
ATOM 1 N91 G 22 3.880 42.390 10.893 0.00 0.00
ATOM 1 C1' A 23 8.843 39.410 12.429 0.00 0.00
ATOM 1 C4' A 23 10.085 40.582 10.829 0.00 0.00
ATOM 1 O5' A 23 8.585 40.826 8.975 0.00 0.00
ATOM 1 N91 A 23 7.551 38.830 12.090 0.00 0.00
ATOM 1 C1' G 24 10.460 34.212 13.294 0.00 0.00
ATOM 1 C4' G 24 12.511 34.982 12.475 0.00 0.00
ATOM 1 O5' G 24 11.932 36.417 10.637 0.00 0.00
ATOM 1 N91 G 24 9.304 34.452 12.456 0.00 0.00
ATOM 1 C1' C 25 9.074 29.543 11.255 0.00 0.00
ATOM 1 C4' C 25 11.388 29.228 11.287 0.00 0.00
ATOM 1 O5' C 25 12.505 31.039 10.183 0.00 0.00
ATOM 1 N91 C 25 8.429 30.574 10.457 0.00 0.00
ATOM 1 C1' A 26 6.285 27.613 6.915 0.00 0.00
ATOM 1 C4' A 26 7.912 26.023 7.462 0.00 0.00
ATOM 1 O5' A 26 10.074 26.991 7.586 0.00 0.00
ATOM 1 N91 A 26 6.662 28.956 6.482 0.00 0.00
ATOM 1 C1' C 28 7.357 29.909 -3.471 0.00 0.00
ATOM 1 C4' C 28 6.559 27.742 -3.837 0.00 0.00
ATOM 1 O5' C 28 7.551 26.203 -2.268 0.00 0.00
ATOM 1 N91 C 28 8.398 30.130 -2.473 0.00 0.00
ATOM 1 C1' A 29 11.605 31.544 -6.772 0.00 0.00
ATOM 1 C4' A 29 10.557 29.923 -8.093 0.00 0.00
ATOM 1 O5' A 29 10.171 27.971 -6.739 0.00 0.00
ATOM 1 N91 A 29 11.959 31.307 -5.388 0.00 0.00
ATOM 1 C1' G 30 16.254 32.437 -7.547 0.00 0.00
ATOM 1 C4' G 30 15.972 31.410 -9.623 0.00 0.00
ATOM 1 O5' G 30 14.909 29.268 -9.325 0.00 0.00
ATOM 1 N91 G 30 16.183 31.733 -6.276 0.00 0.00
ATOM 1 C1' A 31 21.968 32.633 -5.907 0.00 0.00
ATOM 1 C4' A 31 22.011 32.715 -8.247 0.00 0.00
ATOM 1 O5' A 31 20.473 31.005 -8.931 0.00 0.00
ATOM 1 N91 A 31 21.255 31.525 -5.277 0.00 0.00
ATOM 1 C1' C 32 25.931 28.877 -3.938 0.00 0.00
ATOM 1 C4' C 32 26.823 30.043 -5.743 0.00 0.00
ATOM 1 O5' C 32 25.569 29.887 -7.793 0.00 0.00
ATOM 1 N91 C 32 24.865 27.874 -3.905 0.00 0.00
ATOM 1 C1' U 33 26.671 23.429 -4.240 0.00 0.00
ATOM 1 C4' U 33 28.741 24.464 -4.536 0.00 0.00
ATOM 1 O5' U 33 28.670 26.121 -6.268 0.00 0.00
ATOM 1 N91 U 33 25.491 23.659 -5.075 0.00 0.00
ATOM 1 C1' U 35 23.397 17.531 -6.045 0.00 0.00
ATOM 1 C4' U 35 22.606 19.049 -7.658 0.00 0.00
ATOM 1 O5' U 35 24.263 20.796 -7.734 0.00 0.00
ATOM 1 N91 U 35 24.386 17.945 -5.047 0.00 0.00
ATOM 1 C1' U 36 20.082 17.818 -0.749 0.00 0.00
ATOM 1 C4' U 36 18.759 18.313 -2.627 0.00 0.00
ATOM 1 O5' U 36 20.045 19.792 -3.987 0.00 0.00
ATOM 1 N91 U 36 21.360 18.493 -0.500 0.00 0.00
ATOM 1 C1' A 38 22.303 24.915 5.723 0.00 0.00
ATOM 1 C4' A 38 20.330 25.008 6.940 0.00 0.00
ATOM 1 O5' A 38 18.596 24.966 5.335 0.00 0.00
ATOM 1 N91 A 38 22.392 25.245 4.307 0.00 0.00
ATOM 1 C1' C 40 22.152 34.600 1.015 0.00 0.00
ATOM 1 C4' C 40 22.835 35.543 3.050 0.00 0.00
ATOM 1 O5' C 40 21.645 34.338 4.736 0.00 0.00
ATOM 1 N91 C 40 21.021 33.674 0.985 0.00 0.00
ATOM 1 C1' U 41 18.231 37.123 -1.879 0.00 0.00
ATOM 1 C4' U 41 19.401 38.831 -0.786 0.00 0.00
ATOM 1 O5' U 41 19.538 38.280 1.527 0.00 0.00
ATOM 1 N91 U 41 17.588 35.998 -1.197 0.00 0.00
ATOM 1 C1' G 42 13.447 38.159 -3.355 0.00 0.00
ATOM 1 C4' G 42 14.082 40.376 -2.970 0.00 0.00
ATOM 1 O5' G 42 15.153 40.632 -0.843 0.00 0.00
ATOM 1 N91 G 42 13.393 37.099 -2.354 0.00 0.00
ATOM 1 C1' A 43 8.329 37.301 -3.491 0.00 0.00
ATOM 1 C4' A 43 8.296 39.567 -4.056 0.00 0.00
ATOM 1 O5' A 43 9.487 40.609 -2.273 0.00 0.00
ATOM 1 N91 A 43 8.709 36.870 -2.144 0.00 0.00
ATOM 1 C1' G 44 3.803 36.410 -2.514 0.00 0.00
ATOM 1 C4' G 44 2.735 38.258 -3.446 0.00 0.00
ATOM 1 O5' G 44 3.892 40.041 -2.407 0.00 0.00
ATOM 1 N91 G 44 4.486 36.415 -1.226 0.00 0.00
ATOM 1 C1' G 45 0.163 35.352 2.205 0.00 0.00
ATOM 1 C4' G 45 -1.416 35.587 0.495 0.00 0.00
ATOM 1 O5' G 45 -0.732 37.574 -0.587 0.00 0.00
ATOM 1 N91 G 45 1.217 36.309 2.503 0.00 0.00
ATOM 1 C1' A 50 -18.271 37.931 15.601 0.00 0.00
ATOM 1 C4' A 50 -17.413 37.710 13.451 0.00 0.00
ATOM 1 O5' A 50 -15.198 38.489 13.638 0.00 0.00
ATOM 1 N91 A 50 -17.540 38.577 16.685 0.00 0.00
ATOM 1 C1' G 51 -22.478 41.378 16.247 0.00 0.00
ATOM 1 C4' G 51 -22.470 41.010 13.939 0.00 0.00
ATOM 1 O5' G 51 -20.230 41.185 13.122 0.00 0.00
ATOM 1 N91 G 51 -21.222 41.650 16.928 0.00 0.00
ATOM 1 C1' G 52 -23.450 45.804 17.934 0.00 0.00
ATOM 1 C4' G 52 -24.793 46.019 16.035 0.00 0.00
ATOM 1 O5' G 52 -23.419 45.409 14.193 0.00 0.00
ATOM 1 N91 G 52 -21.996 45.726 17.891 0.00 0.00
ATOM 1 C1' G 53 -21.453 50.857 19.925 0.00 0.00
ATOM 1 C4' G 53 -23.545 51.330 19.022 0.00 0.00
ATOM 1 O5' G 53 -23.750 50.442 16.810 0.00 0.00
ATOM 1 N91 G 53 -20.267 50.428 19.196 0.00 0.00
ATOM 1 C1' C 56 -12.893 62.288 11.575 0.00 0.00
ATOM 1 C4' C 56 -15.195 62.115 11.836 0.00 0.00
ATOM 1 O5' C 56 -15.641 62.176 14.175 0.00 0.00
ATOM 1 N91 C 56 -11.969 62.346 12.688 0.00 0.00
ATOM 1 C1' A 57 -10.499 57.513 12.278 0.00 0.00
ATOM 1 C4' A 57 -12.196 56.866 10.809 0.00 0.00
ATOM 1 O5' A 57 -14.271 57.720 11.656 0.00 0.00
ATOM 1 N91 A 57 -10.674 58.054 13.618 0.00 0.00
ATOM 1 C1' G 59 -6.792 45.195 15.483 0.00 0.00
ATOM 1 C4' G 59 -9.025 45.052 14.825 0.00 0.00
ATOM 1 O5' G 59 -9.097 46.790 13.139 0.00 0.00
ATOM 1 N91 G 59 -5.911 46.315 15.191 0.00 0.00
ATOM 1 C1' U 60 -6.651 48.867 19.587 0.00 0.00
ATOM 1 C4' U 60 -7.545 46.768 20.156 0.00 0.00
ATOM 1 O5' U 60 -9.435 47.137 18.794 0.00 0.00
ATOM 1 N91 U 60 -6.568 49.485 18.269 0.00 0.00
ATOM 1 C1' C 61 -11.667 51.503 23.633 0.00 0.00
ATOM 1 C4' C 61 -10.191 50.577 25.176 0.00 0.00
ATOM 1 O5' C 61 -9.307 48.571 24.306 0.00 0.00
ATOM 1 N91 C 61 -11.994 50.942 22.326 0.00 0.00
ATOM 1 C1' C 62 -17.434 49.816 25.528 0.00 0.00
ATOM 1 C4' C 62 -16.091 49.894 27.440 0.00 0.00
ATOM 1 O5' C 62 -14.102 48.655 26.992 0.00 0.00
ATOM 1 N91 C 62 -16.922 49.177 24.307 0.00 0.00
ATOM 1 C1' C 63 -21.212 46.284 25.573 0.00 0.00
ATOM 1 C4' C 63 -20.880 46.477 27.879 0.00 0.00
ATOM 1 O5' C 63 -18.574 46.118 28.482 0.00 0.00
ATOM 1 N91 C 63 -20.174 45.855 24.626 0.00 0.00
ATOM 1 C1' U 64 -23.031 41.009 24.012 0.00 0.00
ATOM 1 C4' U 64 -23.809 41.157 26.213 0.00 0.00
ATOM 1 O5' U 64 -22.076 42.065 27.631 0.00 0.00
ATOM 1 N91 U 64 -21.622 41.357 23.752 0.00 0.00
ATOM 1 C1' G 65 -21.897 36.197 21.884 0.00 0.00
ATOM 1 C4' G 65 -23.470 35.720 23.550 0.00 0.00
ATOM 1 O5' G 65 -22.727 36.833 25.542 0.00 0.00
ATOM 1 N91 G 65 -20.622 36.826 22.207 0.00 0.00
ATOM 1 C1' U 66 -18.481 32.296 20.060 0.00 0.00
ATOM 1 C4' U 66 -20.580 31.307 20.429 0.00 0.00
ATOM 1 O5' U 66 -21.181 32.106 22.604 0.00 0.00
ATOM 1 N91 U 66 -17.808 33.135 21.064 0.00 0.00
ATOM 1 C1' U 67 -14.451 29.861 20.920 0.00 0.00
ATOM 1 C4' U 67 -15.869 28.102 20.299 0.00 0.00
ATOM 1 O5' U 67 -17.791 27.918 21.757 0.00 0.00
ATOM 1 N91 U 67 -14.686 30.722 22.087 0.00 0.00
ATOM 1 C1' C 68 -9.658 27.362 23.166 0.00 0.00
ATOM 1 C4' C 68 -10.489 25.369 22.240 0.00 0.00
ATOM 1 O5' C 68 -12.827 25.396 22.745 0.00 0.00
ATOM 1 N91 C 68 -10.475 28.146 24.098 0.00 0.00
ATOM 1 C1' G 69 -7.349 26.646 28.042 0.00 0.00
ATOM 1 C4' G 69 -7.098 24.456 27.280 0.00 0.00
ATOM 1 O5' G 69 -9.160 23.632 26.391 0.00 0.00
ATOM 1 N91 G 69 -8.617 27.303 28.275 0.00 0.00
ATOM 1 C1' G 70 -7.171 27.028 33.688 0.00 0.00
ATOM 1 C4' G 70 -6.105 24.967 33.455 0.00 0.00
ATOM 1 O5' G 70 -7.346 23.652 31.858 0.00 0.00
ATOM 1 N91 G 70 -8.541 27.141 33.239 0.00 0.00
ATOM 1 C1' G 71 -10.041 27.703 38.685 0.00 0.00
ATOM 1 C4' G 71 -8.265 26.237 39.107 0.00 0.00
ATOM 1 O5' G 71 -8.316 24.498 37.464 0.00 0.00
ATOM 1 N91 G 71 -11.005 27.427 37.632 0.00 0.00
ATOM 1 C1' C 72 -14.526 26.961 40.954 0.00 0.00
ATOM 1 C4' C 72 -13.090 26.097 42.555 0.00 0.00
ATOM 1 O5' C 72 -11.579 24.490 41.588 0.00 0.00
ATOM 1 N91 C 72 -14.874 26.394 39.668 0.00 0.00
ATOM 1 C1' G 73 -19.292 25.225 41.283 0.00 0.00
ATOM 1 C4' G 73 -18.753 25.238 43.535 0.00 0.00
ATOM 1 O5' G 73 -16.926 23.779 43.850 0.00 0.00
ATOM 1 N91 G 73 -18.936 24.356 40.172 0.00 0.00
ATOM 1 C1' C 74 -23.189 21.917 40.030 0.00 0.00
ATOM 1 C4' C 74 -24.075 22.730 42.042 0.00 0.00
ATOM 1 O5' C 74 -22.354 22.373 43.663 0.00 0.00
ATOM 1 N91 C 74 -21.931 21.182 39.942 0.00 0.00
ATOM 1 C1' C 75 -24.015 18.930 48.349 0.00 0.00
ATOM 1 C4' C 75 -24.010 18.376 46.120 0.00 0.00
ATOM 1 O5' C 75 -25.259 19.556 44.434 0.00 0.00
ATOM 1 N91 C 75 -24.951 19.159 49.435 0.00 0.00
ATOM 1 C1' A 76 -21.615 13.544 51.242 0.00 0.00
ATOM 1 C4' A 76 -20.694 13.232 49.104 0.00 0.00
ATOM 1 O5' A 76 -22.260 14.246 47.601 0.00 0.00
ATOM 1 N91 A 76 -22.957 14.091 51.419 0.00 0.00

pred_1fir.pdb

ATOM 1 C1' G 1 -29.773 1.195 26.474 0.00 0.00
ATOM 1 C4' G 1 -28.843 -0.729 25.656 0.00 0.00
ATOM 1 O5' G 1 -26.962 -1.128 26.737 0.00 0.00
ATOM 1 N91 G 1 -29.090 2.209 27.385 0.00 0.00
ATOM 1 C1' C 2 -29.508 5.213 22.598 0.00 0.00
ATOM 1 C4' C 2 -29.347 3.526 20.902 0.00 0.00
ATOM 1 O5' C 2 -27.701 2.185 21.704 0.00 0.00
ATOM 1 N91 C 2 -28.522 5.774 23.833 0.00 0.00
ATOM 1 C1' C 3 -27.111 10.107 20.938 0.00 0.00
ATOM 1 C4' C 3 -27.703 9.047 18.615 0.00 0.00
ATOM 1 O5' C 3 -27.374 6.574 18.740 0.00 0.00
ATOM 1 N91 C 3 -26.302 9.688 22.138 0.00 0.00
ATOM 1 C1' C 4 -22.617 13.372 20.735 0.00 0.00
ATOM 1 C4' C 4 -23.269 13.514 18.055 0.00 0.00
ATOM 1 O5' C 4 -24.284 11.357 17.095 0.00 0.00
ATOM 1 N91 C 4 -22.316 12.033 21.605 0.00 0.00
ATOM 1 C1' G 5 -17.677 13.552 21.113 0.00 0.00
ATOM 1 C4' G 5 -17.971 14.364 18.923 0.00 0.00
ATOM 1 O5' G 5 -19.372 13.347 17.343 0.00 0.00
ATOM 1 N91 G 5 -17.903 12.214 21.532 0.00 0.00
ATOM 1 C1' A 7 -8.439 7.624 22.040 0.00 0.00
ATOM 1 C4' A 7 -7.367 9.419 21.600 0.00 0.00
ATOM 1 O5' A 7 -8.432 10.270 19.809 0.00 0.00
ATOM 1 N91 A 7 -9.563 6.906 21.599 0.00 0.00
ATOM 1 C1' U 8 -1.598 9.605 18.068 0.00 0.00
ATOM 1 C4' U 8 -2.019 8.157 19.681 0.00 0.00
ATOM 1 O5' U 8 -3.184 8.473 21.121 0.00 0.00
ATOM 1 N91 U 8 -1.845 10.751 18.170 0.00 0.00
ATOM 1 C1' A 9 6.152 8.738 20.538 0.00 0.00
ATOM 1 C4' A 9 4.647 7.460 21.502 0.00 0.00
ATOM 1 O5' A 9 2.287 7.976 21.469 0.00 0.00
ATOM 1 N91 A 9 6.269 9.757 20.017 0.00 0.00
ATOM 1 C1' C 11 3.577 13.007 28.483 0.00 0.00
ATOM 1 C4' C 11 2.118 11.307 29.276 0.00 0.00
ATOM 1 O5' C 11 2.385 9.395 27.881 0.00 0.00
ATOM 1 N91 C 11 4.306 13.021 27.182 0.00 0.00
ATOM 1 C1' U 12 0.231 17.011 25.858 0.00 0.00
ATOM 1 C4' U 12 -1.373 15.959 27.370 0.00 0.00
ATOM 1 O5' U 12 -1.600 13.463 27.545 0.00 0.00
ATOM 1 N91 U 12 0.964 16.133 24.895 0.00 0.00
ATOM 1 C1' C 13 -1.321 17.826 20.782 0.00 0.00
ATOM 1 C4' C 13 -3.550 18.342 21.767 0.00 0.00
ATOM 1 O5' C 13 -4.111 17.231 23.482 0.00 0.00
ATOM 1 N91 C 13 -0.768 16.548 20.569 0.00 0.00
ATOM 1 C1' A 14 -1.563 18.772 14.784 0.00 0.00
ATOM 1 C4' A 14 -3.426 19.762 15.541 0.00 0.00
ATOM 1 O5' A 14 -4.541 18.876 17.527 0.00 0.00
ATOM 1 N91 A 14 -1.155 17.521 14.898 0.00 0.00
ATOM 1 C1' G 15 -3.220 15.682 10.819 0.00 0.00
ATOM 1 C4' G 15 -4.287 17.845 10.235 0.00 0.00
ATOM 1 O5' G 15 -5.298 18.383 12.005 0.00 0.00
ATOM 1 N91 G 15 -3.366 14.696 11.910 0.00 0.00
ATOM 1 C1' C 17 -11.104 12.578 2.156 0.00 0.00
ATOM 1 C4' C 17 -10.781 13.185 3.801 0.00 0.00
ATOM 1 O5' C 17 -10.033 14.895 4.885 0.00 0.00
ATOM 1 N91 C 17 -11.120 12.845 1.642 0.00 0.00
ATOM 1 C1' G 18 -5.268 8.830 0.135 0.00 0.00
ATOM 1 C4' G 18 -5.558 10.795 1.712 0.00 0.00
ATOM 1 O5' G 18 -6.871 12.483 1.785 0.00 0.00
ATOM 1 N91 G 18 -5.695 8.394 -0.779 0.00 0.00
ATOM 1 C1' G 19 2.149 9.599 1.256 0.00 0.00
ATOM 1 C4' G 19 1.679 9.731 0.972 0.00 0.00
ATOM 1 O5' G 19 0.333 10.957 -0.081 0.00 0.00
ATOM 1 N91 G 19 1.863 10.196 0.953 0.00 0.00
ATOM 1 C1' A 21 3.333 8.926 10.724 0.00 0.00
ATOM 1 C4' A 21 4.479 9.928 9.336 0.00 0.00
ATOM 1 O5' A 21 5.536 8.837 8.050 0.00 0.00
ATOM 1 N91 A 21 3.666 7.689 11.312 0.00 0.00
ATOM 1 C1' G 22 3.561 16.454 11.589 0.00 0.00
ATOM 1 C4' G 22 5.797 15.753 10.530 0.00 0.00
ATOM 1 O5' G 22 7.149 13.520 10.437 0.00 0.00
ATOM 1 N91 G 22 3.137 15.761 12.581 0.00 0.00
ATOM 1 C1' A 23 5.009 19.477 16.128 0.00 0.00
ATOM 1 C4' A 23 6.840 19.987 14.455 0.00 0.00
ATOM 1 O5' A 23 8.090 18.728 13.525 0.00 0.00
ATOM 1 N91 A 23 4.802 18.446 16.696 0.00 0.00
ATOM 1 C1' G 24 5.683 21.518 21.218 0.00 0.00
ATOM 1 C4' G 24 7.234 23.021 20.040 0.00 0.00
ATOM 1 O5' G 24 8.828 21.953 18.512 0.00 0.00
ATOM 1 N91 G 24 5.755 20.079 21.074 0.00 0.00
ATOM 1 C1' C 25 7.141 20.013 25.808 0.00 0.00
ATOM 1 C4' C 25 8.120 22.194 25.722 0.00 0.00
ATOM 1 O5' C 25 9.576 22.479 23.859 0.00 0.00
ATOM 1 N91 C 25 7.448 18.929 24.957 0.00 0.00
ATOM 1 C1' A 26 9.403 15.549 28.509 0.00 0.00
ATOM 1 C4' A 26 9.618 17.397 29.690 0.00 0.00
ATOM 1 O5' A 26 10.668 19.504 28.658 0.00 0.00
ATOM 1 N91 A 26 9.808 15.484 27.368 0.00 0.00
ATOM 1 C1' C 28 19.471 11.404 26.016 0.00 0.00
ATOM 1 C4' C 28 19.516 10.739 28.121 0.00 0.00
ATOM 1 O5' C 28 18.650 12.543 29.802 0.00 0.00
ATOM 1 N91 C 28 19.007 12.612 25.624 0.00 0.00
ATOM 1 C1' A 29 23.396 13.602 23.743 0.00 0.00
ATOM 1 C4' A 29 24.216 12.410 25.369 0.00 0.00
ATOM 1 O5' A 29 23.104 13.078 27.582 0.00 0.00
ATOM 1 N91 A 29 22.466 14.661 23.999 0.00 0.00
ATOM 1 C1' G 30 26.678 17.438 21.786 0.00 0.00
ATOM 1 C4' G 30 28.162 16.296 22.872 0.00 0.00
ATOM 1 O5' G 30 27.740 15.776 25.234 0.00 0.00
ATOM 1 N91 G 30 25.647 17.948 22.408 0.00 0.00
ATOM 1 C1' A 31 27.762 22.728 20.744 0.00 0.00
ATOM 1 C4' A 31 29.880 22.161 20.297 0.00 0.00
ATOM 1 O5' A 31 30.141 20.967 21.776 0.00 0.00
ATOM 1 N91 A 31 26.832 22.547 21.814 0.00 0.00
ATOM 1 C1' C 32 28.238 28.177 23.161 0.00 0.00
ATOM 1 C4' C 32 30.350 28.331 21.925 0.00 0.00
ATOM 1 O5' C 32 31.246 26.682 22.192 0.00 0.00
ATOM 1 N91 C 32 27.641 27.412 24.010 0.00 0.00
ATOM 1 C1' U 33 28.445 30.820 27.904 0.00 0.00
ATOM 1 C4' U 33 29.720 31.949 26.513 0.00 0.00
ATOM 1 O5' U 33 30.766 31.130 25.333 0.00 0.00
ATOM 1 N91 U 33 28.345 29.723 28.163 0.00 0.00
ATOM 1 C1' U 35 30.043 29.725 37.276 0.00 0.00
ATOM 1 C4' U 35 30.708 29.446 35.515 0.00 0.00
ATOM 1 O5' U 35 31.933 31.152 33.450 0.00 0.00
ATOM 1 N91 U 35 29.971 30.221 37.303 0.00 0.00
ATOM 1 C1' U 36 23.856 29.269 38.344 0.00 0.00
ATOM 1 C4' U 36 24.635 27.902 37.453 0.00 0.00
ATOM 1 O5' U 36 26.776 28.865 36.179 0.00 0.00
ATOM 1 N91 U 36 24.164 30.132 38.105 0.00 0.00
ATOM 1 C1' A 38 18.260 29.476 33.501 0.00 0.00
ATOM 1 C4' A 38 17.389 28.152 34.047 0.00 0.00
ATOM 1 O5' A 38 18.692 27.349 34.857 0.00 0.00
ATOM 1 N91 A 38 19.047 29.735 33.160 0.00 0.00
ATOM 1 C1' C 40 19.456 28.138 22.783 0.00 0.00
ATOM 1 C4' C 40 17.342 29.380 22.623 0.00 0.00
ATOM 1 O5' C 40 15.950 28.703 24.437 0.00 0.00
ATOM 1 N91 C 40 19.713 27.075 23.439 0.00 0.00
ATOM 1 C1' U 41 20.637 24.673 17.969 0.00 0.00
ATOM 1 C4' U 41 19.040 26.160 17.231 0.00 0.00
ATOM 1 O5' U 41 17.341 26.439 18.668 0.00 0.00
ATOM 1 N91 U 41 20.626 23.913 18.974 0.00 0.00
ATOM 1 C1' G 42 20.972 19.389 16.960 0.00 0.00
ATOM 1 C4' G 42 20.302 20.434 14.799 0.00 0.00
ATOM 1 O5' G 42 19.148 21.917 14.518 0.00 0.00
ATOM 1 N91 G 42 20.443 19.312 18.014 0.00 0.00
ATOM 1 C1' A 43 19.325 13.960 17.059 0.00 0.00
ATOM 1 C4' A 43 19.406 14.284 14.406 0.00 0.00
ATOM 1 O5' A 43 18.530 16.485 13.189 0.00 0.00
ATOM 1 N91 A 43 18.408 14.593 17.866 0.00 0.00
ATOM 1 C1' G 44 16.957 10.530 18.752 0.00 0.00
ATOM 1 C4' G 44 17.318 9.330 16.484 0.00 0.00
ATOM 1 O5' G 44 17.135 10.200 14.734 0.00 0.00
ATOM 1 N91 G 44 16.307 11.516 18.952 0.00 0.00
ATOM 1 C1' G 45 12.774 8.636 20.150 0.00 0.00
ATOM 1 C4' G 45 13.272 6.654 19.252 0.00 0.00
ATOM 1 O5' G 45 13.987 6.576 17.618 0.00 0.00
ATOM 1 N91 G 45 12.503 9.662 19.473 0.00 0.00
ATOM 1 C1' A 50 -7.990 -3.313 18.903 0.00 0.00
ATOM 1 C4' A 50 -5.763 -3.256 18.683 0.00 0.00
ATOM 1 O5' A 50 -4.989 -1.001 17.875 0.00 0.00
ATOM 1 N91 A 50 -8.737 -2.329 18.384 0.00 0.00
ATOM 1 C1' G 51 -10.250 -6.990 15.645 0.00 0.00
ATOM 1 C4' G 51 -8.229 -7.823 15.699 0.00 0.00
ATOM 1 O5' G 51 -6.203 -6.073 15.993 0.00 0.00
ATOM 1 N91 G 51 -10.396 -5.624 15.333 0.00 0.00
ATOM 1 C1' G 52 -12.419 -7.150 10.827 0.00 0.00
ATOM 1 C4' G 52 -10.873 -8.944 10.631 0.00 0.00
ATOM 1 O5' G 52 -8.363 -8.674 11.352 0.00 0.00
ATOM 1 N91 G 52 -11.940 -5.810 10.793 0.00 0.00
ATOM 1 C1' G 53 -14.110 -4.937 5.947 0.00 0.00
ATOM 1 C4' G 53 -13.630 -7.093 5.160 0.00 0.00
ATOM 1 O5' G 53 -11.478 -7.981 5.822 0.00 0.00
ATOM 1 N91 G 53 -13.174 -3.996 6.335 0.00 0.00
ATOM 1 C1' C 56 -5.086 0.563 -5.777 0.00 0.00
ATOM 1 C4' C 56 -6.006 -1.152 -5.969 0.00 0.00
ATOM 1 O5' C 56 -8.136 -0.741 -6.009 0.00 0.00
ATOM 1 N91 C 56 -5.546 1.660 -5.757 0.00 0.00
ATOM 1 C1' A 57 -3.711 3.159 -1.275 0.00 0.00
ATOM 1 C4' A 57 -3.135 0.805 -0.577 0.00 0.00
ATOM 1 O5' A 57 -4.885 -0.657 -1.526 0.00 0.00
ATOM 1 N91 A 57 -4.936 3.861 -1.735 0.00 0.00
ATOM 1 C1' G 59 -4.488 7.850 10.987 0.00 0.00
ATOM 1 C4' G 59 -4.635 5.433 10.933 0.00 0.00
ATOM 1 O5' G 59 -3.235 4.663 9.383 0.00 0.00
ATOM 1 N91 G 59 -4.127 8.864 10.128 0.00 0.00
ATOM 1 C1' U 60 -8.370 8.818 7.813 0.00 0.00
ATOM 1 C4' U 60 -9.677 7.890 9.399 0.00 0.00
ATOM 1 O5' U 60 -8.913 6.057 9.454 0.00 0.00
ATOM 1 N91 U 60 -7.105 8.513 7.128 0.00 0.00
ATOM 1 C1' C 61 -13.939 5.457 5.544 0.00 0.00
ATOM 1 C4' C 61 -14.408 7.487 6.108 0.00 0.00
ATOM 1 O5' C 61 -12.675 8.143 7.635 0.00 0.00
ATOM 1 N91 C 61 -13.017 4.767 6.119 0.00 0.00
ATOM 1 C1' C 62 -17.737 1.122 7.592 0.00 0.00
ATOM 1 C4' C 62 -19.035 3.131 7.331 0.00 0.00
ATOM 1 O5' C 62 -17.528 4.901 8.011 0.00 0.00
ATOM 1 N91 C 62 -16.491 1.223 7.992 0.00 0.00
ATOM 1 C1' C 63 -19.061 -1.702 11.330 0.00 0.00
ATOM 1 C4' C 63 -20.939 -0.429 11.090 0.00 0.00
ATOM 1 O5' C 63 -20.275 1.788 10.949 0.00 0.00
ATOM 1 N91 C 63 -17.794 -1.062 11.499 0.00 0.00
ATOM 1 C1' U 64 -18.332 -4.001 15.113 0.00 0.00
ATOM 1 C4' U 64 -20.533 -3.760 15.057 0.00 0.00
ATOM 1 O5' U 64 -21.133 -1.854 14.690 0.00 0.00
ATOM 1 N91 U 64 -17.472 -2.976 15.097 0.00 0.00
ATOM 1 C1' G 65 -15.902 -4.854 20.268 0.00 0.00
ATOM 1 C4' G 65 -18.238 -5.589 20.773 0.00 0.00
ATOM 1 O5' G 65 -19.992 -3.975 20.021 0.00 0.00
ATOM 1 N91 G 65 -15.680 -3.583 19.808 0.00 0.00
ATOM 1 C1' U 66 -13.116 -1.942 24.316 0.00 0.00
ATOM 1 C4' U 66 -14.259 -3.464 25.226 0.00 0.00
ATOM 1 O5' U 66 -16.223 -3.355 24.749 0.00 0.00
ATOM 1 N91 U 66 -13.507 -1.098 23.505 0.00 0.00
ATOM 1 C1' U 67 -12.189 2.514 27.698 0.00 0.00
ATOM 1 C4' U 67 -12.637 1.046 29.225 0.00 0.00
ATOM 1 O5' U 67 -14.406 -0.270 29.023 0.00 0.00
ATOM 1 N91 U 67 -12.806 2.661 26.758 0.00 0.00
ATOM 1 C1' C 68 -12.807 7.462 29.169 0.00 0.00
ATOM 1 C4' C 68 -12.524 6.543 31.163 0.00 0.00
ATOM 1 O5' C 68 -13.622 4.503 31.458 0.00 0.00
ATOM 1 N91 C 68 -13.639 7.105 28.234 0.00 0.00
ATOM 1 C1' G 69 -15.833 12.696 29.138 0.00 0.00
ATOM 1 C4' G 69 -15.071 12.854 31.295 0.00 0.00
ATOM 1 O5' G 69 -15.138 10.912 32.154 0.00 0.00
ATOM 1 N91 G 69 -16.488 11.607 28.497 0.00 0.00
ATOM 1 C1' G 70 -20.332 15.176 28.086 0.00 0.00
ATOM 1 C4' G 70 -19.626 16.122 30.000 0.00 0.00
ATOM 1 O5' G 70 -19.001 14.629 31.565 0.00 0.00
ATOM 1 N91 G 70 -20.571 13.737 27.848 0.00 0.00
ATOM 1 C1' G 71 -25.702 14.569 27.550 0.00 0.00
ATOM 1 C4' G 71 -25.568 16.328 29.077 0.00 0.00
ATOM 1 O5' G 71 -24.277 16.025 30.922 0.00 0.00
ATOM 1 N91 G 71 -25.357 13.214 27.721 0.00 0.00
ATOM 1 C1' C 72 -30.892 11.916 28.051 0.00 0.00
ATOM 1 C4' C 72 -31.343 14.115 28.531 0.00 0.00
ATOM 1 O5' C 72 -30.172 15.167 29.903 0.00 0.00
ATOM 1 N91 C 72 -30.125 11.144 28.745 0.00 0.00
ATOM 1 C1' G 73 -33.774 8.629 28.051 0.00 0.00
ATOM 1 C4' G 73 -35.574 10.382 27.628 0.00 0.00
ATOM 1 O5' G 73 -35.273 11.886 28.653 0.00 0.00
ATOM 1 N91 G 73 -32.749 8.493 28.891 0.00 0.00
ATOM 1 C1' C 74 -36.031 8.704 32.826 0.00 0.00
ATOM 1 C4' C 74 -37.721 8.806 31.740 0.00 0.00
ATOM 1 O5' C 74 -37.586 9.739 31.917 0.00 0.00
ATOM 1 N91 C 74 -35.093 9.647 33.533 0.00 0.00
ATOM 1 C1' C 75 -38.036 5.406 37.594 0.00 0.00
ATOM 1 C4' C 75 -38.814 5.096 36.469 0.00 0.00
ATOM 1 O5' C 75 -38.314 5.967 36.001 0.00 0.00
ATOM 1 N91 C 75 -37.228 6.484 38.042 0.00 0.00
ATOM 1 C1' A 76 -41.570 2.947 35.569 0.00 0.00
ATOM 1 C4' A 76 -42.352 2.862 34.664 0.00 0.00
ATOM 1 O5' A 76 -41.690 3.979 34.281 0.00 0.00
ATOM 1 N91 A 76 -41.392 3.030 35.657 0.00 0.00

mmagnus commented 2 years ago

@pengzhangzhi yeah, sorry for that, ClaRNA program is missing, I'm not sure what was the deal to share the code of the tool, have to check that.

In the meantime, you can use the server

http://rna-tools.online/tools/calc-inf/

or

http://rna-tools.online/tools/clarna/

mmagnus commented 2 years ago

I tried with your files, http://rna-tools.online/tools/calc-inf/761b9b3a but something it's wrong, can you upload the original files and let me know if you get non-0 result

pengzhangzhi commented 2 years ago

I have send you a email: Consulting Problems About rna-tools, where I propose a new problem. The current problem have been solved in a hack way :-)

pengzhangzhi commented 2 years ago

Also, I have a problem which is not regarding to this issue. Do you know any tools (software) that can visualize RNA 3D structure? Sorry for such a stupid question. I am a researcher from computer science, who wants to advance the bio using Machine Learning.

mmagnus commented 2 years ago

It's fine. We all are learing something new ;-) I recommend to use PYMOL https://pymol.org/2/

pengzhangzhi commented 2 years ago

I tried with your files, http://rna-tools.online/tools/calc-inf/761b9b3a but something it's wrong, can you upload the original files and let me know if you get non-0 result

What do you mean original file? The two file are just contains the coordinates of four atoms.

mmagnus commented 2 years ago

Yeah, but I can't open it with PYMOL. This should be the PDB format, the format is a bit old fashion, and needs correct position of x,y,z and other data into like 80-column format.

I guess we lost this information when you copy-pasted the content into this issue: sc 2022-04-08 at 11 05 02 pred_1fir.pdb.zip (you can zip files and attach them here)

pengzhangzhi commented 2 years ago

I give you the original pdb files, which is a little complicated. The native contains bad atoms. The pred predicts four atoms of a bad atoms. So I preprocess the two pdb files (delete bad atoms and corresponding predicted atoms) to match the length. I think this is the problem? My collaborator said we use 80-column format original.zip .

mmagnus commented 2 years ago

How did you get this file? This seems like some coarse-grain representation of a PDB file, only 4 atoms per RNA residue, so it's hard to do INF (because it is based on interactions of "real" residues, you can calculate RMSD, it's a geometrical score of anything, points):

ATOM      1  C1' G    1        -29.773   1.195  26.474  0.00  0.00              
ATOM      1  C4' G    1        -28.843  -0.729  25.656  0.00  0.00              
ATOM      1  O5' G    1        -26.962  -1.128  26.737  0.00  0.00              
ATOM      1  N91 G    1        -29.090   2.209  27.385  0.00  0.00              
ATOM      1  C1' C    2        -29.508   5.213  22.598  0.00  0.00

This should be reconstructed into the full-atom model to be run with our tools on the website.

pengzhangzhi commented 2 years ago

How did you get this file? This seems like some coarse-grain representation of a PDB file, only 4 atoms per RNA residue, so it's hard to do INF (because it is based on interactions of "real" residues, you can calculate RMSD, it's a geometrical score of anything, points):

ATOM      1  C1' G    1        -29.773   1.195  26.474  0.00  0.00              
ATOM      1  C4' G    1        -28.843  -0.729  25.656  0.00  0.00              
ATOM      1  O5' G    1        -26.962  -1.128  26.737  0.00  0.00              
ATOM      1  N91 G    1        -29.090   2.209  27.385  0.00  0.00              
ATOM      1  C1' C    2        -29.508   5.213  22.598  0.00  0.00

This should be reconstructed into the full-atom model to be run with our tools on the website.

I think the same way. Thanks sooo much for your kind response!

mmagnus commented 2 years ago

I have to fix this issue in a better way.