Hi all, This really annoying thing kept happening to me where the H5' hydrogen would fly off when I refined RNA. Now I finally found out why!
After comparing the pdb output from coot (Ideal DNA/RNA tool) with my file (hydrogens added by phenix.ready_set), I noticed that in my structure, the atom name of the H5' atom was differently indented then from the coot file. So I changed from having the extra space before the atom name to after, and then it behaved as expected. I've attached a short PDB file below, where the first nucleotide is "broken" and the second one can be refined/regularized properly without having the H5' fly away. I'm not sure if there is an official stance regarding the spacing of the atom names in the PDB standard and I don't know if the coot or the phenix version is correct, but perhaps coot should be made less sensitive to the atom name spacing to avoid this problem. Regards, Daniel ATOM 10519 P G I 7 170.602 248.626 268.016 1.00115.63 P ATOM 10520 OP1 G I 7 171.072 248.442 266.615 1.00112.87 O ATOM 10521 OP2 G I 7 171.027 247.678 269.076 1.00113.68 O ATOM 10522 O5' G I 7 171.107 250.064 268.478 1.00110.56 O ATOM 10523 C5' G I 7 170.242 251.007 269.081 1.00108.26 C ATOM 10524 C4' G I 7 170.718 251.393 270.456 1.00109.87 C ATOM 10525 O4' G I 7 169.946 250.701 271.478 1.00115.20 O ATOM 10526 C3' G I 7 172.154 251.073 270.834 1.00108.89 C ATOM 10527 O3' G I 7 173.106 251.949 270.289 1.00108.65 O ATOM 10528 C2' G I 7 172.105 251.168 272.348 1.00113.37 C ATOM 10529 O2' G I 7 172.086 252.521 272.785 1.00114.75 O ATOM 10530 C1' G I 7 170.754 250.517 272.632 1.00113.97 C ATOM 10531 N9 G I 7 170.900 249.082 272.931 1.00112.09 N ATOM 10532 C8 G I 7 170.778 247.991 272.098 1.00110.38 C ATOM 10533 N7 G I 7 170.991 246.860 272.717 1.00111.14 N ATOM 10534 C5 G I 7 171.287 247.230 274.030 1.00111.25 C ATOM 10535 C6 G I 7 171.611 246.446 275.174 1.00112.33 C ATOM 10536 O6 G I 7 171.709 245.212 275.269 1.00112.15 O ATOM 10537 N1 G I 7 171.839 247.246 276.297 1.00113.66 N ATOM 10538 C2 G I 7 171.762 248.623 276.326 1.00112.68 C ATOM 10539 N2 G I 7 172.018 249.215 277.502 1.00111.61 N ATOM 10540 N3 G I 7 171.462 249.361 275.266 1.00111.87 N ATOM 10541 C4 G I 7 171.239 248.600 274.170 1.00111.37 C ATOM 10542 H5' G I 7 169.351 250.642 269.149 1.00108.26 H ATOM 10543 H5'' G I 7 170.212 251.802 268.526 1.00108.26 H ATOM 10544 H4' G I 7 170.579 252.340 270.569 1.00109.87 H ATOM 10545 H3' G I 7 172.363 250.162 270.576 1.00108.89 H ATOM 10546 H2' G I 7 172.829 250.669 272.757 1.00113.37 H ATOM 10547 HO2' G I 7 171.299 252.737 272.981 1.00114.75 H ATOM 10548 H1' G I 7 170.337 250.958 273.388 1.00113.97 H ATOM 10549 H8 G I 7 170.549 248.052 271.200 1.00110.38 H ATOM 10550 H1 G I 7 172.041 246.847 277.031 1.00113.66 H ATOM 10551 H21 G I 7 172.213 248.738 278.190 1.00111.61 H ATOM 10552 H22 G I 7 171.987 250.072 277.568 1.00111.61 H ATOM 10553 P C I 8 174.489 251.382 269.706 1.00110.40 P ATOM 10554 OP1 C I 8 175.155 252.470 268.938 1.00110.65 O ATOM 10555 OP2 C I 8 174.263 250.086 269.018 1.00107.72 O ATOM 10556 O5' C I 8 175.298 251.101 271.052 1.00107.15 O ATOM 10557 C5' C I 8 175.702 252.176 271.888 1.00107.36 C ATOM 10558 C4' C I 8 176.085 251.708 273.272 1.00110.04 C ATOM 10559 O4' C I 8 174.983 250.998 273.907 1.00113.31 O ATOM 10560 C3' C I 8 177.216 250.706 273.355 1.00111.09 C ATOM 10561 O3' C I 8 178.482 251.285 273.112 1.00112.60 O ATOM 10562 C2' C I 8 177.026 250.156 274.758 1.00110.67 C ATOM 10563 O2' C I 8 177.417 251.090 275.750 1.00110.46 O ATOM 10564 C1' C I 8 175.503 250.003 274.778 1.00112.45 C ATOM 10565 N1 C I 8 175.083 248.653 274.319 1.00110.99 N ATOM 10566 C2 C I 8 175.114 247.598 275.243 1.00108.78 C ATOM 10567 O2 C I 8 175.450 247.826 276.414 1.00109.82 O ATOM 10568 N3 C I 8 174.764 246.352 274.858 1.00107.91 N ATOM 10569 C4 C I 8 174.409 246.118 273.596 1.00109.91 C ATOM 10570 N4 C I 8 174.067 244.866 273.276 1.00110.74 N ATOM 10571 C5 C I 8 174.379 247.162 272.616 1.00109.08 C ATOM 10572 C6 C I 8 174.729 248.398 273.014 1.00110.01 C ATOM 10573 H5' C I 8 174.971 252.810 271.961 1.00107.36 H ATOM 10574 H5'' C I 8 176.464 252.620 271.484 1.00107.36 H ATOM 10575 H4' C I 8 176.312 252.481 273.812 1.00110.04 H ATOM 10576 H3' C I 8 177.061 249.997 272.711 1.00111.09 H ATOM 10577 H2' C I 8 177.471 249.301 274.870 1.00110.67 H ATOM 10578 HO2' C I 8 178.243 251.227 275.688 1.00110.46 H ATOM 10579 H1' C I 8 175.174 250.158 275.677 1.00112.45 H ATOM 10580 H41 C I 8 173.832 244.677 272.471 1.00110.74 H ATOM 10581 H42 C I 8 174.082 244.250 273.876 1.00110.74 H ATOM 10582 H5 C I 8 174.125 246.992 271.738 1.00109.08 H ATOM 10583 H6 C I 8 174.720 249.095 272.399 1.00110.01 H När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. 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