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[ccp4bb]: Bug in HGEN (fwd)
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>From dpal@imb-jena.de Mon Oct 15 11:56:33 2001
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Date: Mon, 15 Oct 2001 11:56:31 +0200
From: Debnath Pal <dpal@imb-jena.de>
To: Tom Sicker <sicker@fuzzy.imb-jena.de>
Subject: Bug
Message-ID: <Pine.SGI.4.33.0110151122110.64321-100000@fuzzy.imb-jena.de>
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There appears to be a bug in the HGEN program, which is used to fix
stereochemical hydrogen atoms to the heavy atoms in the PDB. The 'TER'
record is misplaced and the last residue is put beyond the 'TER' card.
Also, if there are heteroatom records after the 'TER' card the 'ATOM'
label is replaced by 'HETATM' label.
Input:
ATOM 631 CA ALA A 81 11.405 38.847 4.515 1.00 21.87 C
ATOM 632 C ALA A 81 10.957 39.844 5.588 1.00 21.05 C
ATOM 633 O ALA A 81 9.742 40.080 5.804 1.00 19.43 O
ATOM 634 CB ALA A 81 11.637 39.471 3.131 1.00 22.88 C
ATOM 635 N ALA A 82 11.934 40.303 6.379 1.00 20.38 N
ATOM 636 CA ALA A 82 11.645 41.348 7.407 1.00 20.77 C
ATOM 637 C ALA A 82 11.215 42.634 6.689 1.00 22.11 C
ATOM 638 O ALA A 82 11.514 42.915 5.490 1.00 21.00 O
ATOM 639 CB ALA A 82 12.815 41.482 8.313 1.00 19.87 C
ATOM 640 N PRO A 83 10.223 43.316 7.303 1.00 22.85 N
ATOM 641 CA PRO A 83 9.635 44.502 6.677 1.00 23.42 C
ATOM 642 C PRO A 83 10.678 45.611 6.415 1.00 23.17 C
ATOM 643 O PRO A 83 11.645 45.669 7.203 0.50 19.06 O
ATOM 644 CB PRO A 83 8.488 44.894 7.590 1.00 24.37 C
ATOM 645 CG PRO A 83 8.646 44.090 8.838 1.00 25.23 C
ATOM 646 CD PRO A 83 9.741 43.079 8.659 0.50 23.00 C
ATOM 647 OXT PRO A 83 10.572 46.241 5.325 0.50 15.91 O
TER 648 PRO A 83
ATOM 649 N ASP B 0 25.173 21.699 5.957 1.00 18.03 N
Output:
ATOM 1206 CA ALA A 81 11.405 38.847 4.515 1.00 21.87 C
ATOM 1207 H1A ALA A 81 12.272 38.447 4.811 1.00 21.87 H
ATOM 1208 C ALA A 81 10.957 39.844 5.588 1.00 21.05 C
ATOM 1209 O ALA A 81 9.742 40.080 5.804 1.00 19.43 O
ATOM 1210 CB ALA A 81 11.637 39.471 3.131 1.00 22.88 C
ATOM 1211 H1B ALA A 81 10.788 39.888 2.807 1.00 22.88 H
ATOM 1212 H2B ALA A 81 12.349 40.171 3.196 1.00 22.88 H
ATOM 1213 H3B ALA A 81 11.926 38.761 2.489 1.00 22.88 H
ATOM 1214 N ALA A 82 11.934 40.303 6.379 1.00 20.38 N
ATOM 1215 H1 ALA A 82 12.862 39.945 6.282 1.00 20.38 H
ATOM 1216 CA ALA A 82 11.645 41.348 7.407 1.00 20.77 C
ATOM 1217 H1A ALA A 82 10.758 40.985 7.692 1.00 20.77 H
ATOM 1218 C ALA A 82 11.215 42.634 6.689 1.00 22.11 C
ATOM 1219 O ALA A 82 11.514 42.915 5.490 1.00 21.00 O
ATOM 1220 CB ALA A 82 12.815 41.482 8.313 1.00 19.87 C
ATOM 1221 H1B ALA A 82 13.609 41.791 7.789 1.00 19.87 H
ATOM 1222 H2B ALA A 82 12.608 42.149 9.029 1.00 19.87 H
ATOM 1223 H3B ALA A 82 13.016 40.596 8.731 1.00 19.87 H
TER 648 PRO A 83
ATOM 1224 N PRO A 83 10.223 43.316 7.303 1.00 22.85 N
ATOM 1225 CA PRO A 83 9.635 44.502 6.677 1.00 23.42 C
ATOM 1226 H1A PRO A 83 9.068 44.098 5.959 1.00 23.42 H
ATOM 1227 C PRO A 83 10.678 45.611 6.415 1.00 23.17 C
ATOM 1228 O PRO A 83 11.645 45.669 7.203 0.50 19.06 O
ATOM 1229 CB PRO A 83 8.488 44.894 7.590 1.00 24.37 C
ATOM 1230 H1B PRO A 83 8.532 45.871 7.800 1.00 24.37 H
ATOM 1231 H2B PRO A 83 7.613 44.686 7.154 1.00 24.37 H
ATOM 1232 CG PRO A 83 8.646 44.090 8.838 1.00 25.23 C
ATOM 1233 H1G PRO A 83 8.877 44.698 9.597 1.00 25.23 H
ATOM 1234 H2G PRO A 83 7.788 43.617 9.039 1.00 25.23 H
ATOM 1235 CD PRO A 83 9.741 43.079 8.659 0.50 23.00 C
ATOM 1236 H1D PRO A 83 10.471 43.224 9.326 0.50 23.00 H
ATOM 1237 H2D PRO A 83 9.385 42.149 8.752 0.50 23.00 H
ATOM 1238 OXT PRO A 83 10.572 46.241 5.325 0.50 15.91 O
ATOM 1239 N ASP B 0 25.173 21.699 5.957 1.00 18.03 N
Input:
ATOM 1289 CB ALA B 82 13.908 14.200 11.230 1.00 9.39 C
ATOM 1290 N PRO B 83 16.658 12.888 12.677 1.00 13.07 N
ATOM 1291 CA PRO B 83 17.314 11.618 13.048 1.00 14.99 C
ATOM 1292 C PRO B 83 16.282 10.486 13.227 1.00 14.34 C
ATOM 1293 O PRO B 83 15.111 10.765 13.511 1.00 15.71 O
ATOM 1294 CB PRO B 83 18.088 12.005 14.310 1.00 13.01 C
ATOM 1295 CG PRO B 83 17.039 12.890 14.991 1.00 14.29 C
ATOM 1296 CD PRO B 83 16.613 13.814 13.818 1.00 13.99 C
ATOM 1297 OXT PRO B 83 16.689 9.313 13.016 1.00 16.58 O
TER 1298 PRO B 83
Output:
ATOM 2458 CA ALA B 82 15.443 14.418 11.227 1.00 12.01 C
ATOM 2459 H1A ALA B 82 15.691 15.074 11.940 1.00 12.01 H
ATOM 2460 C ALA B 82 16.164 13.073 11.464 1.00 14.35 C
ATOM 2461 O ALA B 82 16.316 12.250 10.526 1.00 13.20 O
ATOM 2462 CB ALA B 82 13.908 14.200 11.230 1.00 9.39 C
ATOM 2463 H1B ALA B 82 13.661 13.560 10.502 1.00 9.39 H
ATOM 2464 H2B ALA B 82 13.626 13.825 12.113 1.00 9.39 H
ATOM 2465 H3B ALA B 82 13.447 15.074 11.076 1.00 9.39 H
TER 1298 PRO B 83
HETATM 2466 N PRO B 83 16.658 12.888 12.677 1.00 13.07 N
HETATM 2467 CA PRO B 83 17.314 11.618 13.048 1.00 14.99 C
HETATM 2468 H1A PRO B 83 18.105 11.305 12.523 1.00 14.99 H
HETATM 2469 C PRO B 83 16.282 10.486 13.227 1.00 14.34 C
HETATM 2470 O PRO B 83 15.111 10.765 13.511 1.00 15.71 O
HETATM 2471 CB PRO B 83 18.088 12.005 14.310 1.00 13.01 C
HETATM 2472 H1B PRO B 83 18.319 11.206 14.865 1.00 13.01 H
HETATM 2473 H2B PRO B 83 18.922 12.513 14.095 1.00 13.01 H
HETATM 2474 CG PRO B 83 17.039 12.890 14.991 1.00 14.29 C
HETATM 2475 H1G PRO B 83 16.269 12.350 15.330 1.00 14.29 H
HETATM 2476 H2G PRO B 83 17.436 13.414 15.745 1.00 14.29 H
HETATM 2477 CD PRO B 83 16.613 13.814 13.818 1.00 13.99 C
HETATM 2478 H1D PRO B 83 15.692 14.177 13.956 1.00 13.99 H
HETATM 2479 H2D PRO B 83 17.255 14.571 13.699 1.00 13.99 H
HETATM 2480 OXT PRO B 83 16.689 9.313 13.016 1.00 16.58 O
--
Tom Sicker sicker@imb-jena.de
Institut fuer Molekulare Biotechnologie
Beutenbergstrasse 11 Tel.: +49-3641-65-6081
D-07745 Jena, Germany Fax: +49-3641-65-6062