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PDBPARSE documentation |
/ebi/services/idata/pmr/hgmp/test/data/structure/pdb1cs4.ent SEQRESLENDIF 1 (A) ATOMCOL12 429 BADINDEX 1 (A) GAPPEDOK 1 (A) SECSTART 1 1 ILE 384 SECSTART 1 1 ILE 384 // /ebi/services/idata/pmr/hgmp/test/data/structure/pdb1ii7.ent SEQRESLENDIF 1 (A) ATOMCOL12 390 SECBOTH 1 1 SER 57 GLU 73 SECBOTH 1 1 VAL 78 ILE 81 SECBOTH 1 1 LYS 2 LEU 6 // |
ID 1cs4 XX DE MOL_ID: 1; MOLECULE: TYPE V ADENYLATE CYCLASE; XX OS MOL_ID: 1; ORGANISM_SCIENTIFIC: CANIS FAMILIARIS; XX EX METHOD xray; RESO 2.50; NMOD 1; NCHN 1; NGRP 0; XX CN [1] XX IN ID A; NR 52; NL 7; NH 0; NE 0; XX SQ SEQUENCE 52 AA; 5817 MW; 47362A43 CRC32; ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS XX CO 1 1 . P 2 396 . . . . . . D ASP N 51.711 -11.782 62.798 1.00 51.17 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 2 396 . . . . . . D ASP CA 52.810 -11.644 61.848 1.00 54.45 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 2 396 . . . . . . D ASP C 54.137 -11.314 62.530 1.00 55.11 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 2 396 . . . . . . D ASP O 54.175 -10.524 63.469 1.00 55.34 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 2 396 . . . . . . D ASP CB 52.437 -10.555 60.831 1.00 57.50 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 2 396 . . . . . . D ASP CG 53.460 -10.391 59.729 1.00 61.38 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 2 396 . . . . . . D ASP OD1 54.316 -9.485 59.841 1.00 65.55 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 2 396 . . . . . . D ASP OD2 53.390 -11.146 58.736 1.00 63.68 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 3 397 . . . . . . I ILE N 55.216 -11.941 62.066 1.00 57.14 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 3 397 . . . . . . I ILE CA 56.546 -11.705 62.624 1.00 59.46 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 3 397 . . . . . . I ILE C 57.020 -10.305 62.230 1.00 60.12 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 3 397 . . . . . . I ILE O 56.963 -9.927 61.060 1.00 59.12 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 3 397 . . . . . . I ILE CB 57.583 -12.722 62.094 1.00 60.84 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 3 397 . . . . . . I ILE CG1 57.184 -14.163 62.447 1.00 63.12 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 3 397 . . . . . . I ILE CG2 58.975 -12.384 62.632 1.00 61.24 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 3 397 . . . . . . I ILE CD1 57.408 -14.554 63.895 1.00 63.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 4 398 . . . . . . E GLU N 57.492 -9.548 63.212 1.00 60.23 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 4 398 . . . . . . E GLU CA 57.975 -8.198 62.971 1.00 62.14 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 4 398 . . . . . . E GLU C 59.401 -8.277 62.424 1.00 60.59 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 4 398 . . . . . . E GLU O 60.244 -8.972 62.987 1.00 61.84 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 4 398 . . . . . . E GLU CB 57.917 -7.386 64.272 1.00 65.47 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 4 398 . . . . . . E GLU CG 58.037 -5.874 64.091 1.00 70.25 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 4 398 . . . . . . E GLU CD 57.588 -5.089 65.324 1.00 72.94 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 4 398 . . . . . . E GLU OE1 58.262 -5.175 66.377 1.00 70.76 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 4 398 . . . . . . E GLU OE2 56.555 -4.380 65.232 1.00 74.36 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 5 399 H 1 1 1 . . G GLY N 59.642 -7.608 61.298 1.00 57.58 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 5 399 H 1 1 1 . . G GLY CA 60.956 -7.615 60.681 1.00 56.14 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 5 399 H 1 1 1 . . G GLY C 61.452 -8.993 60.265 1.00 58.03 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 5 399 H 1 1 1 . . G GLY O 62.620 -9.322 60.480 1.00 57.47 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 6 400 H 1 1 1 . . F PHE N 60.576 -9.789 59.649 1.00 58.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 6 400 H 1 1 1 . . F PHE CA 60.914 -11.143 59.200 1.00 58.07 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 6 400 H 1 1 1 . . F PHE C 61.995 -11.219 58.117 1.00 58.57 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 6 400 H 1 1 1 . . F PHE O 62.862 -12.091 58.161 1.00 59.44 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 6 400 H 1 1 1 . . F PHE CB 59.657 -11.881 58.734 1.00 59.18 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 6 400 H 1 1 1 . . F PHE CG 59.900 -13.316 58.322 1.00 58.53 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 [Part of this file has been deleted for brevity] CO 1 1 5 H . 1002 . . . . . . . FOK C9 42.200 -11.309 50.489 1.00 41.39 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 1002 . . . . . . . FOK O6 42.275 -12.455 49.593 1.00 43.23 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 1002 . . . . . . . FOK C10 43.008 -11.601 51.811 1.00 39.11 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 1002 . . . . . . . FOK C11 40.680 -11.078 50.616 1.00 44.36 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 1002 . . . . . . . FOK O7 40.106 -10.945 51.688 1.00 48.77 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 1002 . . . . . . . FOK C12 39.943 -11.046 49.301 1.00 40.67 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 1002 . . . . . . . FOK C13 40.595 -10.085 48.292 1.00 41.47 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 1002 . . . . . . . FOK C14 40.276 -10.620 46.930 1.00 46.69 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 1002 . . . . . . . FOK C15 39.971 -11.751 46.590 1.00 53.22 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 1002 . . . . . . . FOK C16 40.047 -8.685 48.426 1.00 42.42 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 1002 . . . . . . . FOK C17 42.671 -8.737 50.253 1.00 39.67 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 1002 . . . . . . . FOK C18 46.732 -13.026 51.827 1.00 35.74 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 1002 . . . . . . . FOK C19 45.859 -11.483 53.586 1.00 34.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 1002 . . . . . . . FOK C20 42.913 -10.426 52.807 1.00 39.44 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 1002 . . . . . . . FOK C21 45.883 -9.553 47.821 1.00 42.15 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 1002 . . . . . . . FOK O5 46.157 -10.520 47.166 1.00 40.91 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 1002 . . . . . . . FOK C22 46.769 -8.315 48.006 1.00 37.08 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1003 . . . . . . . MES O1 45.676 7.326 49.092 1.00 77.86 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1003 . . . . . . . MES C2 44.367 6.816 48.900 1.00 75.17 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1003 . . . . . . . MES C3 44.349 5.317 48.923 1.00 74.42 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1003 . . . . . . . MES N4 44.832 4.804 50.196 1.00 72.45 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1003 . . . . . . . MES C5 46.234 5.425 50.473 1.00 73.23 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1003 . . . . . . . MES C6 46.176 6.914 50.355 1.00 75.06 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1003 . . . . . . . MES C7 44.806 3.336 50.302 1.00 73.39 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1003 . . . . . . . MES C8 44.672 2.791 51.713 1.00 76.85 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1003 . . . . . . . MES S 45.724 1.379 51.967 1.00 78.26 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1003 . . . . . . . MES O1S 47.062 1.828 51.737 1.00 79.39 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1003 . . . . . . . MES O2S 45.303 0.380 51.016 1.00 81.58 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1003 . . . . . . . MES O3S 45.523 0.961 53.326 1.00 80.59 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1004 . . . . . . . MES O1 59.246 -5.152 27.381 1.00 99.99 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1004 . . . . . . . MES C2 60.067 -4.021 27.127 1.00 99.99 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1004 . . . . . . . MES C3 60.447 -3.301 28.378 1.00 99.78 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1004 . . . . . . . MES N4 61.180 -4.156 29.270 1.00 96.33 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1004 . . . . . . . MES C5 60.358 -5.461 29.506 1.00 97.90 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1004 . . . . . . . MES C6 59.965 -6.072 28.203 1.00 99.68 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1004 . . . . . . . MES C7 61.596 -3.484 30.507 1.00 93.33 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1004 . . . . . . . MES C8 61.931 -2.010 30.442 1.00 90.74 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1004 . . . . . . . MES S 60.763 -0.978 31.301 0.50 90.72 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1004 . . . . . . . MES O1S 59.476 -1.170 30.680 0.50 91.60 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1004 . . . . . . . MES O2S 61.249 0.383 31.164 0.50 91.20 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 1004 . . . . . . . MES O3S 60.776 -1.430 32.647 0.50 90.05 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 7 H . 1005 . . . . . . . POP P1 58.812 -7.766 57.091 1.00 57.40 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 7 H . 1005 . . . . . . . POP O1 60.254 -7.589 56.745 1.00 54.93 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 7 H . 1005 . . . . . . . POP O2 58.618 -8.839 58.095 1.00 55.36 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 7 H . 1005 . . . . . . . POP O3 57.949 -8.024 55.908 1.00 55.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 7 H . 1005 . . . . . . . POP O 58.295 -6.370 57.759 1.00 57.30 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 7 H . 1005 . . . . . . . POP P2 56.998 -5.955 58.661 1.00 59.66 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 7 H . 1005 . . . . . . . POP O4 57.491 -5.746 60.070 1.00 54.95 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 7 H . 1005 . . . . . . . POP O5 56.004 -7.075 58.550 1.00 56.24 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 7 H . 1005 . . . . . . . POP O6 56.427 -4.710 58.044 1.00 56.50 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 // |
ID 1ii7 XX DE MOL_ID: 1; MOLECULE: MRE11 NUCLEASE; XX OS MOL_ID: 1; ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; XX EX METHOD xray; RESO 2.20; NMOD 1; NCHN 1; NGRP 0; XX CN [1] XX IN ID A; NR 65; NL 6; NH 0; NE 0; XX SQ SEQUENCE 65 AA; 7396 MW; 0CFB92A3 CRC32; MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT LKKAI XX CO 1 1 . P 8 8 . . . . . . D ASP N 7.977 32.254 19.055 1.00 26.65 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 8 8 . . . . . . D ASP CA 8.882 31.149 19.290 1.00 28.34 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 8 8 . . . . . . D ASP C 10.273 31.305 18.659 1.00 27.71 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 8 8 . . . . . . D ASP O 10.740 30.453 17.907 1.00 29.27 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 8 8 . . . . . . D ASP CB 8.186 29.886 18.777 1.00 30.25 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 8 8 . . . . . . D ASP CG 6.918 29.584 19.554 1.00 34.25 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 8 8 . . . . . . D ASP OD1 7.041 29.177 20.724 1.00 33.37 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 8 8 . . . . . . D ASP OD2 5.801 29.770 19.010 1.00 35.77 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 9 9 . . . . . . I ILE N 10.913 32.423 18.967 1.00 26.84 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 9 9 . . . . . . I ILE CA 12.236 32.739 18.477 1.00 26.52 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 9 9 . . . . . . I ILE C 13.285 31.864 19.173 1.00 28.22 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 9 9 . . . . . . I ILE O 14.257 31.426 18.550 1.00 28.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 9 9 . . . . . . I ILE CB 12.520 34.214 18.759 1.00 27.25 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 9 9 . . . . . . I ILE CG1 11.338 35.051 18.249 1.00 26.35 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 9 9 . . . . . . I ILE CG2 13.823 34.640 18.094 1.00 26.40 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 9 9 . . . . . . I ILE CD1 11.011 34.845 16.725 1.00 25.85 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 10 10 . . . . . . H HIS N 13.072 31.599 20.462 1.00 26.69 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 10 10 . . . . . . H HIS CA 14.009 30.787 21.254 1.00 28.02 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 10 10 . . . . . . H HIS C 15.483 31.203 21.181 1.00 27.57 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 10 10 . . . . . . H HIS O 16.357 30.359 21.019 1.00 23.99 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 10 10 . . . . . . H HIS CB 13.867 29.284 20.899 1.00 27.15 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 10 10 . . . . . . H HIS CG 12.599 28.681 21.415 1.00 28.59 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 10 10 . . . . . . H HIS ND1 12.536 27.980 22.603 1.00 30.06 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 10 10 . . . . . . H HIS CD2 11.319 28.794 20.978 1.00 26.35 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 10 10 . . . . . . H HIS CE1 11.276 27.691 22.875 1.00 27.36 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 10 10 . . . . . . H HIS NE2 10.519 28.180 21.909 1.00 28.44 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 11 11 . . . . . . L LEU N 15.758 32.503 21.303 1.00 26.85 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 11 11 . . . . . . L LEU CA 17.152 32.972 21.286 1.00 27.57 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 11 11 . . . . . . L LEU C 17.879 32.257 22.409 1.00 28.11 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 11 11 . . . . . . L LEU O 17.323 32.093 23.505 1.00 29.47 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 11 11 . . . . . . L LEU CB 17.225 34.494 21.530 1.00 25.89 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 11 11 . . . . . . L LEU CG 16.526 35.348 20.465 1.00 23.73 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 11 11 . . . . . . L LEU CD1 16.604 36.805 20.823 1.00 24.72 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 11 11 . . . . . . L LEU CD2 17.179 35.102 19.081 1.00 22.96 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 [Part of this file has been deleted for brevity] CO 1 1 . P 50 50 . . . . . . L LEU CD2 12.425 39.035 22.798 1.00 23.77 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 1 H . 402 . . . . . . . PO4 P 34.178 32.996 46.387 1.00 60.84 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 1 H . 402 . . . . . . . PO4 O1 35.146 33.243 45.291 1.00 57.95 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 1 H . 402 . . . . . . . PO4 O2 34.912 32.751 47.670 1.00 59.15 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 1 H . 402 . . . . . . . PO4 O3 33.291 34.184 46.538 1.00 58.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 1 H . 402 . . . . . . . PO4 O4 33.352 31.796 46.060 1.00 61.86 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 2 H . 403 . . . . . . . MN MN 8.130 27.788 21.899 1.00 36.09 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 2 H . 404 . . . . . . . MN MN 5.801 27.935 24.271 1.00 39.57 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 3 H . 405 . . . . . . . MN MN 36.023 34.916 44.253 1.00 39.52 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 3 H . 406 . . . . . . . MN MN 33.658 36.365 46.296 1.00 33.69 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 501 . . . . . . . SO4 S 17.175 28.112 32.476 1.00 100.80 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 501 . . . . . . . SO4 O1 18.136 28.230 31.357 1.00 100.18 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 501 . . . . . . . SO4 O2 17.097 26.692 32.887 1.00 100.80 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 501 . . . . . . . SO4 O3 17.633 28.926 33.626 1.00 100.14 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 501 . . . . . . . SO4 O4 15.834 28.575 32.045 1.00 100.56 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 502 . . . . . . . SO4 S 0.566 29.512 36.007 1.00 86.73 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 502 . . . . . . . SO4 O1 1.690 28.556 35.971 1.00 87.27 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 502 . . . . . . . SO4 O2 -0.620 28.803 36.523 1.00 87.87 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 502 . . . . . . . SO4 O3 0.896 30.642 36.905 1.00 86.58 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 502 . . . . . . . SO4 O4 0.287 30.037 34.658 1.00 86.51 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 503 . . . . . . . SO4 S -13.586 39.644 36.031 1.00 100.28 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 503 . . . . . . . SO4 O1 -12.340 39.512 35.250 1.00 100.72 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 503 . . . . . . . SO4 O2 -14.638 38.811 35.421 1.00 100.46 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 503 . . . . . . . SO4 O3 -13.347 39.201 37.420 1.00 99.66 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 5 H . 503 . . . . . . . SO4 O4 -14.020 41.056 36.015 1.00 99.97 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 P 7.599 25.305 23.994 1.00 56.33 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 O1P 8.249 24.467 25.030 1.00 56.70 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 O2P 6.700 26.285 24.649 1.00 54.49 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 O3P 8.637 26.026 23.216 1.00 53.97 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 O5* 7.095 23.970 23.128 1.00 59.20 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 C5* 7.073 23.961 21.762 1.00 66.74 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 C4* 6.041 23.013 21.296 1.00 71.22 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 O4* 6.029 21.855 22.189 1.00 73.78 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 C3* 4.736 23.676 21.350 1.00 73.80 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 O3* 4.355 23.874 19.995 1.00 76.51 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 C2* 3.864 22.749 22.165 1.00 74.04 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 C1* 4.682 21.474 22.506 1.00 74.70 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 N9 4.578 21.123 23.969 1.00 76.71 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 C8 3.630 21.533 24.876 1.00 76.87 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 N7 3.758 21.069 26.081 1.00 77.50 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 C5 4.896 20.300 25.989 1.00 77.78 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 C6 5.570 19.479 26.941 1.00 78.16 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 N6 5.155 19.409 28.200 1.00 78.77 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 N1 6.682 18.805 26.554 1.00 78.32 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 C2 7.090 18.888 25.277 1.00 78.14 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 N3 6.541 19.611 24.271 1.00 78.05 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 6 H . 401 . . . . . . . 101 C4 5.403 20.288 24.700 1.00 78.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 407 . . . . . . . HOH O 5.997 27.242 22.189 1.00 38.84 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 408 . . . . . . . HOH O 35.697 35.756 46.350 1.00 41.39 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 600 . . . . . . . HOH O 20.825 31.690 27.031 1.00 20.90 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 // |
Standard (Mandatory) qualifiers: [-pdbpath] dirlist This option specifies the location of PDB files (input). A PDB file contains protein coordinate and other data. A detailed explanation of the PDB file format is available on the PDB web site http://www.rcsb.org/pdb/info.html. -camask boolean This option specifies whether to to mask non-amino acid groups in protein chains that do not contain a C-alpha atom. If masked, the group will not appear in either the CO or SQ records of the clean coordinate file. -camaska boolean This option specifies whether to mask amino acids in protein chains that do not contain a C-alpha atom. If masked, the amino acid will not appear in the CO record but will still be present in the SQ record of the clean coordinate file. -atommask boolean This option specifies whether to mask amino acid residues in protein chains with a single atom only. If masked, the amino acid will appear not appear in the CO record but will still be present in the SQ record of the clean coordinate file. [-ccfoutdir] outdir This option specifies the location of CCF files (clean coordinate files) (output). A 'protein clean cordinate file' contains protein coordinate and other data for a single PDB file. The files, generated by using PDBPARSE, are in CCF format (EMBL-like) and contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. -errfile outfile This option specifies tame of the log file for the build. The log file may contain messages about inconsistencies or errors in the PDB files that were parsed. Additional (Optional) qualifiers: -[no]ccfnaming boolean This option specifies whether to use pdbid code to name the output files. If set, the PDB identifier code (from the PDB file) is used to name the file. Otherwise, the output files have the same names as the input files. -chnsiz integer Minimum number of amino acid residues in a chain for it to be parsed. -maxmis integer Maximum number of permissible mismatches between the ATOM and SEQRES sequences. -maxtrim integer Max. no. residues to trim when checking for missing C-terminal SEQRES sequences. Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-errfile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report deaths
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-pdbpath] (Parameter 1) |
This option specifies the location of PDB files (input). A PDB file contains protein coordinate and other data. A detailed explanation of the PDB file format is available on the PDB web site http://www.rcsb.org/pdb/info.html. | Directory with files | ./ |
-camask | This option specifies whether to to mask non-amino acid groups in protein chains that do not contain a C-alpha atom. If masked, the group will not appear in either the CO or SQ records of the clean coordinate file. | Boolean value Yes/No | No |
-camaska | This option specifies whether to mask amino acids in protein chains that do not contain a C-alpha atom. If masked, the amino acid will not appear in the CO record but will still be present in the SQ record of the clean coordinate file. | Boolean value Yes/No | No |
-atommask | This option specifies whether to mask amino acid residues in protein chains with a single atom only. If masked, the amino acid will appear not appear in the CO record but will still be present in the SQ record of the clean coordinate file. | Boolean value Yes/No | No |
[-ccfoutdir] (Parameter 2) |
This option specifies the location of CCF files (clean coordinate files) (output). A 'protein clean cordinate file' contains protein coordinate and other data for a single PDB file. The files, generated by using PDBPARSE, are in CCF format (EMBL-like) and contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. | Output directory | ./ |
-errfile | This option specifies tame of the log file for the build. The log file may contain messages about inconsistencies or errors in the PDB files that were parsed. | Output file | pdbparse.log |
Additional (Optional) qualifiers | Allowed values | Default | |
-[no]ccfnaming | This option specifies whether to use pdbid code to name the output files. If set, the PDB identifier code (from the PDB file) is used to name the file. Otherwise, the output files have the same names as the input files. | Boolean value Yes/No | Yes |
-chnsiz | Minimum number of amino acid residues in a chain for it to be parsed. | Any integer value | 5 |
-maxmis | Maximum number of permissible mismatches between the ATOM and SEQRES sequences. | Any integer value | 3 |
-maxtrim | Max. no. residues to trim when checking for missing C-terminal SEQRES sequences. | Any integer value | 10 |
Advanced (Unprompted) qualifiers | Allowed values | Default | |
(none) |
% pdbparse Parses PDB files and writes CCF files (clean coordinate files) for proteins. Location of PDB files (input) [./]: structure Mask non-amino acid groups in protein chains that do not contain a C-alpha atom. [N]: Mask amino acids in protein chains that do not contain a C-alpha atom. [N]: Y Mask amino acid residues in protein chains with a single atom only. [N]: Location of CCF files (clean coordinate files) (output) [./]: Name of log file for the build. [pdbparse.log]: Processing /ebi/services/idata/pmr/hgmp/test/data/structure/pdb1cs4.ent Processing /ebi/services/idata/pmr/hgmp/test/data/structure/pdb1ii7.ent |
Go to the output files for this example
The PDB files pdb1ii7.ent and pdb1cs4.ent were read. The protein clean
coordinate files 1cs4.ccf and 1ii7.ccf are written. A log file called
/test_data/pdbparse/pdbparse.log was also written.
FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
Clean coordinate file (for protein) | CCF format (EMBL-like format for protein coordinate and derived data). | Coordinate and other data for a single PDB file. The data are 'cleaned-up': self-consistent and error-corrected. | PDBPARSE | Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. |
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Program name | Description |
---|---|
aaindexextract | Extract data from AAINDEX |
allversusall | Does an all-versus-all global alignment for each set of sequences in an input directory and writes files of sequence similarity values |
cathparse | Reads raw CATH classification files and writes DCF file (domain classification file) |
cutgextract | Extract data from CUTG |
domainer | Reads CCF files (clean coordinate files) for proteins and writes CCF files for domains, taken from a DCF file (domain classification file) |
domainnr | Removes redundant domains from a DCF file (domain classification file). The file must contain domain sequence information, which can be added by using DOMAINSEQS |
domainseqs | Adds sequence records to a DCF file (domain classification file) |
domainsse | Adds secondary structure records to a DCF file (domain classification file) |
hetparse | Converts raw dictionary of heterogen groups to a file in EMBL-like format |
pdbplus | Add residue solvent accessibility and secondary structure data to a CCF file (clean coordinate file) for a protein or domain |
pdbtosp | Convert raw swissprot:PDB equivalence file to EMBL-like format |
printsextract | Extract data from PRINTS |
prosextract | Builds the PROSITE motif database for patmatmotifs to search |
rebaseextract | Extract data from REBASE |
scopparse | Reads raw SCOP classification files and writes a DCF file (domain classification file) |
seqnr | Removes redundancy from DHF files (domain hits files) or other files of sequences |
sites | Reads CCF files (clean coordinate files) and writes CON files (contact files) of residue-ligand contact data for domains in a DCF file (domain classification file) |
ssematch | Searches a DCF file (domain classification file) for secondary structure matches |
tfextract | Extract data from TRANSFAC |
FILE_OPEN my.file my.file could not be opened for reading or writing. The file is ignored. File FILE_READ my.file my.file could not be read. The file is ignored. File NO_OUTPUT my.file No clean coordinate file was generated for my.file. This will happen if there was a FILE_READ error on the raw PDB file, or a NOSEQRES, NOATOM or NOPROTEINS error when reading the file. File FILE_WRITE my.file my.file could not be written. The file is ignored. File. BADINDEX 1 (A) Raw residue numbering from ATOM records does not give the correct index into the SEQRES sequence for chain 1 ('A'). The correct alignment of the ATOM and SEQRES sequences is found by string handling (see 'Parsing methodology' in the text). Chain NEGNUM 1 (A) 123 Negative residue number found for chain 1 ('A') on line 123. Chain ZERNUM 1 (A) 123 Residue number of zero found for chain 1 ('A') on line 123. Chain ODDNUM 1 (A) 123 Possible residue heterogeneity or alternative residue numbering scheme for chain 1 ('A') on line 123. Chain NONSQNTL 1 (A) 123 Possible case of non-sequential numbering error for chain 1 ('A') on line 123. Chain HETEROK 1 (A) Correct alignment of ATOM and SEQRES sequences of chain 1 ('A') found by presuming an alternative residue numbering scheme. Chain ALTERNOK 1 (A) Correct alignment of ATOM and SEQRES sequences of chain 1 ('A') found by presuming one or more instances of heterogeneity. Chain MISSNTERM 1 (A) 3 SEQRES records appeared to be missing 3 N-terminal residues relative to ATOM sequence for chain 1 ('A'). The missing residues are added to the sequence. Chain MISSCTERM 1 (A) 3 SEQRES records appeared to be missing 3 C-terminal residues relative to ATOM sequence for chain 1 ('A'). The missing residues are added to the sequence. Chain GAPPEDOK 1 (A) Correct alignment of ATOM and SEQRES sequences of chain 1 ('A') found by gap insertion with no mismatches. Chain MISMATCH 1 (A) 2 ALA 2 ARG 6; ALA 12 TYR 16 Correct alignment of ATOM and SEQRES sequences of chain 1 ('A') found without gap insertion but contained 2 mismatches (ALA 2 versus ARG 6 and ALA 12 versus TYR 16). Chain GAPPED 1 (A) 2 ALA 2 ARG 6; ALA 12 TYR 16 Correct alignment of ATOM and SEQRES sequences of chain 1 ('A') found by gap insertion but contained 2 mismatches (ALA 2 versus ARG 6 and ALA 12 versus TYR 16). Chain NOMATCH 1 (A) Correct alignment of ATOM and SEQRES sequences of chain 1 ('A') could not be found by string handling (see 'Parsing methodology' in the text). The raw sequence from the ATOM records is taken to be the true sequence and the SEQRES sequence is discarded. Chain DUPATOMRES 3 Multiple sets of coordinates were given for an individual atom or whole residues, first instance on line 3. The first set of coordinates are used and the others discarded. Residue NOATOMRESID 123 No atom or residue identifier specified, first instance on line 123. All such lines are discarded. Residue SEQRESLENDIF 1(A) Indicated and actual length of SEQRES sequence differs for chain 1 (chain identifier 'A'). The actual length of the sequence is used. Chain CHAINIDS 1 (A) 2 (A) Chain identifiers of chains 1 and 2 are not unique ('A' in both cases). Both chains are discarded. File CHAINIDSPC Space (' ') and non-space characters are both used for chain identifiers in a single file. Chains in ATOM records are identified by reference to the TER records as well as chain identifiers. File CHAINORDER 123 The order of the chains in the ATOM records is inconsistent with that in the SEQRES records, first instance on line 123. Coordinates are assigned to the correct chain by reference to the chain identifier. File TERNONE No TER records were found. The chains in the ATOM records are identified by reference to the chain identifiers. File TERTOOMANY Number of TER records is greater than the number of chains; possible digest. File TERTOOFEW Number of TER records is less than the number of chains. File TERMISSHET 123 124 A chain is not separated from its heterogen group by a TER record between lines 123 and 124. Coordinates for the chain and heterogen are distinguished by reference to the chain identifier and residue numbers. Chain TERMISSCHN 123 124 Two chains are not separated by TER records between lines 123 and 124. Chain SEQRESNOAA 1 (A) No known amino acids found in the SEQRES records for chain 1 ('A'). The chain is discarded. Chain SEQRESFEWAA 1 (A) Fewer than the user-specified minimum number (5) of known amino acids were found in the SEQRES records for chain 1 ('A'). The chain is discarded. Chain NOPROTEINS No chains were found with at least the user-specified minimum number (5) of known amino acids. The file is not parsed and no output file is generated. File ATOMFEWAA 1 (A) 3 Fewer than the user-specified minimum number of known amino acids found in the ATOM records for chain 1 ('A'), model 3. The chain is discarded. Chain SECMISS 123 One or more standard records (e.g. for residue identity) were missing for an SSE on line 123. The element(s) are discarded. Line SECBOTH 1 2 ALA 2 ARG 6 The start and end residues (ALA 2 ARG 6) of an element given in the HELIX, SHEET or TURN records was not found in the ATOM records of chain 1, model 2. The element is discarded. Element SECSTART 1 2 ALA 2 The start residue (ALA 2) of an element was not found in the ATOM records of chain 1, model 2. The element is discarded. Element SECEND 1 2 ARG 6 The end residue (ARG 6) of an element was not found in the ATOM records of chain 1, model 2. The element is discarded. Element SECCHAIN A Chain identifier ('A') specified for an element not found in PDB file. The element is discarded. Element SECTWOCHN A B 2 chain identifiers ('A' and 'B') specified for an element. The element is discarded. Element NOSEQRES No SEQRES records. The file is not parsed and no output file is generated. File NOATOM No ATOM records. The file is not parsed and no output file is generated. File RESOLMOD A value for the RESOLUTION record is given but MODEL records are also found. The file is presumed to contain an NMR structure or model. File NORESOLUTION RESOLUTION record not found. The file is presumed to contain an NMR structure or model. File NOMODEL NMR structure with no MODEL records. The number of models is determined by reference to the TER records. File MODELDUP 123 Duplicate MODEL records on line 123. The duplicate record is disregarded. File |
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