stride output for: /ebi/services/idata/pmr/hgmp/test/data/structure/1cs4.ent // stride data for: /ebi/services/idata/pmr/hgmp/test/data/structure/1cs4.ent // naccess output for: /ebi/services/idata/pmr/hgmp/test/data/structure/1cs4.ent // naccess data for: /ebi/services/idata/pmr/hgmp/test/data/structure/1cs4.ent // stride output for: /ebi/services/idata/pmr/hgmp/test/data/structure/1ii7.ent // stride data for: /ebi/services/idata/pmr/hgmp/test/data/structure/1ii7.ent // naccess output for: /ebi/services/idata/pmr/hgmp/test/data/structure/1ii7.ent // naccess data for: /ebi/services/idata/pmr/hgmp/test/data/structure/1ii7.ent // STRIDE failures: 0 NACCESS failures: 0 |
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naccess: using defualt vdw.radii naccess: using default STD FILE naccess: using defualt vdw.radii naccess: using default STD FILE |
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 2; NE 0; XX SQ SEQUENCE 52 AA; 5817 MW; 47362A43 CRC32; ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS XX CO 1 1 . P 2 396 . . . . C . D ASP N 51.711 -11.782 62.798 1.00 51.17 360.00 138.76 146.70 139.38 99.30 65.52 63.80 73.85 195.90 37.10 75.30 102.28 112.20 CO 1 1 . P 2 396 . . . . C . D ASP CA 52.810 -11.644 61.848 1.00 54.45 360.00 138.76 146.70 139.38 99.30 65.52 63.80 73.85 195.90 37.10 75.30 102.28 112.20 CO 1 1 . P 2 396 . . . . C . D ASP C 54.137 -11.314 62.530 1.00 55.11 360.00 138.76 146.70 139.38 99.30 65.52 63.80 73.85 195.90 37.10 75.30 102.28 112.20 CO 1 1 . P 2 396 . . . . C . D ASP O 54.175 -10.524 63.469 1.00 55.34 360.00 138.76 146.70 139.38 99.30 65.52 63.80 73.85 195.90 37.10 75.30 102.28 112.20 CO 1 1 . P 2 396 . . . . C . D ASP CB 52.437 -10.555 60.831 1.00 57.50 360.00 138.76 146.70 139.38 99.30 65.52 63.80 73.85 195.90 37.10 75.30 102.28 112.20 CO 1 1 . P 2 396 . . . . C . D ASP CG 53.460 -10.391 59.729 1.00 61.38 360.00 138.76 146.70 139.38 99.30 65.52 63.80 73.85 195.90 37.10 75.30 102.28 112.20 CO 1 1 . P 2 396 . . . . C . D ASP OD1 54.316 -9.485 59.841 1.00 65.55 360.00 138.76 146.70 139.38 99.30 65.52 63.80 73.85 195.90 37.10 75.30 102.28 112.20 CO 1 1 . P 2 396 . . . . C . D ASP OD2 53.390 -11.146 58.736 1.00 63.68 360.00 138.76 146.70 139.38 99.30 65.52 63.80 73.85 195.90 37.10 75.30 102.28 112.20 CO 1 1 . P 3 397 . . . . T . I ILE N 55.216 -11.941 62.066 1.00 57.14 -70.66 130.71 41.60 42.25 24.10 39.03 28.30 3.22 8.70 39.03 28.10 3.22 9.00 CO 1 1 . P 3 397 . . . . T . I ILE CA 56.546 -11.705 62.624 1.00 59.46 -70.66 130.71 41.60 42.25 24.10 39.03 28.30 3.22 8.70 39.03 28.10 3.22 9.00 CO 1 1 . P 3 397 . . . . T . I ILE C 57.020 -10.305 62.230 1.00 60.12 -70.66 130.71 41.60 42.25 24.10 39.03 28.30 3.22 8.70 39.03 28.10 3.22 9.00 CO 1 1 . P 3 397 . . . . T . I ILE O 56.963 -9.927 61.060 1.00 59.12 -70.66 130.71 41.60 42.25 24.10 39.03 28.30 3.22 8.70 39.03 28.10 3.22 9.00 CO 1 1 . P 3 397 . . . . T . I ILE CB 57.583 -12.722 62.094 1.00 60.84 -70.66 130.71 41.60 42.25 24.10 39.03 28.30 3.22 8.70 39.03 28.10 3.22 9.00 CO 1 1 . P 3 397 . . . . T . I ILE CG1 57.184 -14.163 62.447 1.00 63.12 -70.66 130.71 41.60 42.25 24.10 39.03 28.30 3.22 8.70 39.03 28.10 3.22 9.00 CO 1 1 . P 3 397 . . . . T . I ILE CG2 58.975 -12.384 62.632 1.00 61.24 -70.66 130.71 41.60 42.25 24.10 39.03 28.30 3.22 8.70 39.03 28.10 3.22 9.00 CO 1 1 . P 3 397 . . . . T . I ILE CD1 57.408 -14.554 63.895 1.00 63.92 -70.66 130.71 41.60 42.25 24.10 39.03 28.30 3.22 8.70 39.03 28.10 3.22 9.00 CO 1 1 . P 4 398 . . . . T . E GLU N 57.492 -9.548 63.212 1.00 60.23 -80.63 128.14 189.80 172.42 100.10 152.25 113.00 20.18 53.80 71.11 118.00 101.31 90.50 CO 1 1 . P 4 398 . . . . T . E GLU CA 57.975 -8.198 62.971 1.00 62.14 -80.63 128.14 189.80 172.42 100.10 152.25 113.00 20.18 53.80 71.11 118.00 101.31 90.50 CO 1 1 . P 4 398 . . . . T . E GLU C 59.401 -8.277 62.424 1.00 60.59 -80.63 128.14 189.80 172.42 100.10 152.25 113.00 20.18 53.80 71.11 118.00 101.31 90.50 CO 1 1 . P 4 398 . . . . T . E GLU O 60.244 -8.972 62.987 1.00 61.84 -80.63 128.14 189.80 172.42 100.10 152.25 113.00 20.18 53.80 71.11 118.00 101.31 90.50 CO 1 1 . P 4 398 . . . . T . E GLU CB 57.917 -7.386 64.272 1.00 65.47 -80.63 128.14 189.80 172.42 100.10 152.25 113.00 20.18 53.80 71.11 118.00 101.31 90.50 CO 1 1 . P 4 398 . . . . T . E GLU CG 58.037 -5.874 64.091 1.00 70.25 -80.63 128.14 189.80 172.42 100.10 152.25 113.00 20.18 53.80 71.11 118.00 101.31 90.50 CO 1 1 . P 4 398 . . . . T . E GLU CD 57.588 -5.089 65.324 1.00 72.94 -80.63 128.14 189.80 172.42 100.10 152.25 113.00 20.18 53.80 71.11 118.00 101.31 90.50 CO 1 1 . P 4 398 . . . . T . E GLU OE1 58.262 -5.175 66.377 1.00 70.76 -80.63 128.14 189.80 172.42 100.10 152.25 113.00 20.18 53.80 71.11 118.00 101.31 90.50 CO 1 1 . P 4 398 . . . . T . E GLU OE2 56.555 -4.380 65.232 1.00 74.36 -80.63 128.14 189.80 172.42 100.10 152.25 113.00 20.18 53.80 71.11 118.00 101.31 90.50 CO 1 1 . P 5 399 H 1 1 1 T . G GLY N 59.642 -7.608 61.298 1.00 57.58 60.62 44.06 47.30 46.32 57.80 33.67 104.20 12.64 26.50 33.67 89.70 12.64 29.70 CO 1 1 . P 5 399 H 1 1 1 T . G GLY CA 60.956 -7.615 60.681 1.00 56.14 60.62 44.06 47.30 46.32 57.80 33.67 104.20 12.64 26.50 33.67 89.70 12.64 29.70 CO 1 1 . P 5 399 H 1 1 1 T . G GLY C 61.452 -8.993 60.265 1.00 58.03 60.62 44.06 47.30 46.32 57.80 33.67 104.20 12.64 26.50 33.67 89.70 12.64 29.70 CO 1 1 . P 5 399 H 1 1 1 T . G GLY O 62.620 -9.322 60.480 1.00 57.47 60.62 44.06 47.30 46.32 57.80 33.67 104.20 12.64 26.50 33.67 89.70 12.64 29.70 CO 1 1 . P 6 400 H 1 1 1 H 1 F PHE N 60.576 -9.789 59.649 1.00 58.00 -63.71 -43.06 38.10 42.33 21.20 38.88 23.70 3.46 9.80 38.88 23.50 3.46 10.10 CO 1 1 . P 6 400 H 1 1 1 H 1 F PHE CA 60.914 -11.143 59.200 1.00 58.07 -63.71 -43.06 38.10 42.33 21.20 38.88 23.70 3.46 9.80 38.88 23.50 3.46 10.10 CO 1 1 . P 6 400 H 1 1 1 H 1 F PHE C 61.995 -11.219 58.117 1.00 58.57 -63.71 -43.06 38.10 42.33 21.20 38.88 23.70 3.46 9.80 38.88 23.50 3.46 10.10 CO 1 1 . P 6 400 H 1 1 1 H 1 F PHE O 62.862 -12.091 58.161 1.00 59.44 -63.71 -43.06 38.10 42.33 21.20 38.88 23.70 3.46 9.80 38.88 23.50 3.46 10.10 CO 1 1 . P 6 400 H 1 1 1 H 1 F PHE CB 59.657 -11.881 58.734 1.00 59.18 -63.71 -43.06 38.10 42.33 21.20 38.88 23.70 3.46 9.80 38.88 23.50 3.46 10.10 CO 1 1 . P 6 400 H 1 1 1 H 1 F PHE CG 59.900 -13.316 58.322 1.00 58.53 -63.71 -43.06 38.10 42.33 21.20 38.88 23.70 3.46 9.80 38.88 23.50 3.46 10.10 [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 5; NH 1; 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 . . . . C . D ASP N 7.977 32.254 19.055 1.00 26.65 360.00 53.69 128.30 117.77 83.90 84.46 82.20 33.31 88.40 34.39 69.80 83.38 91.50 CO 1 1 . P 8 8 . . . . C . D ASP CA 8.882 31.149 19.290 1.00 28.34 360.00 53.69 128.30 117.77 83.90 84.46 82.20 33.31 88.40 34.39 69.80 83.38 91.50 CO 1 1 . P 8 8 . . . . C . D ASP C 10.273 31.305 18.659 1.00 27.71 360.00 53.69 128.30 117.77 83.90 84.46 82.20 33.31 88.40 34.39 69.80 83.38 91.50 CO 1 1 . P 8 8 . . . . C . D ASP O 10.740 30.453 17.907 1.00 29.27 360.00 53.69 128.30 117.77 83.90 84.46 82.20 33.31 88.40 34.39 69.80 83.38 91.50 CO 1 1 . P 8 8 . . . . C . D ASP CB 8.186 29.886 18.777 1.00 30.25 360.00 53.69 128.30 117.77 83.90 84.46 82.20 33.31 88.40 34.39 69.80 83.38 91.50 CO 1 1 . P 8 8 . . . . C . D ASP CG 6.918 29.584 19.554 1.00 34.25 360.00 53.69 128.30 117.77 83.90 84.46 82.20 33.31 88.40 34.39 69.80 83.38 91.50 CO 1 1 . P 8 8 . . . . C . D ASP OD1 7.041 29.177 20.724 1.00 33.37 360.00 53.69 128.30 117.77 83.90 84.46 82.20 33.31 88.40 34.39 69.80 83.38 91.50 CO 1 1 . P 8 8 . . . . C . D ASP OD2 5.801 29.770 19.010 1.00 35.77 360.00 53.69 128.30 117.77 83.90 84.46 82.20 33.31 88.40 34.39 69.80 83.38 91.50 CO 1 1 . P 9 9 . . . . C . I ILE N 10.913 32.423 18.967 1.00 26.84 -72.50 -37.00 42.90 42.38 24.20 41.07 29.80 1.31 3.50 41.07 29.50 1.31 3.60 CO 1 1 . P 9 9 . . . . C . I ILE CA 12.236 32.739 18.477 1.00 26.52 -72.50 -37.00 42.90 42.38 24.20 41.07 29.80 1.31 3.50 41.07 29.50 1.31 3.60 CO 1 1 . P 9 9 . . . . C . I ILE C 13.285 31.864 19.173 1.00 28.22 -72.50 -37.00 42.90 42.38 24.20 41.07 29.80 1.31 3.50 41.07 29.50 1.31 3.60 CO 1 1 . P 9 9 . . . . C . I ILE O 14.257 31.426 18.550 1.00 28.01 -72.50 -37.00 42.90 42.38 24.20 41.07 29.80 1.31 3.50 41.07 29.50 1.31 3.60 CO 1 1 . P 9 9 . . . . C . I ILE CB 12.520 34.214 18.759 1.00 27.25 -72.50 -37.00 42.90 42.38 24.20 41.07 29.80 1.31 3.50 41.07 29.50 1.31 3.60 CO 1 1 . P 9 9 . . . . C . I ILE CG1 11.338 35.051 18.249 1.00 26.35 -72.50 -37.00 42.90 42.38 24.20 41.07 29.80 1.31 3.50 41.07 29.50 1.31 3.60 CO 1 1 . P 9 9 . . . . C . I ILE CG2 13.823 34.640 18.094 1.00 26.40 -72.50 -37.00 42.90 42.38 24.20 41.07 29.80 1.31 3.50 41.07 29.50 1.31 3.60 CO 1 1 . P 9 9 . . . . C . I ILE CD1 11.011 34.845 16.725 1.00 25.85 -72.50 -37.00 42.90 42.38 24.20 41.07 29.80 1.31 3.50 41.07 29.50 1.31 3.60 CO 1 1 . P 10 10 . . . . T . H HIS N 13.072 31.599 20.462 1.00 26.69 50.63 45.81 76.20 75.98 41.50 75.67 51.40 0.31 0.90 48.67 50.10 27.31 31.90 CO 1 1 . P 10 10 . . . . T . H HIS CA 14.009 30.787 21.254 1.00 28.02 50.63 45.81 76.20 75.98 41.50 75.67 51.40 0.31 0.90 48.67 50.10 27.31 31.90 CO 1 1 . P 10 10 . . . . T . H HIS C 15.483 31.203 21.181 1.00 27.57 50.63 45.81 76.20 75.98 41.50 75.67 51.40 0.31 0.90 48.67 50.10 27.31 31.90 CO 1 1 . P 10 10 . . . . T . H HIS O 16.357 30.359 21.019 1.00 23.99 50.63 45.81 76.20 75.98 41.50 75.67 51.40 0.31 0.90 48.67 50.10 27.31 31.90 CO 1 1 . P 10 10 . . . . T . H HIS CB 13.867 29.284 20.899 1.00 27.15 50.63 45.81 76.20 75.98 41.50 75.67 51.40 0.31 0.90 48.67 50.10 27.31 31.90 CO 1 1 . P 10 10 . . . . T . H HIS CG 12.599 28.681 21.415 1.00 28.59 50.63 45.81 76.20 75.98 41.50 75.67 51.40 0.31 0.90 48.67 50.10 27.31 31.90 CO 1 1 . P 10 10 . . . . T . H HIS ND1 12.536 27.980 22.603 1.00 30.06 50.63 45.81 76.20 75.98 41.50 75.67 51.40 0.31 0.90 48.67 50.10 27.31 31.90 CO 1 1 . P 10 10 . . . . T . H HIS CD2 11.319 28.794 20.978 1.00 26.35 50.63 45.81 76.20 75.98 41.50 75.67 51.40 0.31 0.90 48.67 50.10 27.31 31.90 CO 1 1 . P 10 10 . . . . T . H HIS CE1 11.276 27.691 22.875 1.00 27.36 50.63 45.81 76.20 75.98 41.50 75.67 51.40 0.31 0.90 48.67 50.10 27.31 31.90 CO 1 1 . P 10 10 . . . . T . H HIS NE2 10.519 28.180 21.909 1.00 28.44 50.63 45.81 76.20 75.98 41.50 75.67 51.40 0.31 0.90 48.67 50.10 27.31 31.90 CO 1 1 . P 11 11 . . . . T . L LEU N 15.758 32.503 21.303 1.00 26.85 -57.60 139.21 78.50 79.58 44.50 55.49 39.30 24.09 64.20 56.43 39.70 23.15 63.70 CO 1 1 . P 11 11 . . . . T . L LEU CA 17.152 32.972 21.286 1.00 27.57 -57.60 139.21 78.50 79.58 44.50 55.49 39.30 24.09 64.20 56.43 39.70 23.15 63.70 CO 1 1 . P 11 11 . . . . T . L LEU C 17.879 32.257 22.409 1.00 28.11 -57.60 139.21 78.50 79.58 44.50 55.49 39.30 24.09 64.20 56.43 39.70 23.15 63.70 CO 1 1 . P 11 11 . . . . T . L LEU O 17.323 32.093 23.505 1.00 29.47 -57.60 139.21 78.50 79.58 44.50 55.49 39.30 24.09 64.20 56.43 39.70 23.15 63.70 CO 1 1 . P 11 11 . . . . T . L LEU CB 17.225 34.494 21.530 1.00 25.89 -57.60 139.21 78.50 79.58 44.50 55.49 39.30 24.09 64.20 56.43 39.70 23.15 63.70 CO 1 1 . P 11 11 . . . . T . L LEU CG 16.526 35.348 20.465 1.00 23.73 -57.60 139.21 78.50 79.58 44.50 55.49 39.30 24.09 64.20 56.43 39.70 23.15 63.70 CO 1 1 . P 11 11 . . . . T . L LEU CD1 16.604 36.805 20.823 1.00 24.72 -57.60 139.21 78.50 79.58 44.50 55.49 39.30 24.09 64.20 56.43 39.70 23.15 63.70 CO 1 1 . P 11 11 . . . . T . L LEU CD2 17.179 35.102 19.081 1.00 22.96 -57.60 139.21 78.50 79.58 44.50 55.49 39.30 24.09 64.20 56.43 39.70 23.15 63.70 [Part of this file has been deleted for brevity] CO 1 1 . P 50 50 . . . . C . L LEU CD2 12.425 39.035 22.798 1.00 23.77 -69.71 360.00 98.90 101.26 56.70 78.17 55.40 23.09 61.60 96.01 67.50 5.25 14.50 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 4 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 4 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 4 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 4 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 4 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 4 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 4 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 4 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 4 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 4 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 4 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 4 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 4 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 4 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 4 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 (* if not always prompted): [-ccfinpath] dirlist This option specifies the location of CCF files (clean coordinate files) (input). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), 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. [-pdbindir] directory 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 -pdbprefix string This option specifies the file prefix of PDB files (if any) -mode menu This option specifies the mode of operation. * -thresholdsize integer This option specifies the threshold size for SSEs (secondary structure elements) [-ccfoutdir] outdir This option specifies the location of CCF files (clean coordinate files) (output). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), 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 the name of the log file for PDBPLUS * -serrfile outfile This option specifies the name of the log file for STRIDE * -nerrfile outfile This option specifies the name of the log file for NACCESS Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-errfile" associated qualifiers -odirectory string Output directory "-serrfile" associated qualifiers -odirectory string Output directory "-nerrfile" 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 | |||||||
---|---|---|---|---|---|---|---|---|---|
[-ccfinpath] (Parameter 1) |
This option specifies the location of CCF files (clean coordinate files) (input). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), 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. | Directory with files | ./ | ||||||
[-pdbindir] (Parameter 2) |
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 | ./ | ||||||
-pdbprefix | This option specifies the file prefix of PDB files (if any) | Any string is accepted | An empty string is accepted | ||||||
-mode | This option specifies the mode of operation. |
|
1 | ||||||
-thresholdsize | This option specifies the threshold size for SSEs (secondary structure elements) | Any integer value | 4 | ||||||
[-ccfoutdir] (Parameter 3) |
This option specifies the location of CCF files (clean coordinate files) (output). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), 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 the name of the log file for PDBPLUS | Output file | pdbplus.log | ||||||
-serrfile | This option specifies the name of the log file for STRIDE | Output file | stride.log | ||||||
-nerrfile | This option specifies the name of the log file for NACCESS | Output file | naccess.log | ||||||
Additional (Optional) qualifiers | Allowed values | Default | |||||||
(none) | |||||||||
Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||
(none) |
% pdbplus Add residue solvent accessibility and secondary structure data to a CCF file (clean coordinate file) for a protein or domain. Location of CCF files (clean coordinate files) (input) [./]: pdbplus Location of PDB files (input) [./]: File prefix of PDB files (if any): Mode of operation 1 : Use STRIDE only 2 : Use NACCESS only 3 : Use STRIDE and NACCESS Select mode [1]: 3 Threshold size for SSEs (secondary structure elements) [4]: 4 Location of CCF files (clean coordinate files) (output) [./]: Name of log file for PDBPLUS [pdbplus.log]: Name of log file for STRIDE [stride.log]: Name of log file for NACCESS [naccess.log]: Processing /ebi/services/idata/pmr/hgmp/test/data/structure/pdbplus/1cs4.ccf stride /ebi/services/idata/pmr/hgmp/test/data/structure/1cs4.ent -f./pdbplus-1108721730.13957 >> stride.log 2>&1 naccess /ebi/services/idata/pmr/hgmp/test/data/structure/1cs4.ent >> naccess.log 2>&1 Processing /ebi/services/idata/pmr/hgmp/test/data/structure/pdbplus/1ii7.ccf stride /ebi/services/idata/pmr/hgmp/test/data/structure/1ii7.ent -f./pdbplus-1108721730.13957 >> stride.log 2>&1 naccess /ebi/services/idata/pmr/hgmp/test/data/structure/1ii7.ent >> naccess.log 2>&1 STRIDE failures: 0 NACCESS failures: 0 |
Go to the output files for this example
All CCF files were read from testdata/pdbplus/ccfin and CCF files (annotated with values for secondary structure and solvent accessibility) were written to testdata/pdbplus/ccfout. The STRIDE and NACCESS programs ran on PDB files within testdata/. Three log files (pdbplus.log, naccess.log and stride.log) were written. The threshold size for secondary structure elements was 4 residues. File extension of all input and output files would be set in the ACD file.
FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
Clean coordinate file (for protein) | CCF format (EMBL-like). | Protein coordinate and derived 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. |
Clean coordinate file (for domain) | CCF format (EMBL-like). | Protein coordinate and derived data for a single domain from SCOP or CATH. The data are 'cleaned-up': self-consistent and error-corrected. | DOMAINER | Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. |
PDB file | PDB format. | Protein coordinate data in PDB format. | N.A. | N.A. |
Domain PDB file | PDB format. | Protein coordinate data for a single domain from SCOP or CATH. | DOMAINER | N.A. |
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 |
pdbparse | Parses PDB files and writes CCF files (clean coordinate files) for proteins |
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 |
1. Frishman, D. & Argos, P. (1995). Knowledge-Based Secondary Structure Assignment. Proteins 23:566-579. 2. Hubbard,S.J. & Thornton, J.M. (1993), 'NACCESS', Computer Program, Department of Biochemistry and Molecular Biology, University College London.