PDBPLUS documentation |
stride output for: /homes/user/test/data/structure/1cs4.ent // stride data for: /homes/user/test/data/structure/1cs4.ent // naccess output for: /homes/user/test/data/structure/1cs4.ent // naccess data for: /homes/user/test/data/structure/1cs4.ent // stride output for: /homes/user/test/data/structure/1ii7.ent // stride data for: /homes/user/test/data/structure/1ii7.ent // naccess output for: /homes/user/test/data/structure/1ii7.ent // naccess data for: /homes/user/test/data/structure/1ii7.ent // stride output for: /homes/user/test/data/structure/2hhb.ent // stride data for: /homes/user/test/data/structure/2hhb.ent // naccess output for: /homes/user/test/data/structure/2hhb.ent // naccess data for: /homes/user/test/data/structure/2hhb.ent // STRIDE failures: 0 NACCESS failures: 0 |
|
naccess: using defualt vdw.radii naccess: using default STD FILE 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; D8CCAE0E1FC0849A CRC64; ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS XX RE 1 1 2 396 D ASP . . . . . C 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 RE 1 1 3 397 I ILE . . . . . T -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 RE 1 1 4 398 E GLU . . . . . T -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 RE 1 1 5 399 G GLY 1 1 H 1 . T 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 RE 1 1 6 400 F PHE 1 1 H 1 1 H -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 RE 1 1 7 401 T THR 1 1 H 1 1 H -63.13 -33.45 122.50 117.00 84.00 113.46 111.60 3.54 9.40 81.54 107.70 35.46 55.80 RE 1 1 8 402 S SER 1 1 H 1 1 H -69.61 -44.64 76.80 69.25 59.40 66.11 84.60 3.14 8.20 36.50 75.20 32.75 48.20 RE 1 1 9 403 L LEU 1 1 H 1 1 H -63.95 -53.38 81.30 81.72 45.70 81.25 57.60 0.47 1.30 81.25 57.10 0.47 1.30 RE 1 1 10 404 A ALA 1 1 H 1 1 H -67.72 -13.25 35.90 35.58 33.00 16.63 24.00 18.95 49.20 18.20 25.50 17.38 47.50 RE 1 1 11 405 S SER 1 1 H 1 . T -82.48 -15.19 100.90 90.08 77.30 61.12 78.20 28.96 75.40 25.90 53.40 64.18 94.40 RE 1 1 12 406 Q GLN . . . . . T -95.87 -61.03 151.90 142.66 79.90 109.97 78.00 32.69 87.10 49.16 94.10 93.49 74.00 RE 1 1 13 407 C CYS . . . . . T -79.87 165.96 32.00 36.35 27.10 27.88 28.80 8.47 22.60 29.04 29.70 7.31 20.10 RE 1 1 14 408 T THR 2 2 H 1 . C -67.21 155.23 79.50 78.09 56.10 73.27 72.00 4.82 12.80 53.17 70.20 24.92 39.20 RE 1 1 15 409 A ALA 2 2 H 1 2 H -61.46 -26.61 74.80 80.21 74.30 71.49 103.00 8.72 22.60 72.91 102.10 7.31 20.00 RE 1 1 16 410 Q GLN 2 2 H 1 2 H -69.67 -54.28 138.50 127.16 71.20 124.25 88.10 2.91 7.80 46.24 88.60 80.92 64.10 RE 1 1 17 411 E GLU 2 2 H 1 2 H -57.11 -42.09 104.70 89.88 52.20 89.35 66.30 0.53 1.40 31.77 52.70 58.11 51.90 RE 1 1 18 412 L LEU 2 2 H 1 2 H -57.70 -47.91 25.70 25.00 14.00 25.00 17.70 0.00 0.00 25.00 17.60 0.00 0.00 RE 1 1 19 413 V VAL 2 2 H 1 2 H -66.05 -30.11 88.20 90.90 60.00 90.80 79.50 0.10 0.30 90.90 78.70 0.00 0.00 RE 1 1 20 414 M MET 2 2 H 1 2 H -69.27 -42.21 124.20 127.92 65.90 122.84 78.40 5.08 13.50 124.37 78.80 3.54 9.80 RE 1 1 21 415 T THR 2 2 H 1 2 H -65.51 -37.49 81.70 78.15 56.10 76.18 74.90 1.96 5.20 56.58 74.70 21.56 33.90 RE 1 1 22 416 L LEU 2 2 H 1 2 H -74.87 -41.05 26.30 23.57 13.20 23.31 16.50 0.26 0.70 23.57 16.60 0.00 0.00 RE 1 1 23 417 N ASN 2 2 H 1 2 H -67.86 -35.26 113.60 101.30 70.40 99.87 94.00 1.43 3.80 18.39 39.80 82.91 84.80 RE 1 1 24 418 E GLU 2 2 H 1 2 H -65.83 -40.82 113.30 100.53 58.40 99.74 74.00 0.79 2.10 38.76 64.30 61.77 55.20 RE 1 1 25 419 L LEU 2 2 H 1 2 H -72.73 -52.39 57.40 57.47 32.20 57.33 40.60 0.14 0.40 57.33 40.30 0.14 0.40 RE 1 1 26 420 F PHE 2 2 H 1 2 H -70.80 -21.35 27.00 28.81 14.40 27.76 16.90 1.06 3.00 28.81 17.40 0.00 0.00 RE 1 1 27 421 A ALA 2 2 H 1 2 H -69.34 -45.28 29.90 35.82 33.20 34.83 50.20 1.00 2.60 34.83 48.80 1.00 2.70 RE 1 1 28 422 R ARG 2 2 H 1 2 H -61.82 -45.79 136.10 134.66 56.40 134.62 66.90 0.03 0.10 47.36 60.90 87.30 54.20 RE 1 1 29 423 F PHE 2 2 H 1 2 H -57.44 -43.57 101.50 99.54 49.90 95.45 58.20 4.09 11.60 96.26 58.30 3.28 9.60 RE 1 1 30 424 D ASP 2 2 H 1 2 H -62.18 -31.31 60.50 54.34 38.70 42.49 41.40 11.84 31.40 25.02 50.80 29.31 32.20 RE 1 1 31 425 K LYS 2 2 H 1 2 H -78.40 -41.15 135.60 131.47 65.50 129.94 79.60 1.53 4.10 94.19 80.80 37.29 44.30 RE 1 1 32 426 L LEU 2 2 H 1 2 H -64.72 -26.22 81.20 86.96 48.70 86.30 61.20 0.66 1.80 86.96 61.10 0.00 0.00 RE 1 1 33 427 A ALA 2 2 H 1 2 H -69.69 -37.04 17.80 18.88 17.50 18.70 26.90 0.18 0.50 18.70 26.20 0.18 0.50 RE 1 1 34 428 A ALA 2 2 H 1 2 H -70.19 -38.47 77.30 79.34 73.50 60.25 86.80 19.09 49.50 61.54 86.20 17.79 48.60 RE 1 1 35 429 E GLU 2 2 H 1 2 H -66.66 -43.34 133.10 123.38 71.60 108.84 80.80 14.54 38.80 51.79 85.90 71.59 63.90 RE 1 1 36 430 N ASN 2 2 H 1 2 H -85.82 10.44 105.20 96.15 66.80 83.39 78.50 12.75 33.80 21.86 47.30 74.28 76.00 [Part of this file has been deleted for brevity] AT 1 1 5 . 1002 . FOK H C9 42.200 -11.309 50.489 1.00 41.39 AT 1 1 5 . 1002 . FOK H O6 42.275 -12.455 49.593 1.00 43.23 AT 1 1 5 . 1002 . FOK H C10 43.008 -11.601 51.811 1.00 39.11 AT 1 1 5 . 1002 . FOK H C11 40.680 -11.078 50.616 1.00 44.36 AT 1 1 5 . 1002 . FOK H O7 40.106 -10.945 51.688 1.00 48.77 AT 1 1 5 . 1002 . FOK H C12 39.943 -11.046 49.301 1.00 40.67 AT 1 1 5 . 1002 . FOK H C13 40.595 -10.085 48.292 1.00 41.47 AT 1 1 5 . 1002 . FOK H C14 40.276 -10.620 46.930 1.00 46.69 AT 1 1 5 . 1002 . FOK H C15 39.971 -11.751 46.590 1.00 53.22 AT 1 1 5 . 1002 . FOK H C16 40.047 -8.685 48.426 1.00 42.42 AT 1 1 5 . 1002 . FOK H C17 42.671 -8.737 50.253 1.00 39.67 AT 1 1 5 . 1002 . FOK H C18 46.732 -13.026 51.827 1.00 35.74 AT 1 1 5 . 1002 . FOK H C19 45.859 -11.483 53.586 1.00 34.48 AT 1 1 5 . 1002 . FOK H C20 42.913 -10.426 52.807 1.00 39.44 AT 1 1 5 . 1002 . FOK H C21 45.883 -9.553 47.821 1.00 42.15 AT 1 1 5 . 1002 . FOK H O5 46.157 -10.520 47.166 1.00 40.91 AT 1 1 5 . 1002 . FOK H C22 46.769 -8.315 48.006 1.00 37.08 AT 1 1 6 . 1003 . MES H O1 45.676 7.326 49.092 1.00 77.86 AT 1 1 6 . 1003 . MES H C2 44.367 6.816 48.900 1.00 75.17 AT 1 1 6 . 1003 . MES H C3 44.349 5.317 48.923 1.00 74.42 AT 1 1 6 . 1003 . MES H N4 44.832 4.804 50.196 1.00 72.45 AT 1 1 6 . 1003 . MES H C5 46.234 5.425 50.473 1.00 73.23 AT 1 1 6 . 1003 . MES H C6 46.176 6.914 50.355 1.00 75.06 AT 1 1 6 . 1003 . MES H C7 44.806 3.336 50.302 1.00 73.39 AT 1 1 6 . 1003 . MES H C8 44.672 2.791 51.713 1.00 76.85 AT 1 1 6 . 1003 . MES H S 45.724 1.379 51.967 1.00 78.26 AT 1 1 6 . 1003 . MES H O1S 47.062 1.828 51.737 1.00 79.39 AT 1 1 6 . 1003 . MES H O2S 45.303 0.380 51.016 1.00 81.58 AT 1 1 6 . 1003 . MES H O3S 45.523 0.961 53.326 1.00 80.59 AT 1 1 6 . 1004 . MES H O1 59.246 -5.152 27.381 1.00 99.99 AT 1 1 6 . 1004 . MES H C2 60.067 -4.021 27.127 1.00 99.99 AT 1 1 6 . 1004 . MES H C3 60.447 -3.301 28.378 1.00 99.78 AT 1 1 6 . 1004 . MES H N4 61.180 -4.156 29.270 1.00 96.33 AT 1 1 6 . 1004 . MES H C5 60.358 -5.461 29.506 1.00 97.90 AT 1 1 6 . 1004 . MES H C6 59.965 -6.072 28.203 1.00 99.68 AT 1 1 6 . 1004 . MES H C7 61.596 -3.484 30.507 1.00 93.33 AT 1 1 6 . 1004 . MES H C8 61.931 -2.010 30.442 1.00 90.74 AT 1 1 6 . 1004 . MES H S 60.763 -0.978 31.301 0.50 90.72 AT 1 1 6 . 1004 . MES H O1S 59.476 -1.170 30.680 0.50 91.60 AT 1 1 6 . 1004 . MES H O2S 61.249 0.383 31.164 0.50 91.20 AT 1 1 6 . 1004 . MES H O3S 60.776 -1.430 32.647 0.50 90.05 AT 1 1 7 . 1005 . POP H P1 58.812 -7.766 57.091 1.00 57.40 AT 1 1 7 . 1005 . POP H O1 60.254 -7.589 56.745 1.00 54.93 AT 1 1 7 . 1005 . POP H O2 58.618 -8.839 58.095 1.00 55.36 AT 1 1 7 . 1005 . POP H O3 57.949 -8.024 55.908 1.00 55.10 AT 1 1 7 . 1005 . POP H O 58.295 -6.370 57.759 1.00 57.30 AT 1 1 7 . 1005 . POP H P2 56.998 -5.955 58.661 1.00 59.66 AT 1 1 7 . 1005 . POP H O4 57.491 -5.746 60.070 1.00 54.95 AT 1 1 7 . 1005 . POP H O5 56.004 -7.075 58.550 1.00 56.24 AT 1 1 7 . 1005 . POP H O6 56.427 -4.710 58.044 1.00 56.50 // |
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 1; NE 0; XX SQ SEQUENCE 65 AA; 7395 MW; 75FBE75B22FD3678 CRC64; MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT LKKAI XX RE 1 1 8 8 D ASP . . . . . C 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 RE 1 1 9 9 I ILE . . . . . C -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 RE 1 1 10 10 H HIS . . . . . T 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 RE 1 1 11 11 L LEU . . . . . T -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 RE 1 1 12 12 G GLY . . . . . T 91.01 -4.77 47.80 51.11 63.80 23.22 71.80 27.90 58.40 27.09 72.10 24.02 56.50 RE 1 1 13 13 Y TYR . . . . . T -74.99 115.31 107.80 100.62 47.30 100.09 56.40 0.52 1.50 66.13 48.50 34.48 45.20 RE 1 1 14 14 E GLU 1 1 H 5 . C -96.17 74.41 82.00 71.84 41.70 61.45 45.60 10.39 27.70 17.84 29.60 54.00 48.20 RE 1 1 15 15 Q GLN 1 1 H 5 . G -56.45 130.81 34.70 33.39 18.70 33.39 23.70 0.00 0.00 0.31 0.60 33.08 26.20 RE 1 1 16 16 F PHE 1 1 H 5 . G 57.56 29.90 146.10 150.86 75.60 136.18 83.00 14.68 41.50 136.40 82.50 14.46 42.20 RE 1 1 17 17 H HIS 1 1 H 5 . G 55.61 29.81 160.00 158.76 86.80 143.03 97.20 15.72 43.90 93.02 95.70 65.74 76.70 RE 1 1 18 18 K LYS 2 A E . . C -111.48 108.83 115.50 109.57 54.60 109.57 67.10 0.00 0.00 67.34 57.80 42.23 50.10 RE 1 1 19 19 P PRO 2 A E . 1 H -54.76 -17.53 74.50 83.79 61.60 82.99 69.20 0.80 4.90 82.99 68.60 0.80 5.30 RE 1 1 20 20 Q GLN 2 A E . 1 H -73.35 -35.75 120.10 112.90 63.30 111.79 79.30 1.11 3.00 28.62 54.80 84.28 66.70 RE 1 1 21 21 R ARG 2 A E . 1 H -68.53 -38.89 82.60 84.22 35.30 84.22 41.80 0.00 0.00 22.91 29.40 61.31 38.10 RE 1 1 22 22 E GLU 2 A E . 1 H -56.60 -42.19 71.00 59.66 34.60 59.41 44.10 0.25 0.70 17.46 29.00 42.20 37.70 RE 1 1 23 23 E GLU 2 A E . 1 H -66.34 -36.55 123.60 108.67 63.10 104.55 77.60 4.12 11.00 54.20 89.90 54.47 48.60 RE 1 1 24 24 E GLU 2 A E . 1 H -71.24 -35.34 80.40 71.99 41.80 67.32 50.00 4.67 12.40 41.76 69.30 30.23 27.00 RE 1 1 25 25 F PHE 2 A E . 1 H -63.59 -40.62 41.80 41.19 20.60 39.81 24.30 1.38 3.90 39.81 24.10 1.38 4.00 RE 1 1 26 26 A ALA 2 A E . 1 H -66.25 -43.69 46.10 46.40 43.00 41.37 59.60 5.03 13.10 42.55 59.60 3.85 10.50 RE 1 1 27 27 E GLU 2 A E . 1 H -60.95 -39.89 91.00 84.33 49.00 83.96 62.30 0.36 1.00 41.68 69.10 42.65 38.10 RE 1 1 28 28 A ALA 2 A E . 1 H -58.03 -47.16 55.00 58.08 53.80 52.98 76.30 5.10 13.20 54.38 76.20 3.70 10.10 RE 1 1 29 29 F PHE 2 A E . 1 H -61.12 -42.56 38.50 33.87 17.00 33.36 20.30 0.51 1.40 33.36 20.20 0.51 1.50 RE 1 1 30 30 K LYS 2 A E . 1 H -63.44 -42.40 104.70 105.98 52.80 105.45 64.60 0.53 1.40 58.41 50.10 47.56 56.50 RE 1 1 31 31 N ASN 2 A E . 1 H -60.26 -47.05 77.00 73.22 50.90 72.53 68.30 0.70 1.80 23.06 49.90 50.16 51.30 RE 1 1 32 32 A ALA 2 A E . 1 H -58.51 -48.57 56.20 56.15 52.00 49.87 71.80 6.28 16.30 51.18 71.70 4.97 13.60 RE 1 1 33 33 L LEU 2 A E . 1 H -61.69 -37.59 59.70 59.93 33.60 59.56 42.20 0.38 1.00 59.93 42.10 0.00 0.00 RE 1 1 34 34 E GLU 2 A E . 1 H -68.18 -35.02 87.40 76.92 44.70 76.19 56.50 0.74 2.00 33.77 56.00 43.15 38.50 RE 1 1 35 35 I ILE 2 A E . 1 H -69.89 -35.85 89.80 96.84 55.30 96.84 70.20 0.00 0.00 96.84 69.60 0.00 0.00 RE 1 1 36 36 A ALA 2 A E . 1 H -61.30 -45.01 19.20 19.50 18.10 19.22 27.70 0.27 0.70 19.22 26.90 0.27 0.70 RE 1 1 37 37 V VAL 2 A E . 1 H -64.92 -44.30 109.50 111.45 73.60 102.58 89.80 8.87 23.90 102.58 88.80 8.87 24.70 RE 1 1 38 38 Q GLN 2 A E . 1 H -59.93 -32.77 145.80 140.48 78.70 113.02 80.20 27.46 73.20 49.34 94.50 91.14 72.20 RE 1 1 39 39 E GLU 2 A E . 1 H -83.49 5.97 133.40 118.49 68.80 99.06 73.50 19.43 51.80 31.08 51.60 87.41 78.10 RE 1 1 40 40 N ASN . . . . . C 54.97 43.05 136.50 126.77 88.10 116.79 109.90 9.98 26.50 31.92 69.00 94.86 97.10 RE 1 1 41 41 V VAL . . . . . C -70.50 156.23 65.90 69.23 45.70 50.82 44.50 18.40 49.50 50.86 44.00 18.36 51.10 [Part of this file has been deleted for brevity] AT 1 1 . 50 50 L LEU P CD2 12.425 39.035 22.798 1.00 23.77 AT 1 1 1 . 402 . PO4 H P 34.178 32.996 46.387 1.00 60.84 AT 1 1 1 . 402 . PO4 H O1 35.146 33.243 45.291 1.00 57.95 AT 1 1 1 . 402 . PO4 H O2 34.912 32.751 47.670 1.00 59.15 AT 1 1 1 . 402 . PO4 H O3 33.291 34.184 46.538 1.00 58.92 AT 1 1 1 . 402 . PO4 H O4 33.352 31.796 46.060 1.00 61.86 AT 1 1 2 . 403 . MN H MN 8.130 27.788 21.899 1.00 36.09 AT 1 1 2 . 404 . MN H MN 5.801 27.935 24.271 1.00 39.57 AT 1 1 3 . 405 . MN H MN 36.023 34.916 44.253 1.00 39.52 AT 1 1 3 . 406 . MN H MN 33.658 36.365 46.296 1.00 33.69 AT 1 1 5 . 501 . SO4 H S 17.175 28.112 32.476 1.00 100.80 AT 1 1 5 . 501 . SO4 H O1 18.136 28.230 31.357 1.00 100.18 AT 1 1 5 . 501 . SO4 H O2 17.097 26.692 32.887 1.00 100.80 AT 1 1 5 . 501 . SO4 H O3 17.633 28.926 33.626 1.00 100.14 AT 1 1 5 . 501 . SO4 H O4 15.834 28.575 32.045 1.00 100.56 AT 1 1 5 . 502 . SO4 H S 0.566 29.512 36.007 1.00 86.73 AT 1 1 5 . 502 . SO4 H O1 1.690 28.556 35.971 1.00 87.27 AT 1 1 5 . 502 . SO4 H O2 -0.620 28.803 36.523 1.00 87.87 AT 1 1 5 . 502 . SO4 H O3 0.896 30.642 36.905 1.00 86.58 AT 1 1 5 . 502 . SO4 H O4 0.287 30.037 34.658 1.00 86.51 AT 1 1 5 . 503 . SO4 H S -13.586 39.644 36.031 1.00 100.28 AT 1 1 5 . 503 . SO4 H O1 -12.340 39.512 35.250 1.00 100.72 AT 1 1 5 . 503 . SO4 H O2 -14.638 38.811 35.421 1.00 100.46 AT 1 1 5 . 503 . SO4 H O3 -13.347 39.201 37.420 1.00 99.66 AT 1 1 5 . 503 . SO4 H O4 -14.020 41.056 36.015 1.00 99.97 AT 1 1 6 . 401 . 101 H P 7.599 25.305 23.994 1.00 56.33 AT 1 1 6 . 401 . 101 H O1P 8.249 24.467 25.030 1.00 56.70 AT 1 1 6 . 401 . 101 H O2P 6.700 26.285 24.649 1.00 54.49 AT 1 1 6 . 401 . 101 H O3P 8.637 26.026 23.216 1.00 53.97 AT 1 1 6 . 401 . 101 H O5* 7.095 23.970 23.128 1.00 59.20 AT 1 1 6 . 401 . 101 H C5* 7.073 23.961 21.762 1.00 66.74 AT 1 1 6 . 401 . 101 H C4* 6.041 23.013 21.296 1.00 71.22 AT 1 1 6 . 401 . 101 H O4* 6.029 21.855 22.189 1.00 73.78 AT 1 1 6 . 401 . 101 H C3* 4.736 23.676 21.350 1.00 73.80 AT 1 1 6 . 401 . 101 H O3* 4.355 23.874 19.995 1.00 76.51 AT 1 1 6 . 401 . 101 H C2* 3.864 22.749 22.165 1.00 74.04 AT 1 1 6 . 401 . 101 H C1* 4.682 21.474 22.506 1.00 74.70 AT 1 1 6 . 401 . 101 H N9 4.578 21.123 23.969 1.00 76.71 AT 1 1 6 . 401 . 101 H C8 3.630 21.533 24.876 1.00 76.87 AT 1 1 6 . 401 . 101 H N7 3.758 21.069 26.081 1.00 77.50 AT 1 1 6 . 401 . 101 H C5 4.896 20.300 25.989 1.00 77.78 AT 1 1 6 . 401 . 101 H C6 5.570 19.479 26.941 1.00 78.16 AT 1 1 6 . 401 . 101 H N6 5.155 19.409 28.200 1.00 78.77 AT 1 1 6 . 401 . 101 H N1 6.682 18.805 26.554 1.00 78.32 AT 1 1 6 . 401 . 101 H C2 7.090 18.888 25.277 1.00 78.14 AT 1 1 6 . 401 . 101 H N3 6.541 19.611 24.271 1.00 78.05 AT 1 1 6 . 401 . 101 H C4 5.403 20.288 24.700 1.00 78.10 AT 1 . . . 407 . HOH W O 5.997 27.242 22.189 1.00 38.84 AT 1 . . . 408 . HOH W O 35.697 35.756 46.350 1.00 41.39 AT 1 . . . 600 . HOH W O 20.825 31.690 27.031 1.00 20.90 // |
ID 2hhb XX DE HEMOGLOBIN (DEOXY) XX OS HUMAN (HOMO SAPIENS) XX EX METHOD xray; RESO 1.74; NMOD 1; NCHN 4; NGRP 0; XX CN [1] XX IN ID A; NR 141; NL 1; NH 7; NE 0; XX SQ SEQUENCE 141 AA; 15126 MW; 34D13618E62A33C1 CRC64; VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SVSTVLTSKY R XX CN [2] XX IN ID B; NR 146; NL 1; NH 8; NE 0; XX SQ SEQUENCE 146 AA; 15867 MW; EACBC707CFD466A1 CRC64; VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK EFTPPVQAAY QKVVAGVANA LAHKYH XX CN [3] XX IN ID C; NR 141; NL 1; NH 7; NE 0; XX SQ SEQUENCE 141 AA; 15126 MW; 34D13618E62A33C1 CRC64; VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SVSTVLTSKY R XX CN [4] XX IN ID D; NR 146; NL 2; NH 8; NE 0; XX SQ SEQUENCE 146 AA; 15867 MW; EACBC707CFD466A1 CRC64; VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK EFTPPVQAAY QKVVAGVANA LAHKYH XX RE 1 1 1 1 V VAL . . . . . C 360.00 130.57 137.00 142.86 94.30 113.45 99.30 29.40 79.10 113.56 98.30 29.29 81.40 RE 1 1 2 2 L LEU . . . . . C -80.50 121.94 16.80 18.20 10.20 7.73 5.50 10.48 27.90 7.73 5.40 10.48 28.80 RE 1 1 3 3 S SER 1 AA H 1 . C -71.32 164.78 44.40 44.59 38.30 44.42 56.90 0.17 0.40 39.26 80.90 5.34 7.90 RE 1 1 4 4 P PRO 1 AA H 1 1 H -62.31 -35.05 99.60 105.25 77.30 103.02 85.90 2.23 13.70 103.65 85.70 1.60 10.50 RE 1 1 5 5 A ALA 1 AA H 1 1 H -65.00 -41.52 59.80 65.59 60.80 64.35 92.70 1.24 3.20 64.35 90.20 1.24 3.40 RE 1 1 6 6 D ASP 1 AA H 1 1 H -56.29 -42.84 13.60 13.83 9.90 13.80 13.40 0.03 0.10 0.44 0.90 13.39 14.70 [Part of this file has been deleted for brevity] AT 1 . . . 174 . HOH W O -4.764 -6.228 5.515 8.00 40.89 AT 1 . . . 175 . HOH W O 23.809 19.925 1.758 8.00 39.37 AT 1 . . . 176 . HOH W O -7.871 -9.078 2.406 8.00 43.37 AT 1 . . . 177 . HOH W O 4.693 12.083 7.558 8.00 40.24 AT 1 . . . 178 . HOH W O 8.775 -23.438 16.055 8.00 42.33 AT 1 . . . 179 . HOH W O -7.480 -10.898 17.998 8.00 38.06 AT 1 . . . 180 . HOH W O -4.731 16.453 2.295 8.00 36.37 AT 1 . . . 181 . HOH W O -1.055 11.866 -0.448 8.00 43.19 AT 1 . . . 182 . HOH W O -27.610 -10.991 5.353 8.00 43.46 AT 1 . . . 183 . HOH W O 26.015 11.766 5.159 8.00 40.95 AT 1 . . . 184 . HOH W O -18.517 -8.355 15.267 8.00 35.55 AT 1 . . . 185 . HOH W O -14.034 2.806 -30.367 8.00 41.77 AT 1 . . . 186 . HOH W O -32.905 -9.033 0.480 8.00 43.68 AT 1 . . . 187 . HOH W O -28.749 -13.315 1.938 8.00 45.36 AT 1 . . . 188 . HOH W O 0.516 -8.074 -26.354 8.00 41.53 AT 1 . . . 189 . HOH W O -20.080 -9.873 -22.862 8.00 36.25 AT 1 . . . 190 . HOH W O -13.442 9.778 -13.572 8.00 39.70 AT 1 . . . 191 . HOH W O -24.804 -2.608 -15.488 8.00 37.79 AT 1 . . . 192 . HOH W O 6.547 9.706 16.296 8.00 41.86 AT 1 . . . 193 . HOH W O 0.029 22.606 14.164 8.00 43.02 AT 1 . . . 194 . HOH W O -11.367 0.306 28.463 8.00 44.30 AT 1 . . . 195 . HOH W O -19.950 -10.635 14.301 8.00 40.17 AT 1 . . . 196 . HOH W O -7.047 -6.324 20.098 8.00 36.98 AT 1 . . . 197 . HOH W O -23.876 1.108 14.102 8.00 33.31 AT 1 . . . 198 . HOH W O -34.199 8.033 11.037 8.00 40.72 AT 1 . . . 199 . HOH W O -14.173 13.393 -8.778 8.00 43.21 AT 1 . . . 200 . HOH W O 11.388 -11.044 24.763 8.00 39.34 AT 1 . . . 201 . HOH W O 3.735 -3.643 2.734 8.00 42.17 AT 1 . . . 202 . HOH W O 3.149 -0.692 2.083 8.00 41.40 AT 1 . . . 203 . HOH W O 4.511 -25.886 13.006 8.00 39.83 AT 1 . . . 204 . HOH W O 8.712 -21.655 3.577 8.00 43.08 AT 1 . . . 205 . HOH W O 22.926 -4.304 24.079 8.00 38.10 AT 1 . . . 206 . HOH W O 11.435 9.654 20.618 8.00 40.23 AT 1 . . . 207 . HOH W O 18.099 5.542 27.744 8.00 39.03 AT 1 . . . 208 . HOH W O 12.174 9.951 9.804 8.00 44.34 AT 1 . . . 209 . HOH W O 24.745 -2.501 15.270 8.00 39.78 AT 1 . . . 210 . HOH W O 24.231 0.100 14.764 8.00 42.94 AT 1 . . . 211 . HOH W O 23.324 -18.136 10.981 8.00 53.60 AT 1 . . . 212 . HOH W O 25.576 -22.211 6.309 8.00 45.18 AT 1 . . . 213 . HOH W O 14.639 24.823 -4.300 8.00 41.35 AT 1 . . . 214 . HOH W O 14.903 5.393 -23.047 8.00 37.45 AT 1 . . . 215 . HOH W O 16.650 -5.137 -16.717 8.00 39.12 AT 1 . . . 216 . HOH W O 7.424 -6.700 -20.085 8.00 38.62 AT 1 . . . 217 . HOH W O -1.263 -2.837 -21.251 8.00 45.10 AT 1 . . . 218 . HOH W O 23.120 -3.118 -12.992 8.00 37.05 AT 1 . . . 219 . HOH W O 23.664 0.968 -14.389 8.00 36.25 AT 1 . . . 220 . HOH W O 25.698 7.981 -15.362 8.00 35.85 AT 1 . . . 221 . HOH W O 30.009 16.347 -6.794 8.00 37.62 AT 1 . . . 222 . HOH W O 27.728 16.677 -1.376 8.00 42.54 AT 1 . . . 223 . HOH W O 8.142 18.836 1.041 8.00 39.90 // |
Add accessibility and secondary structure to a CCF file. Version: EMBOSS:6.4.0.0 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) (Any string) -mode menu [1] This option specifies the mode of operation. (Values: 1 (Use STRIDE only); 2 (Use NACCESS only); 3 (Use STRIDE and NACCESS)) * -thresholdsize integer [4] This option specifies the threshold size for SSEs (secondary structure elements) (Any integer value) [-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. -logfile outfile [pdbplus.log] This option specifies the name of the log file for PDBPLUS * -slogfile outfile [stride.log] This option specifies the name of the log file for STRIDE * -nlogfile outfile [naccess.log] This option specifies the name of the log file for NACCESS Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-ccfinpath" associated qualifiers -extension1 string Default file extension "-pdbindir" associated qualifiers -extension2 string Default file extension "-ccfoutdir" associated qualifiers -extension3 string Default file extension "-logfile" associated qualifiers -odirectory string Output directory "-slogfile" associated qualifiers -odirectory string Output directory "-nlogfile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to 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 and exit. 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 dying program messages -version boolean Report version number and exit
Qualifier | Type | Description | Allowed values | Default | ||||||
---|---|---|---|---|---|---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||||||||
[-ccfinpath] (Parameter 1) |
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. | Directory with files | ./ | ||||||
[-pdbindir] (Parameter 2) |
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 | Directory | ./ | ||||||
-pdbprefix | string | This option specifies the file prefix of PDB files (if any) | Any string | |||||||
-mode | list | This option specifies the mode of operation. |
|
1 | ||||||
-thresholdsize | integer | This option specifies the threshold size for SSEs (secondary structure elements) | Any integer value | 4 | ||||||
[-ccfoutdir] (Parameter 3) |
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. | Output directory | ./ | ||||||
-logfile | outfile | This option specifies the name of the log file for PDBPLUS | Output file | pdbplus.log | ||||||
-slogfile | outfile | This option specifies the name of the log file for STRIDE | Output file | stride.log | ||||||
-nlogfile | outfile | This option specifies the name of the log file for NACCESS | Output file | naccess.log | ||||||
Additional (Optional) qualifiers | ||||||||||
(none) | ||||||||||
Advanced (Unprompted) qualifiers | ||||||||||
(none) | ||||||||||
Associated qualifiers | ||||||||||
"-ccfinpath" associated dirlist qualifiers | ||||||||||
-extension1 -extension_ccfinpath |
string | Default file extension | Any string | ccf | ||||||
"-pdbindir" associated directory qualifiers | ||||||||||
-extension2 -extension_pdbindir |
string | Default file extension | Any string | ent | ||||||
"-ccfoutdir" associated outdir qualifiers | ||||||||||
-extension3 -extension_ccfoutdir |
string | Default file extension | Any string | ccf | ||||||
"-logfile" associated outfile qualifiers | ||||||||||
-odirectory | string | Output directory | Any string | |||||||
"-slogfile" associated outfile qualifiers | ||||||||||
-odirectory | string | Output directory | Any string | |||||||
"-nlogfile" associated outfile qualifiers | ||||||||||
-odirectory | string | Output directory | Any string | |||||||
General qualifiers | ||||||||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||
-warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||
-error | boolean | Report errors | Boolean value Yes/No | Y | ||||||
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||
-die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
% pdbplus Add accessibility and secondary structure to a CCF file. Clean protein structure coordinates directories [./]: ../pdbparse-keep/ Pdb entry directory [./]: 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 Clean protein structure coordinates file output directory [./]: Domainatrix log output file [pdbplus.log]: Stride program log output file [stride.log]: Naccess program log output file [naccess.log]: Processing /homes/user/test/qa/pdbparse-keep/1cs4.ccf /shared/software/bin/stride /homes/user/test/data/structure/1cs4.ent -f./pdbplus-1234567890.1234 /shared/software/bin/naccess /homes/user/test/data/structure/1cs4.ent Processing /homes/user/test/qa/pdbparse-keep/1ii7.ccf /shared/software/bin/stride /homes/user/test/data/structure/1ii7.ent -f./pdbplus-1234567890.1234 /shared/software/bin/naccess /homes/user/test/data/structure/1ii7.ent Processing /homes/user/test/qa/pdbparse-keep/2hhb.ccf /shared/software/bin/stride /homes/user/test/data/structure/2hhb.ent -f./pdbplus-1234567890.1234 /shared/software/bin/naccess /homes/user/test/data/structure/2hhb.ent STRIDE failures: 0 NACCESS failures: 0 |
Go to the output files for this example
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 amino acid property data from AAINDEX |
allversusall | Sequence similarity data from all-versus-all comparison |
cathparse | Generates DCF file from raw CATH files |
cutgextract | Extract codon usage tables from CUTG database |
domainer | Generates domain CCF files from protein CCF files |
domainnr | Removes redundant domains from a DCF file |
domainseqs | Adds sequence records to a DCF file |
domainsse | Add secondary structure records to a DCF file |
hetparse | Converts heterogen group dictionary to EMBL-like format |
jaspextract | Extract data from JASPAR |
pdbparse | Parses PDB files and writes protein CCF files |
pdbtosp | Convert swissprot:PDB codes file to EMBL-like format |
printsextract | Extract data from PRINTS database for use by pscan |
prosextract | Processes the PROSITE motif database for use by patmatmotifs |
rebaseextract | Process the REBASE database for use by restriction enzyme applications |
scopparse | Generate DCF file from raw SCOP files |
seqnr | Removes redundancy from DHF files |
sites | Generate residue-ligand CON files from CCF files |
ssematch | Search a DCF file for secondary structure matches |
tfextract | Process TRANSFAC transcription factor database for use by tfscan |
See also http://emboss.sourceforge.net/
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.