Running PDBSTAT from Linux Ayuda is on: /farm/software/PdbStat/PdbStat-5.7 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2012 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.7-exp dom mar 10 23:17:04 UTC 2013 ** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ===============> W E L C O M E to PDBStat <================ PDBStat has become a tool able (between other things) of: a) read and interconvert between DISMAN, DYANA, PDB, DISCOVER, IMPACT b) elaborate some info about the molecule as MW, Radius of gyration, .. c) investigate the setereochemical quality of a protein by evaluating phi, psi, chi1, impropers and chirality The sequence of acts should be: 1.- read a file (coords, constr) 2.- read a sequence file (can be free format) 3.- Follow menu (calculating, writing ...) NOTE: Be aware that if you read in a constraint file you *ALWAYS* need to read a sequence file also HAVE FUN AND ENJOY !! **** For more info type `help' or `menu' **** --> ... Reading/Loading Distances file ... 125 distance records read --> ... Reading/Loading Dihedral Library .. 1119 library records read PdbStat> [rea]d [hel]p [his]tory [men]u [phi] [qui]t... PdbStat> leyendo PDB > locate_file(): file `DRR147D_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP.PDB, 20 MODEL/S TEMP.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 155 MET GLY GLU THR VAL VAL ARG ASP ALA VAL THR ILE GLY 1 > ReadCoordsPdb(): Counting models in file `DRR147D_R3_em_bcr3.pdb'; Model: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 > ReadCoordsPdb(): After scanning there is(are) 20 model(s) > ReadCoordsPdb(): what model do you want [(1 to 20) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file DRR147D_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 48780 ATOM records read from file > ReadCoordsPdb(): --> 48780 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > ReadCoordsPdb(): ** monomer, 1 [1] chains ** PdbStat> > calc_order_parameters(): ... Evaluating Dihedrals CHAIN .GT. SUM.GT. RES ID DIH S(phi) S(psi) S(chi1) S(chi2) S(chi3) S(chi4) S(chi5) 0.90 1.6 ----------------------------------------------------------------------------------- MET A 1 0.324 0.605 0.368 0.267 GLY A 2 0.326 0.325 GLU A 3 0.515 0.776 0.493 0.794 0.842 THR A 4 0.895 0.963 0.864 4 VAL A 5 0.959 0.996 1.000 5 5 VAL A 6 0.948 0.972 0.779 6 6 ARG A 7 0.939 0.970 0.596 0.945 0.441 0.904 1.000 7 7 ASP A 8 0.976 0.986 0.879 0.905 8 8 ALA A 9 0.962 0.998 9 9 VAL A 10 0.991 0.981 0.619 10 10 THR A 11 0.987 0.998 0.799 11 11 ILE A 12 0.995 0.998 0.999 0.847 12 12 GLY A 13 0.998 0.946 13 13 LYS A 14 0.951 0.993 0.996 0.594 0.827 0.818 14 14 PRO A 15 0.998 0.998 0.983 0.970 15 15 ALA A 16 0.989 0.988 16 16 GLU A 17 0.988 0.984 0.584 0.847 0.964 17 17 GLN A 18 0.972 0.976 0.999 0.663 0.898 18 18 LEU A 19 0.980 0.958 0.999 0.998 19 19 TYR A 20 0.971 0.952 0.358 0.880 20 20 ALA A 21 0.976 0.876 21 VAL A 22 0.946 0.978 0.520 22 22 TRP A 23 0.957 0.972 0.708 0.350 23 23 ARG A 24 0.969 0.235 0.861 0.606 0.713 0.537 1.000 ASP A 25 0.115 0.551 0.394 0.937 LEU A 26 0.414 0.778 0.602 0.607 PRO A 27 0.983 0.469 0.903 0.845 GLY A 28 0.172 0.530 LEU A 29 0.557 0.807 0.735 0.758 PRO A 30 0.996 0.763 0.998 1.000 LEU A 31 0.278 0.759 0.849 0.864 LEU A 32 0.392 0.556 0.856 0.721 MET A 33 0.272 0.158 0.599 0.717 0.264 THR A 34 0.572 0.153 0.563 HIS A 35 0.389 0.083 0.424 0.279 LEU A 36 0.567 0.364 0.531 0.580 ARG A 37 0.216 0.342 0.440 0.808 0.496 0.829 1.000 SER A 38 0.384 0.205 0.047 VAL A 39 0.725 0.278 0.542 GLU A 40 0.547 0.350 0.874 0.497 0.937 VAL A 41 0.868 0.776 0.794 LEU A 42 0.789 0.965 0.467 0.571 ASP A 43 0.379 0.214 0.404 0.890 ASP A 44 0.629 0.812 0.217 0.935 LYS A 45 0.944 0.750 0.706 0.564 0.925 0.589 ARG A 46 0.505 0.927 0.724 0.811 0.053 0.536 1.000 SER A 47 0.472 0.374 0.134 ARG A 48 0.284 0.277 0.252 0.653 0.525 0.725 1.000 TRP A 49 0.230 0.144 0.422 0.237 THR A 50 0.332 0.162 0.494 VAL A 51 0.291 0.410 0.452 GLU A 52 0.612 0.514 0.751 0.732 0.910 ALA A 53 0.440 0.803 PRO A 54 0.990 0.895 0.934 0.889 54 ALA A 55 0.278 0.822 PRO A 56 0.988 0.979 0.900 0.824 56 56 LEU A 57 0.965 0.921 0.340 0.700 57 57 GLY A 58 0.138 0.290 ALA A 59 0.268 0.640 VAL A 60 0.699 0.190 0.533 SER A 61 0.325 0.252 0.159 TRP A 62 0.598 0.298 0.111 0.233 GLU A 63 0.791 0.966 0.212 0.136 0.713 ALA A 64 0.890 0.893 64 GLU A 65 0.899 0.950 0.930 0.823 0.774 65 LEU A 66 0.956 0.966 0.606 0.655 66 66 THR A 67 0.951 0.976 0.479 67 67 ALA A 68 0.968 0.987 68 68 ASP A 69 0.974 0.875 0.506 0.976 69 GLU A 70 0.887 0.918 0.848 0.409 0.716 70 PRO A 71 0.990 0.415 0.908 0.833 GLY A 72 0.193 0.939 LYS A 73 0.957 0.973 0.595 0.934 1.000 1.000 73 73 ARG A 74 0.985 0.979 0.503 0.995 0.482 0.547 1.000 74 74 ILE A 75 0.981 0.984 0.727 0.782 75 75 ALA A 76 0.956 0.982 76 76 TRP A 77 0.919 0.893 0.073 0.310 77 ARG A 78 0.970 0.945 0.176 0.571 0.500 0.657 1.000 78 78 SER A 79 0.880 0.453 0.164 LEU A 80 0.560 0.984 0.869 0.792 PRO A 81 0.994 0.991 0.937 0.887 81 81 GLY A 82 0.972 0.919 82 82 ALA A 83 0.889 0.507 ARG A 84 0.664 0.319 0.569 0.806 0.861 0.889 1.000 ILE A 85 0.687 0.389 0.586 0.777 GLU A 86 0.472 0.255 0.655 0.695 0.885 ASN A 87 0.888 0.874 0.649 0.443 87 SER A 88 0.862 0.940 0.113 88 GLY A 89 0.826 0.707 GLU A 90 0.935 0.971 0.472 0.995 0.917 90 90 VAL A 91 0.986 0.997 0.920 91 91 LEU A 92 0.994 0.993 0.459 0.591 92 92 PHE A 93 0.994 0.981 0.996 0.868 93 93 ARG A 94 0.956 0.970 0.576 0.929 0.674 0.943 1.000 94 94 PRO A 95 0.994 0.991 0.920 0.844 95 95 ALA A 96 0.995 0.983 96 96 PRO A 97 0.995 0.985 0.950 0.912 97 97 GLY A 98 0.898 0.581 ALA A 99 0.317 0.984 ARG A 100 0.967 0.897 0.775 0.858 0.505 0.827 1.000 100 GLY A 101 0.814 0.972 101 THR A 102 0.991 0.997 1.000 102 102 GLU A 103 0.989 0.993 0.865 0.998 0.776 103 103 VAL A 104 0.992 0.995 1.000 104 104 VAL A 105 0.995 0.997 1.000 105 105 VAL A 106 0.994 0.990 1.000 106 106 ARG A 107 0.972 0.965 0.601 0.995 0.529 0.574 1.000 107 107 LEU A 108 0.976 0.972 0.278 0.659 108 108 THR A 109 0.914 0.986 1.000 109 109 TYR A 110 0.908 0.870 0.130 0.788 110 ARG A 111 0.880 0.955 0.440 0.874 0.657 0.732 1.000 111 PRO A 112 0.988 0.965 0.898 0.820 112 112 PRO A 113 0.988 0.181 0.905 0.838 GLY A 114 0.295 0.155 GLY A 115 0.153 0.285 SER A 116 0.976 0.980 0.493 116 116 ALA A 117 0.997 0.994 117 117 GLY A 118 0.997 0.990 118 118 ALA A 119 0.995 0.993 119 119 VAL A 120 0.998 0.999 1.000 120 120 ILE A 121 0.995 0.986 0.649 0.878 121 121 ALA A 122 0.996 0.997 122 122 ARG A 123 0.979 0.986 0.671 0.999 0.868 0.883 1.000 123 123 MET A 124 0.997 0.984 0.714 0.655 0.209 124 124 PHE A 125 0.442 0.107 0.484 0.832 ASN A 126 0.369 0.145 0.638 0.871 GLN A 127 0.416 0.177 0.482 0.711 0.909 GLU A 128 0.227 0.865 0.511 0.559 0.884 PRO A 129 0.982 0.305 0.896 0.835 SER A 130 0.344 0.317 0.212 GLN A 131 0.358 0.099 0.857 0.459 0.860 GLN A 132 0.293 0.372 0.583 0.404 0.626 LEU A 133 0.526 0.588 0.698 0.886 ARG A 134 0.490 0.611 0.255 0.741 0.708 0.623 1.000 ASP A 135 0.990 0.984 0.736 0.882 135 135 ASP A 136 0.982 0.985 0.955 0.944 136 136 LEU A 137 0.987 0.974 0.664 0.547 137 137 MET A 138 0.994 0.985 0.671 0.304 0.270 138 138 ARG A 139 0.984 0.994 0.512 0.929 0.791 0.723 1.000 139 139 PHE A 140 0.986 0.991 0.578 0.735 140 140 LYS A 141 0.995 0.987 0.880 0.907 0.996 0.552 141 141 ARG A 142 0.979 0.973 0.672 0.999 0.638 0.711 1.000 142 142 GLU A 143 0.988 0.985 0.998 0.772 0.953 143 143 GLN A 144 0.985 0.985 0.705 0.350 0.725 144 144 GLU A 145 0.971 0.957 0.218 0.921 0.842 145 145 LEU A 146 0.975 0.972 0.924 0.933 146 146 GLY A 147 0.232 0.227 LEU A 148 0.415 0.345 0.603 0.644 GLU A 149 0.366 0.155 0.493 0.661 0.887 HIS A 150 0.426 0.462 0.421 0.548 HIS A 151 0.563 0.531 0.519 0.225 HIS A 152 0.679 0.378 0.403 0.409 HIS A 153 0.427 0.356 0.328 0.313 HIS A 154 0.447 0.095 0.550 0.665 HIS A 155 0.876 0.528 0.273 Ranges: 10 from: A 5 to A 20 from: A 22 to A 23 from: A 56 to A 57 from: A 66 to A 68 from: A 73 to A 76 from: A 81 to A 82 from: A 90 to A 97 from: A 102 to A 109 from: A 116 to A 124 from: A 135 to A 146 PdbStat> > do_average_coords(): Making average for backbone atoms > do_average_coords(): Calculating center of masses > do_average_coords(): Calling optimal rotation for backbone onto model 1 > do_average_coords(): Calc. average coordinates backbone > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 1 is: 3.196 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 2 is: 5.273 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 3 is: 6.192 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 4 is: 2.648 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 5 is: 4.089 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 6 is: 2.519 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 7 is: 3.139 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 8 is: 4.385 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 9 is: 4.172 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 10 is: 4.383 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 11 is: 3.436 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 12 is: 4.061 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 13 is: 2.867 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 14 is: 4.060 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 15 is: 3.074 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 16 is: 4.614 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 17 is: 2.271 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 18 is: 4.400 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 19 is: 3.018 > Kabsch RMSD of backbone atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 20 is: 1.656 (*) > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[5..20],[22..23],[56..57],[66..68],[73..76],[81..82],[90..97],[102..109],[116..124],[135..146], is: 3.673 > Range of RMSD values to reference struct. is 1.656 to 6.192 > do_average_coords(): Making average for heavy atoms > do_average_coords(): Calculating center of masses > do_average_coords(): Calling optimal rotation for heavy onto model 1 > do_average_coords(): Calc. average coordinates heavy > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 1 is: 3.432 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 2 is: 5.247 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 3 is: 6.187 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 4 is: 2.888 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 5 is: 4.575 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 6 is: 2.785 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 7 is: 3.460 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 8 is: 4.394 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 9 is: 4.444 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 10 is: 4.502 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 11 is: 3.582 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 12 is: 4.247 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 13 is: 3.337 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 14 is: 4.154 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 15 is: 3.372 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 16 is: 4.743 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 17 is: 2.805 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 18 is: 4.677 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 19 is: 3.389 > Kabsch RMSD of heavy atoms in res. A[5..20],A[22..23],A[56..57],A[66..68],A[73..76],A[81..82],A[90..97],A[102..109],A[116..124],A[135..146],for model 20 is: 2.225 (*) > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[5..20],[22..23],[56..57],[66..68],[73..76],[81..82],[90..97],[102..109],[116..124],[135..146], is: 3.922 > Range of RMSD values to reference struct. is 2.225 to 6.187 PdbStat> PdbStat> *END* of program detected, BYE! ...