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_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 19 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 18 MODEL/S TEMP_BCM_111.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_R3Cons_em_bcr3.pdb'; Model: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 > ReadCoordsPdb(): After scanning there is(are) 18 model(s) > ReadCoordsPdb(): what model do you want [(1 to 18) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file DRR147D_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (18) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 43902 ATOM records read from file > ReadCoordsPdb(): --> 43902 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 0.304 0.860 0.695 0.491 GLY A 2 0.325 0.384 GLU A 3 0.488 0.695 0.574 0.923 0.863 THR A 4 0.983 0.999 1.000 4 4 VAL A 5 0.990 0.994 0.558 5 5 VAL A 6 0.995 0.998 0.841 6 6 ARG A 7 0.995 0.995 0.999 1.000 0.594 0.938 1.000 7 7 ASP A 8 0.988 0.996 0.825 0.888 8 8 ALA A 9 0.991 0.998 9 9 VAL A 10 0.999 1.000 0.999 10 10 THR A 11 0.998 0.999 1.000 11 11 ILE A 12 0.998 1.000 0.924 0.276 12 12 GLY A 13 0.995 0.943 13 13 LYS A 14 0.959 0.999 0.998 0.830 0.740 0.313 14 14 PRO A 15 0.997 1.000 0.983 0.968 15 15 ALA A 16 0.994 0.993 16 16 GLU A 17 1.000 0.999 0.833 0.999 0.950 17 17 GLN A 18 0.996 0.997 1.000 0.942 0.897 18 18 LEU A 19 0.999 0.994 0.999 0.999 19 19 TYR A 20 0.999 0.998 0.734 0.917 20 20 ALA A 21 0.999 0.991 21 21 VAL A 22 0.999 0.999 0.997 22 22 TRP A 23 0.995 0.997 0.659 0.347 23 23 ARG A 24 0.976 0.188 0.615 0.417 0.308 0.533 1.000 ASP A 25 0.091 0.699 0.998 0.951 LEU A 26 0.545 0.778 0.773 0.752 PRO A 27 0.979 0.535 0.887 0.825 GLY A 28 0.211 0.488 LEU A 29 0.516 0.811 0.916 0.924 PRO A 30 0.995 0.761 0.979 0.965 LEU A 31 0.248 0.725 0.973 0.620 LEU A 32 0.282 0.609 0.810 0.759 MET A 33 0.170 0.104 0.690 0.998 0.346 THR A 34 0.582 0.177 0.505 HIS A 35 0.442 0.103 0.425 0.320 LEU A 36 0.582 0.419 0.660 0.622 ARG A 37 0.202 0.396 0.525 0.922 0.685 0.689 1.000 SER A 38 0.341 0.305 0.166 VAL A 39 0.740 0.336 0.456 GLU A 40 0.652 0.487 0.853 0.854 0.877 VAL A 41 0.894 0.762 0.856 LEU A 42 0.801 0.986 0.470 0.589 42 ASP A 43 0.443 0.332 0.374 0.878 ASP A 44 0.725 0.857 0.548 0.811 LYS A 45 0.959 0.791 0.800 0.510 0.138 0.749 ARG A 46 0.490 0.965 0.569 0.813 0.307 0.589 1.000 SER A 47 0.700 0.435 0.030 ARG A 48 0.342 0.253 0.337 0.656 0.459 0.661 1.000 TRP A 49 0.237 0.149 0.559 0.197 THR A 50 0.384 0.152 0.528 VAL A 51 0.329 0.397 0.439 GLU A 52 0.586 0.611 0.738 0.998 0.959 ALA A 53 0.542 0.816 PRO A 54 0.993 0.968 0.947 0.907 54 54 ALA A 55 0.305 0.855 PRO A 56 0.992 0.985 0.913 0.842 56 56 LEU A 57 0.962 0.940 0.288 0.488 57 57 GLY A 58 0.045 0.279 ALA A 59 0.250 0.665 VAL A 60 0.698 0.277 0.444 SER A 61 0.308 0.250 0.027 TRP A 62 0.598 0.384 0.667 0.387 GLU A 63 0.911 0.980 0.631 0.341 0.754 63 63 ALA A 64 0.932 0.984 64 64 GLU A 65 0.977 0.992 0.882 0.839 0.741 65 65 LEU A 66 0.952 0.981 0.715 0.842 66 66 THR A 67 0.965 0.986 0.618 67 67 ALA A 68 0.979 0.992 68 68 ASP A 69 0.993 0.899 0.545 0.994 69 GLU A 70 0.925 0.895 0.996 0.506 0.833 70 PRO A 71 0.992 0.418 0.912 0.827 GLY A 72 0.317 0.925 LYS A 73 0.962 0.980 0.568 0.998 1.000 0.999 73 73 ARG A 74 0.991 0.995 0.999 0.952 0.574 0.623 1.000 74 74 ILE A 75 0.996 0.999 0.998 0.913 75 75 ALA A 76 0.979 0.996 76 76 TRP A 77 0.950 0.995 0.172 0.520 77 77 ARG A 78 0.967 0.965 0.317 0.832 0.476 0.871 1.000 78 78 SER A 79 0.926 0.410 0.228 LEU A 80 0.525 1.000 0.996 0.997 PRO A 81 0.989 0.992 0.892 0.816 81 81 GLY A 82 0.969 0.933 82 82 ALA A 83 0.924 0.485 ARG A 84 0.664 0.312 0.579 0.918 0.828 0.818 1.000 ILE A 85 0.629 0.420 0.372 1.000 GLU A 86 0.518 0.402 0.726 0.993 0.923 ASN A 87 0.942 0.993 0.685 0.617 87 87 SER A 88 0.940 0.993 0.289 88 88 GLY A 89 0.919 0.684 GLU A 90 0.978 0.996 0.789 0.996 0.830 90 90 VAL A 91 0.997 1.000 0.614 91 91 LEU A 92 0.995 0.998 0.978 0.987 92 92 PHE A 93 0.997 0.998 0.996 0.993 93 93 ARG A 94 0.996 1.000 0.683 0.997 0.795 0.996 1.000 94 94 PRO A 95 0.992 0.997 0.912 0.829 95 95 ALA A 96 0.966 1.000 96 96 PRO A 97 0.994 0.987 0.945 0.904 97 97 GLY A 98 0.899 0.816 98 ALA A 99 0.464 0.972 ARG A 100 0.987 0.969 0.996 0.997 0.776 0.996 1.000 100 100 GLY A 101 0.916 0.987 101 101 THR A 102 0.998 0.998 1.000 102 102 GLU A 103 0.997 0.997 0.866 0.998 0.839 103 103 VAL A 104 0.998 0.992 0.998 104 104 VAL A 105 0.997 0.999 1.000 105 105 VAL A 106 0.999 0.999 0.917 106 106 ARG A 107 0.996 0.991 0.998 0.994 0.635 0.649 1.000 107 107 LEU A 108 0.996 0.998 0.919 0.931 108 108 THR A 109 0.971 0.981 0.556 109 109 TYR A 110 0.972 0.977 0.401 0.884 110 110 ARG A 111 0.935 0.999 0.918 0.995 0.688 0.831 1.000 111 111 PRO A 112 0.995 0.999 0.939 0.883 112 112 PRO A 113 0.983 0.095 0.908 0.846 GLY A 114 0.462 0.128 GLY A 115 0.354 0.214 SER A 116 0.999 0.991 0.487 116 116 ALA A 117 1.000 0.999 117 117 GLY A 118 1.000 0.999 118 118 ALA A 119 0.999 1.000 119 119 VAL A 120 1.000 1.000 1.000 120 120 ILE A 121 1.000 1.000 1.000 1.000 121 121 ALA A 122 1.000 0.999 122 122 ARG A 123 0.999 0.996 0.866 0.998 0.934 0.992 1.000 123 123 MET A 124 1.000 0.998 0.663 0.994 0.551 124 124 PHE A 125 0.504 0.121 0.411 0.857 ASN A 126 0.394 0.092 0.671 0.889 GLN A 127 0.471 0.159 0.587 0.999 0.937 GLU A 128 0.343 0.862 0.663 0.715 0.897 PRO A 129 0.977 0.357 0.884 0.818 SER A 130 0.328 0.482 0.292 GLN A 131 0.515 0.104 0.850 0.639 0.831 GLN A 132 0.336 0.376 0.785 0.699 0.788 LEU A 133 0.507 0.615 0.827 0.808 ARG A 134 0.440 0.584 0.234 0.779 0.502 0.747 1.000 ASP A 135 1.000 0.998 0.807 0.896 135 135 ASP A 136 0.999 0.999 0.778 0.826 136 136 LEU A 137 0.999 0.998 0.930 0.998 137 137 MET A 138 1.000 0.999 0.703 0.595 0.910 138 138 ARG A 139 0.999 0.995 0.654 0.996 0.694 0.690 1.000 139 139 PHE A 140 1.000 0.998 0.704 0.855 140 140 LYS A 141 0.997 0.999 0.929 0.946 0.868 0.446 141 141 ARG A 142 0.999 0.991 0.707 0.916 0.764 0.760 1.000 142 142 GLU A 143 1.000 0.999 0.999 0.993 0.982 143 143 GLN A 144 0.997 0.996 0.695 0.626 0.795 144 144 GLU A 145 0.992 0.996 0.897 0.995 0.794 145 145 LEU A 146 0.988 0.974 0.582 0.570 146 146 GLY A 147 0.132 0.216 LEU A 148 0.476 0.284 0.526 0.589 GLU A 149 0.332 0.157 0.534 0.681 0.834 HIS A 150 0.372 0.485 0.296 0.360 HIS A 151 0.564 0.527 0.414 0.034 HIS A 152 0.645 0.326 0.513 0.608 HIS A 153 0.331 0.388 0.526 0.241 HIS A 154 0.344 0.130 0.528 0.599 HIS A 155 0.910 0.553 0.142 Ranges: 10 from: A 4 to A 23 from: A 56 to A 57 from: A 63 to A 68 from: A 73 to A 78 from: A 81 to A 82 from: A 87 to A 88 from: A 90 to A 97 from: A 100 to A 112 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[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 1 is: 1.959 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 2 is: 3.712 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 3 is: 3.294 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 4 is: 2.398 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 5 is: 3.901 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 6 is: 2.544 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 7 is: 3.908 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 8 is: 2.619 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 9 is: 3.279 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 10 is: 2.714 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 11 is: 2.832 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 12 is: 2.177 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 13 is: 3.445 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 14 is: 3.748 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 15 is: 2.717 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 16 is: 1.592 (*) > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 17 is: 3.628 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 18 is: 4.486 > > Kabsch RMSD statistics for 18 structures: > Mean RMSD using as refer. str. `average' for res.[4..23],[56..57],[63..68],[73..78],[81..82],[87..88],[90..97],[100..112],[116..124],[135..146], is: 3.053 > Range of RMSD values to reference struct. is 1.592 to 4.486 > 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[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 1 is: 2.458 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 2 is: 3.985 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 3 is: 3.443 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 4 is: 2.961 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 5 is: 4.150 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 6 is: 2.836 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 7 is: 4.110 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 8 is: 2.902 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 9 is: 3.692 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 10 is: 3.078 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 11 is: 3.202 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 12 is: 2.657 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 13 is: 3.620 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 14 is: 3.807 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 15 is: 2.998 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 16 is: 1.987 (*) > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 17 is: 3.878 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[63..68],A[73..78],A[81..82],A[87..88],A[90..97],A[100..112],A[116..124],A[135..146],for model 18 is: 4.612 > > Kabsch RMSD statistics for 18 structures: > Mean RMSD using as refer. str. `average' for res.[4..23],[56..57],[63..68],[73..78],[81..82],[87..88],[90..97],[100..112],[116..124],[135..146], is: 3.354 > Range of RMSD values to reference struct. is 1.987 to 4.612 PdbStat> PdbStat> *END* of program detected, BYE! ...