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 `BER31_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 01-APR-08 2K2E > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF BORDETELLA PERTUSSIS PROTEIN > ReadCoordsPdb(): >> TITLE 2 BP2786, A MTH938-LIKE DOMAIN. NORTHEAST STRUCTURAL > ReadCoordsPdb(): >> TITLE 3 GENOMICS CONSORTIUM TARGET BER31 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `BER31_NMR_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 BER31_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 47340 ATOM records read from file > ReadCoordsPdb(): --> 47340 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 0.429 0.849 0.662 0.472 LYS A 2 0.803 0.434 0.619 0.846 0.790 0.216 LEU A 3 0.945 0.516 0.756 0.551 HIS A 4 0.862 0.438 0.649 0.386 THR A 5 0.881 0.583 0.541 ASP A 6 0.635 0.910 0.380 0.218 PRO A 7 0.972 0.406 0.920 0.876 ALA A 8 0.571 0.439 THR A 9 0.938 0.445 0.742 ALA A 10 0.758 0.286 LEU A 11 0.815 0.765 0.865 0.785 ASN A 12 0.764 0.943 0.613 0.614 THR A 13 0.946 0.991 0.997 13 13 VAL A 14 0.997 0.986 0.922 14 14 THR A 15 0.985 0.977 0.841 15 15 ALA A 16 0.963 0.932 16 16 TYR A 17 0.943 0.424 0.627 0.424 GLY A 18 0.373 0.537 ASP A 19 0.780 0.257 0.580 0.517 GLY A 20 0.309 0.861 TYR A 21 0.945 0.967 0.993 0.091 21 21 ILE A 22 0.979 0.985 0.998 0.941 22 22 GLU A 23 0.990 0.996 0.996 0.769 0.240 23 23 VAL A 24 0.988 0.984 0.999 24 24 ASN A 25 0.998 0.552 0.640 0.309 GLN A 26 0.410 0.968 0.921 0.923 0.854 VAL A 27 0.967 0.994 0.999 27 27 ARG A 28 0.994 0.993 0.595 0.987 0.350 0.518 0.999 28 28 PHE A 29 0.993 0.969 0.999 0.996 29 29 SER A 30 0.993 0.931 0.650 30 30 HIS A 31 0.969 0.989 0.790 0.567 31 31 ALA A 32 0.989 0.987 32 32 ILE A 33 0.993 0.992 1.000 1.000 33 33 ALA A 34 0.995 0.993 34 34 PHE A 35 0.993 0.997 0.999 1.000 35 35 ALA A 36 0.983 0.998 36 36 PRO A 37 0.992 0.836 0.937 0.860 37 GLU A 38 0.843 0.788 0.523 0.651 0.317 GLY A 39 0.807 0.882 39 PRO A 40 0.972 0.936 0.977 0.975 40 40 VAL A 41 0.976 0.987 1.000 41 41 ALA A 42 0.968 0.966 42 42 SER A 43 0.972 0.985 0.302 43 43 TRP A 44 0.991 0.990 0.899 0.987 44 44 PRO A 45 0.995 0.962 0.956 0.891 45 45 VAL A 46 0.982 0.977 0.996 46 46 GLN A 47 0.978 0.952 0.794 0.727 0.847 47 47 ARG A 48 0.958 0.979 0.659 0.819 0.461 0.566 0.998 48 48 PRO A 49 0.998 0.973 0.945 0.861 49 49 ALA A 50 0.994 0.983 50 50 ASP A 51 0.965 0.906 0.942 0.694 51 51 ILE A 52 0.954 0.991 0.999 1.000 52 52 THR A 53 0.978 0.991 0.649 53 53 ALA A 54 0.996 0.994 54 54 SER A 55 0.999 0.997 0.777 55 55 LEU A 56 0.999 0.997 0.998 0.998 56 56 LEU A 57 0.998 0.999 0.999 1.000 57 57 GLN A 58 0.999 0.998 0.938 0.999 0.900 58 58 GLN A 59 0.999 0.999 0.996 0.998 0.975 59 59 ALA A 60 0.996 0.993 60 60 ALA A 61 0.997 0.994 61 61 GLY A 62 0.985 0.960 62 62 LEU A 63 0.991 0.863 0.929 0.938 63 ALA A 64 0.847 0.340 GLU A 65 0.952 0.391 0.595 0.538 0.271 VAL A 66 0.923 0.681 0.637 VAL A 67 0.858 0.509 0.577 ARG A 68 0.755 0.362 0.809 0.993 0.235 0.629 0.999 ASP A 69 0.572 0.630 0.568 0.304 PRO A 70 0.973 0.499 0.924 0.885 LEU A 71 0.979 0.942 0.704 0.358 71 71 ALA A 72 0.842 0.440 PHE A 73 0.923 0.287 0.642 0.713 LEU A 74 0.775 0.122 0.645 0.631 ASP A 75 0.717 0.195 0.281 0.274 GLU A 76 0.364 0.829 0.513 0.496 0.342 PRO A 77 0.952 0.292 0.933 0.896 GLU A 78 0.734 0.091 0.626 0.655 0.280 ALA A 79 0.864 0.329 GLY A 80 0.135 0.202 ALA A 81 0.769 0.349 GLY A 82 0.341 0.142 ALA A 83 0.382 0.209 ARG A 84 0.943 0.951 0.438 0.786 0.128 0.745 0.999 84 84 PRO A 85 0.979 0.328 0.937 0.892 ALA A 86 0.562 0.759 ASN A 87 0.427 0.790 0.565 0.388 ALA A 88 0.805 0.952 88 PRO A 89 0.987 0.959 0.937 0.861 89 89 GLU A 90 0.985 0.996 0.522 0.853 0.430 90 90 VAL A 91 0.997 0.998 0.999 91 91 LEU A 92 0.998 0.996 0.932 0.949 92 92 LEU A 93 0.997 0.993 0.999 1.000 93 93 VAL A 94 0.995 0.994 1.000 94 94 GLY A 95 0.990 0.985 95 95 THR A 96 0.957 0.735 0.833 GLY A 97 0.532 0.796 ARG A 98 0.924 0.825 0.540 0.909 0.540 0.601 0.998 98 ARG A 99 0.782 0.893 0.413 0.722 0.744 0.488 0.998 GLN A 100 0.984 0.960 0.577 0.815 0.743 100 100 HIS A 101 0.940 0.955 0.718 0.208 101 101 LEU A 102 0.977 0.962 0.552 0.396 102 102 LEU A 103 0.985 0.946 0.997 0.999 103 103 GLY A 104 1.000 0.981 104 104 PRO A 105 0.995 0.972 0.936 0.862 105 105 GLU A 106 0.972 0.984 0.587 0.280 0.352 106 106 GLN A 107 0.984 0.977 0.998 0.993 0.900 107 107 VAL A 108 0.987 0.977 0.941 108 108 ARG A 109 0.998 0.997 0.697 0.765 0.211 0.713 0.999 109 109 PRO A 110 0.997 0.997 0.949 0.888 110 110 LEU A 111 0.995 0.997 0.998 0.999 111 111 LEU A 112 0.999 0.998 0.935 0.857 112 112 ALA A 113 0.998 0.993 113 113 MET A 114 0.993 0.979 0.998 0.999 0.858 114 114 GLY A 115 0.980 0.989 115 115 VAL A 116 0.989 0.993 0.999 116 116 GLY A 117 0.994 0.970 117 117 VAL A 118 0.981 0.991 0.923 118 118 GLU A 119 0.984 0.975 0.898 0.444 0.315 119 119 ALA A 120 0.988 0.989 120 120 MET A 121 0.997 0.986 0.797 0.999 0.927 121 121 ASP A 122 0.981 0.993 0.493 0.327 122 122 THR A 123 0.997 0.993 0.725 123 123 GLN A 124 0.994 0.996 0.804 0.855 0.742 124 124 ALA A 125 0.999 0.998 125 125 ALA A 126 0.999 0.998 126 126 ALA A 127 0.999 0.997 127 127 ARG A 128 0.998 0.997 0.626 0.990 0.250 0.686 0.999 128 128 THR A 129 0.999 0.998 0.952 129 129 TYR A 130 0.999 0.999 0.991 0.997 130 130 ASN A 131 0.998 0.996 0.603 0.445 131 131 ILE A 132 0.998 0.998 0.999 0.921 132 132 LEU A 133 0.998 0.997 0.878 0.775 133 133 MET A 134 0.999 0.995 0.931 0.996 0.668 134 134 ALA A 135 0.996 0.993 135 135 GLU A 136 0.991 0.983 0.559 0.588 0.402 136 136 GLY A 137 0.938 0.958 137 137 ARG A 138 0.970 0.962 0.605 0.919 0.520 0.691 0.997 138 138 ARG A 139 0.963 0.968 0.936 0.500 0.265 0.573 0.998 139 139 VAL A 140 0.988 0.997 1.000 140 140 VAL A 141 0.995 0.996 0.999 141 141 VAL A 142 0.996 0.998 0.999 142 142 ALA A 143 0.995 0.997 143 143 LEU A 144 0.995 0.994 0.999 1.000 144 144 LEU A 145 0.987 0.949 0.855 0.957 145 145 PRO A 146 0.983 0.756 0.945 0.908 ASP A 147 0.622 0.394 0.625 0.346 GLY A 148 0.922 0.924 148 148 ASP A 149 0.484 0.189 0.430 0.432 SER A 150 0.855 0.203 0.591 LEU A 151 0.865 0.204 0.557 0.473 GLU A 152 0.956 0.626 0.481 0.669 0.288 HIS A 153 0.924 0.681 0.783 0.179 HIS A 154 0.930 0.284 0.665 0.387 HIS A 155 0.952 0.575 0.715 0.259 HIS A 156 0.809 0.338 0.675 0.250 HIS A 157 0.931 0.158 0.534 0.206 HIS A 158 0.786 0.411 0.370 Ranges: 6 from: A 13 to A 16 from: A 21 to A 24 from: A 27 to A 36 from: A 40 to A 62 from: A 89 to A 95 from: A 100 to A 145 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[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 1 is: 0.567 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 2 is: 0.594 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 3 is: 0.581 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 4 is: 0.626 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 5 is: 0.548 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 6 is: 0.524 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 7 is: 0.537 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 8 is: 0.565 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 9 is: 0.601 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 10 is: 0.489 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 11 is: 0.449 (*) > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 12 is: 0.628 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 13 is: 0.681 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 14 is: 0.645 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 15 is: 0.548 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 16 is: 0.548 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 17 is: 0.680 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 18 is: 0.652 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 19 is: 0.706 > Kabsch RMSD of backbone atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 20 is: 0.713 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[13..16],[21..24],[27..36],[40..62],[89..95],[100..145], is: 0.594 > Range of RMSD values to reference struct. is 0.449 to 0.713 > 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[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 1 is: 0.974 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 2 is: 0.918 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 3 is: 0.929 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 4 is: 1.005 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 5 is: 0.887 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 6 is: 0.885 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 7 is: 0.914 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 8 is: 1.086 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 9 is: 1.065 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 10 is: 0.881 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 11 is: 0.865 (*) > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 12 is: 0.962 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 13 is: 1.073 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 14 is: 1.067 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 15 is: 1.051 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 16 is: 1.009 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 17 is: 1.082 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 18 is: 0.975 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 19 is: 1.618 > Kabsch RMSD of heavy atoms in res. A[13..16],A[21..24],A[27..36],A[40..62],A[89..95],A[100..145],for model 20 is: 1.016 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[13..16],[21..24],[27..36],[40..62],[89..95],[100..145], is: 1.013 > Range of RMSD values to reference struct. is 0.865 to 1.618 PdbStat> PdbStat> *END* of program detected, BYE! ...