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_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 158 MET LYS LEU HIS THR ASP PRO ALA THR ALA LEU ASN THR 1 > ReadCoordsPdb(): Counting models in file `BER31_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 BER31_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 47160 ATOM records read from file > ReadCoordsPdb(): --> 47160 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 0.467 0.800 0.530 0.256 LYS A 2 0.872 0.428 0.693 0.999 1.000 0.999 LEU A 3 0.955 0.528 0.663 0.687 HIS A 4 0.892 0.499 0.412 0.501 THR A 5 0.883 0.595 0.273 ASP A 6 0.588 0.886 0.669 0.962 PRO A 7 0.987 0.231 0.904 0.836 ALA A 8 0.556 0.379 THR A 9 0.910 0.464 0.474 ALA A 10 0.744 0.182 LEU A 11 0.844 0.676 0.796 0.743 ASN A 12 0.759 0.871 0.697 0.864 THR A 13 0.816 0.951 0.329 13 VAL A 14 0.977 0.994 0.873 14 14 THR A 15 0.980 0.964 0.510 15 15 ALA A 16 0.968 0.926 16 16 TYR A 17 0.919 0.454 0.408 0.989 GLY A 18 0.356 0.552 ASP A 19 0.819 0.271 0.534 0.938 GLY A 20 0.256 0.881 TYR A 21 0.923 0.993 0.771 0.930 21 21 ILE A 22 0.989 0.987 0.999 0.654 22 22 GLU A 23 0.995 0.997 0.873 0.989 0.873 23 23 VAL A 24 0.988 0.994 1.000 24 24 ASN A 25 0.994 0.503 0.635 0.812 GLN A 26 0.335 0.968 0.844 0.808 0.935 VAL A 27 0.991 0.995 1.000 27 27 ARG A 28 0.992 0.975 0.710 0.998 0.580 0.817 1.000 28 28 PHE A 29 0.975 0.982 0.998 0.999 29 29 SER A 30 0.962 0.938 0.781 30 30 HIS A 31 0.968 0.996 0.700 0.813 31 31 ALA A 32 0.998 0.991 32 32 ILE A 33 0.994 0.982 0.936 0.760 33 33 ALA A 34 0.980 0.993 34 34 PHE A 35 0.995 0.996 0.997 0.999 35 35 ALA A 36 0.953 0.998 36 36 PRO A 37 0.992 0.876 0.900 0.818 37 GLU A 38 0.840 0.775 0.790 0.783 0.896 GLY A 39 0.807 0.802 39 PRO A 40 0.989 0.975 0.944 0.913 40 40 VAL A 41 0.970 0.994 1.000 41 41 ALA A 42 0.990 0.981 42 42 SER A 43 0.981 0.986 0.533 43 43 TRP A 44 0.980 0.957 0.722 0.949 44 44 PRO A 45 0.980 0.786 0.868 0.817 VAL A 46 0.877 0.991 0.998 46 GLN A 47 0.974 0.956 0.859 0.395 0.793 47 47 ARG A 48 0.931 0.966 0.167 0.686 0.438 0.785 1.000 48 48 PRO A 49 0.991 0.987 0.902 0.815 49 49 ALA A 50 0.988 0.981 50 50 ASP A 51 0.955 0.869 0.874 0.954 51 ILE A 52 0.968 0.997 0.999 1.000 52 52 THR A 53 0.968 0.994 0.722 53 53 ALA A 54 0.998 0.995 54 54 SER A 55 0.992 0.994 0.480 55 55 LEU A 56 0.991 0.994 0.924 0.853 56 56 LEU A 57 0.998 0.998 0.988 0.914 57 57 GLN A 58 0.998 0.996 0.603 0.998 0.929 58 58 GLN A 59 0.997 0.998 0.816 0.704 0.896 59 59 ALA A 60 0.996 0.991 60 60 ALA A 61 0.992 0.987 61 61 GLY A 62 0.975 0.979 62 62 LEU A 63 0.967 0.891 0.999 0.999 63 ALA A 64 0.711 0.224 GLU A 65 0.904 0.386 0.658 0.868 0.982 VAL A 66 0.932 0.675 0.655 VAL A 67 0.821 0.557 0.562 ARG A 68 0.734 0.289 0.545 0.864 0.637 0.658 1.000 ASP A 69 0.580 0.625 0.641 0.918 PRO A 70 0.982 0.259 0.905 0.847 LEU A 71 0.958 0.915 0.926 0.930 71 71 ALA A 72 0.819 0.362 PHE A 73 0.864 0.320 0.654 0.849 LEU A 74 0.812 0.127 0.670 0.694 ASP A 75 0.731 0.242 0.432 0.920 GLU A 76 0.326 0.772 0.566 0.706 0.884 PRO A 77 0.987 0.264 0.930 0.888 GLU A 78 0.696 0.056 0.463 0.786 0.919 ALA A 79 0.892 0.284 GLY A 80 0.161 0.203 ALA A 81 0.735 0.257 GLY A 82 0.313 0.096 ALA A 83 0.399 0.232 ARG A 84 0.884 0.943 0.524 0.572 0.944 0.539 1.000 84 PRO A 85 0.983 0.253 0.890 0.814 ALA A 86 0.526 0.710 ASN A 87 0.383 0.802 0.676 0.749 ALA A 88 0.812 0.946 88 PRO A 89 0.989 0.948 0.907 0.838 89 89 GLU A 90 0.958 0.998 0.861 0.996 0.774 90 90 VAL A 91 0.998 0.996 1.000 91 91 LEU A 92 0.996 0.996 0.921 0.930 92 92 LEU A 93 0.989 0.978 0.999 0.999 93 93 VAL A 94 0.987 0.993 1.000 94 94 GLY A 95 0.984 0.972 95 95 THR A 96 0.955 0.742 0.998 GLY A 97 0.529 0.649 ARG A 98 0.899 0.794 0.521 0.878 0.636 0.649 1.000 ARG A 99 0.789 0.873 0.447 0.521 0.857 0.706 1.000 GLN A 100 0.961 0.973 0.813 0.862 0.906 100 100 HIS A 101 0.945 0.892 0.565 0.461 101 LEU A 102 0.943 0.973 0.523 0.565 102 102 LEU A 103 0.983 0.945 0.997 0.911 103 103 GLY A 104 0.991 0.971 104 104 PRO A 105 1.000 0.999 1.000 1.000 105 105 GLU A 106 0.989 0.991 0.845 0.453 0.887 106 106 GLN A 107 0.988 0.983 0.998 0.633 0.872 107 107 VAL A 108 0.979 0.963 0.999 108 108 ARG A 109 0.998 0.997 0.882 0.932 0.640 0.774 1.000 109 109 PRO A 110 0.996 0.996 0.964 0.935 110 110 LEU A 111 0.993 0.996 0.985 0.598 111 111 LEU A 112 0.998 0.999 1.000 1.000 112 112 ALA A 113 0.999 0.996 113 113 MET A 114 0.989 0.980 0.999 0.592 0.441 114 114 GLY A 115 0.984 0.997 115 115 VAL A 116 0.988 0.981 1.000 116 116 GLY A 117 0.999 0.948 117 117 VAL A 118 0.969 0.997 1.000 118 118 GLU A 119 0.991 0.986 0.808 0.869 0.957 119 119 ALA A 120 0.989 0.986 120 120 MET A 121 0.977 0.993 0.584 0.887 0.744 121 121 ASP A 122 0.980 0.980 0.511 0.756 122 122 THR A 123 0.993 0.998 0.998 123 123 GLN A 124 0.995 0.997 0.636 0.999 0.955 124 124 ALA A 125 0.999 0.998 125 125 ALA A 126 1.000 0.998 126 126 ALA A 127 1.000 0.999 127 127 ARG A 128 0.995 0.993 0.594 0.999 0.930 0.998 1.000 128 128 THR A 129 0.999 0.999 1.000 129 129 TYR A 130 1.000 0.999 0.999 0.996 130 130 ASN A 131 0.998 0.999 0.942 0.956 131 131 ILE A 132 1.000 0.998 1.000 1.000 132 132 LEU A 133 0.995 0.995 0.999 0.999 133 133 MET A 134 0.998 0.997 0.626 0.659 0.496 134 134 ALA A 135 1.000 1.000 135 135 GLU A 136 0.997 0.998 0.620 0.645 0.900 136 136 GLY A 137 0.953 0.969 137 137 ARG A 138 0.987 0.965 0.915 0.574 0.352 0.720 1.000 138 138 ARG A 139 0.977 0.949 0.578 0.785 0.161 0.473 1.000 139 139 VAL A 140 0.983 0.981 0.510 140 140 VAL A 141 0.971 0.996 0.927 141 141 VAL A 142 0.997 0.997 0.530 142 142 ALA A 143 0.995 0.989 143 143 LEU A 144 0.994 0.981 0.999 0.999 144 144 LEU A 145 0.975 0.945 0.495 0.531 145 145 PRO A 146 0.986 0.862 0.928 0.893 146 ASP A 147 0.642 0.386 0.566 0.908 GLY A 148 0.649 0.894 ASP A 149 0.533 0.371 0.576 0.911 SER A 150 0.852 0.142 0.572 LEU A 151 0.843 0.086 0.788 0.804 GLU A 152 0.931 0.648 0.545 0.672 0.974 HIS A 153 0.905 0.531 0.640 0.550 HIS A 154 0.901 0.297 0.429 0.690 HIS A 155 0.905 0.523 0.570 0.932 HIS A 156 0.820 0.429 0.623 0.606 HIS A 157 0.917 0.354 0.851 0.447 HIS A 158 0.813 0.587 0.676 Ranges: 8 from: A 14 to A 16 from: A 21 to A 24 from: A 27 to A 36 from: A 40 to A 44 from: A 47 to A 50 from: A 52 to A 62 from: A 89 to A 95 from: A 102 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[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 1 is: 0.816 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 2 is: 0.826 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 3 is: 0.982 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 4 is: 0.658 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 5 is: 0.952 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 6 is: 0.922 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 7 is: 1.168 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 8 is: 0.774 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 9 is: 0.910 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 10 is: 0.657 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 11 is: 0.868 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 12 is: 0.851 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 13 is: 0.636 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 14 is: 0.624 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 15 is: 0.796 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 16 is: 0.625 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 17 is: 0.889 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 18 is: 0.761 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 19 is: 0.853 > Kabsch RMSD of backbone atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 20 is: 0.489 (*) > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[14..16],[21..24],[27..36],[40..44],[47..50],[52..62],[89..95],[102..145], is: 0.803 > Range of RMSD values to reference struct. is 0.489 to 1.168 > 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[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 1 is: 1.148 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 2 is: 1.068 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 3 is: 1.259 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 4 is: 0.988 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 5 is: 1.271 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 6 is: 1.195 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 7 is: 1.415 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 8 is: 1.145 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 9 is: 1.280 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 10 is: 1.154 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 11 is: 1.301 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 12 is: 1.286 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 13 is: 0.967 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 14 is: 1.232 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 15 is: 1.125 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 16 is: 1.127 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 17 is: 1.189 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 18 is: 1.676 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 19 is: 1.238 > Kabsch RMSD of heavy atoms in res. A[14..16],A[21..24],A[27..36],A[40..44],A[47..50],A[52..62],A[89..95],A[102..145],for model 20 is: 0.886 (*) > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[14..16],[21..24],[27..36],[40..44],[47..50],[52..62],[89..95],[102..145], is: 1.198 > Range of RMSD values to reference struct. is 0.886 to 1.676 PdbStat> PdbStat> *END* of program detected, BYE! ...