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 `SGR209C_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 PRO GLN SER TYR PHE ASN ALA ALA ALA LYS ARG GLN LYS 1 > ReadCoordsPdb(): Counting models in file `SGR209C_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 SGR209C_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 50200 ATOM records read from file > ReadCoordsPdb(): --> 50200 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 ----------------------------------------------------------------------------------- PRO A 1 0.596 0.985 0.969 GLN A 2 0.664 0.323 0.693 0.455 0.878 SER A 3 0.453 0.403 0.210 TYR A 4 0.407 0.249 0.496 0.870 PHE A 5 0.697 0.370 0.548 0.850 ASN A 6 0.331 0.583 0.632 0.880 ALA A 7 0.743 0.314 ALA A 8 0.705 0.185 ALA A 9 0.540 0.174 LYS A 10 0.359 0.259 0.693 0.819 0.996 0.998 ARG A 11 0.396 0.581 0.606 0.791 0.691 0.848 1.000 GLN A 12 0.548 0.731 0.364 0.248 0.747 LYS A 13 0.681 0.834 0.684 0.787 0.883 0.828 TYR A 14 0.920 0.911 0.993 0.932 14 14 ALA A 15 0.937 0.992 15 15 MET A 16 0.984 0.924 0.868 0.291 0.473 16 16 LYS A 17 0.900 0.991 0.460 0.746 0.999 0.862 17 17 PRO A 18 0.993 0.889 0.905 0.822 18 GLY A 19 0.874 0.948 19 LEU A 20 0.979 0.994 0.875 0.875 20 20 SER A 21 0.996 0.990 0.939 21 21 ALA A 22 0.999 0.999 22 22 LEU A 23 0.995 0.999 0.930 0.930 23 23 GLU A 24 0.999 0.998 1.000 0.916 0.945 24 24 LYS A 25 0.997 0.998 0.941 0.997 0.739 0.995 25 25 ASN A 26 0.999 0.997 0.842 0.879 26 26 ALA A 27 0.998 0.999 27 27 VAL A 28 0.994 1.000 1.000 28 28 ILE A 29 0.990 0.993 0.917 1.000 29 29 LYS A 30 0.996 0.993 0.612 0.928 0.999 0.849 30 30 ALA A 31 0.998 0.998 31 31 ALA A 32 0.997 0.997 32 32 TYR A 33 0.992 0.992 0.927 0.524 33 33 ARG A 34 0.989 0.985 0.704 0.928 0.447 0.985 1.000 34 34 GLN A 35 0.975 0.973 0.817 0.693 0.527 35 35 ILE A 36 0.968 0.986 0.918 0.999 36 36 PHE A 37 0.994 0.962 0.999 0.693 37 37 GLU A 38 0.995 0.978 0.925 0.868 0.873 38 38 ARG A 39 0.552 0.580 0.465 0.928 0.269 0.877 1.000 ASP A 40 0.658 0.423 0.545 0.957 ILE A 41 0.647 0.789 0.422 0.805 THR A 42 0.700 0.790 0.088 LYS A 43 0.537 0.309 0.755 0.999 1.000 0.998 ALA A 44 0.263 0.830 TYR A 45 0.657 0.258 0.440 0.769 SER A 46 0.364 0.372 0.601 GLN A 47 0.444 0.867 0.873 0.783 0.950 SER A 48 0.980 0.992 0.836 48 48 ILE A 49 0.975 0.996 0.998 0.426 49 49 SER A 50 0.997 0.995 0.683 50 50 TYR A 51 0.993 0.992 0.782 0.850 51 51 LEU A 52 0.997 0.996 0.937 0.939 52 52 GLU A 53 0.997 0.994 0.862 0.995 0.878 53 53 SER A 54 0.994 0.993 0.483 54 54 GLN A 55 0.993 0.968 0.998 0.771 0.796 55 55 VAL A 56 0.967 0.987 0.309 56 56 ARG A 57 0.994 0.991 0.617 0.996 0.580 0.439 1.000 57 57 ASN A 58 0.990 0.990 1.000 0.999 58 58 GLY A 59 0.992 0.988 59 59 ASP A 60 0.990 0.997 0.998 0.944 60 60 ILE A 61 0.999 0.999 1.000 1.000 61 61 SER A 62 0.991 0.995 0.858 62 62 MET A 63 0.995 0.995 0.849 0.844 0.731 63 63 LYS A 64 0.996 0.984 0.861 0.889 0.507 0.796 64 64 GLU A 65 0.989 0.996 0.627 0.378 0.883 65 65 PHE A 66 0.999 0.998 0.998 0.994 66 66 VAL A 67 0.997 0.997 0.917 67 67 ARG A 68 0.996 0.988 0.814 0.987 0.706 0.632 1.000 68 68 ARG A 69 0.997 0.996 0.998 0.742 0.860 0.711 1.000 69 69 LEU A 70 0.994 0.992 0.991 0.847 70 70 ALA A 71 0.995 0.991 71 71 LYS A 72 0.985 0.964 0.554 0.995 0.614 0.796 72 72 SER A 73 0.993 0.992 0.639 73 73 PRO A 74 0.997 0.998 0.951 0.910 74 74 LEU A 75 0.993 0.993 0.686 0.689 75 75 TYR A 76 0.987 0.982 0.938 0.994 76 76 ARG A 77 0.985 0.977 0.534 0.989 0.415 0.664 1.000 77 77 LYS A 78 0.976 0.966 0.870 0.999 0.999 0.999 78 78 GLN A 79 0.964 0.073 0.802 0.606 0.652 PHE A 80 0.185 0.747 0.997 0.725 PHE A 81 0.810 0.990 0.996 0.954 81 GLU A 82 0.913 0.902 0.681 0.793 0.928 82 82 PRO A 83 0.992 0.941 0.958 0.935 83 83 PHE A 84 0.991 0.904 0.997 0.994 84 84 ILE A 85 0.905 0.970 0.486 1.000 85 85 ASN A 86 0.997 0.999 0.922 0.899 86 86 SER A 87 0.998 0.994 0.683 87 87 ARG A 88 0.996 0.998 1.000 1.000 0.999 0.942 1.000 88 88 ALA A 89 0.998 0.998 89 89 LEU A 90 0.997 0.994 0.869 0.873 90 90 GLU A 91 0.998 0.997 0.680 0.999 0.949 91 91 LEU A 92 0.997 0.994 0.918 0.694 92 92 ALA A 93 0.998 0.998 93 93 PHE A 94 0.994 0.989 0.977 0.616 94 94 ARG A 95 0.980 0.974 0.809 0.996 0.455 0.694 1.000 95 95 HIS A 96 0.982 0.970 0.770 0.308 96 96 ILE A 97 0.978 0.994 0.997 0.504 97 97 LEU A 98 0.981 0.984 0.569 0.580 98 98 GLY A 99 0.969 0.958 99 99 ARG A 100 0.926 0.223 0.217 0.871 0.523 0.685 1.000 GLY A 101 0.147 0.982 PRO A 102 0.991 0.906 0.914 0.838 102 102 SER A 103 0.972 0.975 0.513 103 103 SER A 104 0.884 0.983 0.623 104 ARG A 105 0.997 0.999 1.000 1.000 1.000 1.000 1.000 105 105 GLU A 106 0.998 0.997 0.668 1.000 1.000 106 106 GLU A 107 0.999 0.996 0.586 0.759 0.775 107 107 VAL A 108 0.997 0.996 1.000 108 108 GLN A 109 0.999 0.999 1.000 1.000 1.000 109 109 LYS A 110 0.998 0.997 0.666 0.999 0.998 0.993 110 110 TYR A 111 0.992 0.994 0.995 0.788 111 111 PHE A 112 0.999 0.999 0.999 1.000 112 112 SER A 113 1.000 0.999 1.000 113 113 ILE A 114 0.998 0.999 0.999 0.919 114 114 VAL A 115 0.998 0.998 0.999 115 115 SER A 116 0.999 0.975 0.329 116 116 SER A 117 0.984 0.995 0.569 117 117 GLY A 118 0.982 0.941 118 118 GLY A 119 0.947 0.985 119 119 LEU A 120 0.999 0.998 0.941 0.930 120 120 PRO A 121 0.995 0.993 0.931 0.861 121 121 ALA A 122 0.999 0.999 122 122 LEU A 123 0.999 0.999 0.999 0.999 123 123 VAL A 124 0.997 0.998 1.000 124 124 ASP A 125 0.998 0.997 0.841 0.884 125 125 ALA A 126 0.998 0.995 126 126 LEU A 127 0.987 0.995 0.999 0.999 127 127 VAL A 128 0.988 0.991 0.917 128 128 ASP A 129 0.975 0.937 0.850 0.910 129 129 SER A 130 0.983 0.960 0.534 130 130 GLN A 131 0.990 0.979 0.584 0.262 0.743 131 131 GLU A 132 0.994 0.997 0.589 0.998 0.998 132 132 TYR A 133 0.971 0.981 0.604 0.815 133 133 ALA A 134 0.997 0.992 134 134 ASP A 135 0.979 0.967 0.938 0.916 135 135 TYR A 136 0.981 0.973 0.598 0.760 136 136 PHE A 137 0.911 0.972 0.542 0.858 137 137 GLY A 138 0.956 0.952 138 138 GLU A 139 0.967 0.978 0.693 0.928 0.900 139 139 GLU A 140 0.979 0.964 0.830 0.875 0.959 140 140 THR A 141 0.958 0.980 0.633 141 141 VAL A 142 0.968 0.994 0.937 142 142 PRO A 143 0.981 0.883 0.892 0.835 143 TYR A 144 0.874 0.639 0.021 0.806 LEU A 145 0.860 0.479 0.487 0.552 ARG A 146 0.523 0.229 0.470 0.651 0.567 0.781 1.000 GLY A 147 0.293 0.260 LEU A 148 0.365 0.383 0.781 0.680 GLU A 149 0.743 0.427 0.449 0.728 0.849 HIS A 150 0.663 0.423 0.574 0.487 HIS A 151 0.507 0.197 0.342 0.519 HIS A 152 0.690 0.534 0.490 0.527 HIS A 153 0.703 0.198 0.576 0.707 HIS A 154 0.567 0.372 0.386 0.540 HIS A 155 0.760 0.580 0.556 Ranges: 6 from: A 14 to A 17 from: A 20 to A 38 from: A 48 to A 78 from: A 82 to A 99 from: A 102 to A 103 from: A 105 to A 142 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..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 1 is: 1.102 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 2 is: 1.025 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 3 is: 1.106 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 4 is: 1.172 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 5 is: 1.110 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 6 is: 0.984 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 7 is: 0.683 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 8 is: 0.664 (*) > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 9 is: 1.034 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 10 is: 0.763 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 11 is: 1.053 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 12 is: 1.342 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 13 is: 0.847 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 14 is: 1.139 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 15 is: 0.691 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 16 is: 1.077 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 17 is: 0.679 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 18 is: 0.965 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 19 is: 0.836 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 20 is: 2.063 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[14..17],[20..38],[48..78],[82..99],[102..103],[105..142], is: 1.017 > Range of RMSD values to reference struct. is 0.664 to 2.063 > 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..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 1 is: 1.477 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 2 is: 1.610 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 3 is: 1.542 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 4 is: 1.627 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 5 is: 1.469 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 6 is: 1.610 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 7 is: 1.139 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 8 is: 1.141 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 9 is: 1.401 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 10 is: 1.315 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 11 is: 1.448 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 12 is: 1.709 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 13 is: 1.203 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 14 is: 1.519 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 15 is: 1.082 (*) > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 16 is: 1.415 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 17 is: 1.087 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 18 is: 1.409 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 19 is: 1.221 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..99],A[102..103],A[105..142],for model 20 is: 2.459 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[14..17],[20..38],[48..78],[82..99],[102..103],[105..142], is: 1.444 > Range of RMSD values to reference struct. is 1.082 to 2.459 PdbStat> PdbStat> *END* of program detected, BYE! ...