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 `HR1958_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 143 MET ARG LYS ILE ASP LEU CYS LEU SER SER GLU GLY SER 1 > ReadCoordsPdb(): Counting models in file `HR1958_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 HR1958_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (18) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 40518 ATOM records read from file > ReadCoordsPdb(): --> 40518 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 0.306 0.717 0.315 0.271 ARG A 2 0.524 0.350 0.840 0.997 0.499 0.937 1.000 LYS A 3 0.155 0.963 0.915 0.862 0.999 0.928 ILE A 4 0.990 0.979 0.622 1.000 4 4 ASP A 5 0.991 0.990 0.692 0.980 5 5 LEU A 6 0.993 0.979 0.997 0.999 6 6 CYS A 7 0.995 0.995 0.998 7 7 LEU A 8 0.998 0.999 0.999 0.998 8 8 SER A 9 0.999 0.999 0.906 9 9 SER A 10 0.999 1.000 1.000 10 10 GLU A 11 0.996 0.995 0.994 0.988 1.000 11 11 GLY A 12 1.000 0.999 12 12 SER A 13 0.999 0.993 0.735 13 13 GLU A 14 0.995 0.987 0.550 0.999 0.889 14 14 VAL A 15 0.996 0.999 1.000 15 15 ILE A 16 0.999 0.981 0.916 1.000 16 16 LEU A 17 0.993 0.294 0.580 0.619 ALA A 18 0.301 0.912 THR A 19 0.991 0.980 0.631 19 19 SER A 20 0.984 0.844 0.482 20 SER A 21 0.850 0.970 0.390 21 ASP A 22 0.986 0.993 0.999 0.590 22 22 GLU A 23 0.999 0.999 1.000 1.000 1.000 23 23 LYS A 24 1.000 0.997 1.000 1.000 1.000 1.000 24 24 HIS A 25 0.998 0.999 0.925 0.999 25 25 PRO A 26 0.995 0.989 0.960 0.930 26 26 PRO A 27 0.993 0.994 0.933 0.879 27 27 GLU A 28 1.000 0.999 0.681 0.538 0.977 28 28 ASN A 29 0.996 0.996 0.945 0.965 29 29 ILE A 30 0.998 0.990 0.868 1.000 30 30 ILE A 31 0.986 0.672 0.637 1.000 ASP A 32 0.441 0.973 0.669 0.762 GLY A 33 0.985 0.976 33 33 ASN A 34 0.969 0.984 0.571 0.882 34 34 PRO A 35 0.981 0.989 0.896 0.836 35 35 GLU A 36 0.996 0.982 0.860 0.999 0.999 36 36 THR A 37 0.980 0.990 0.681 37 37 PHE A 38 0.993 0.986 0.925 0.887 38 38 TRP A 39 0.974 0.984 0.998 0.998 39 39 THR A 40 0.994 0.989 0.435 40 40 THR A 41 0.992 0.981 0.659 41 41 THR A 42 0.997 0.979 0.999 42 42 GLY A 43 0.993 0.987 43 43 MET A 44 0.987 0.981 1.000 0.514 0.311 44 44 PHE A 45 0.986 0.999 0.999 0.991 45 45 PRO A 46 0.999 0.997 0.999 1.000 46 46 GLN A 47 0.979 0.972 0.671 0.423 0.378 47 47 GLU A 48 0.991 0.992 0.578 0.939 0.798 48 48 PHE A 49 0.999 0.998 1.000 1.000 49 49 ILE A 50 0.998 1.000 0.999 0.826 50 50 ILE A 51 0.999 0.999 1.000 0.917 51 51 CYS A 52 0.999 0.999 0.831 52 52 PHE A 53 0.999 0.998 0.999 0.618 53 53 HIS A 54 0.999 0.998 0.997 0.792 54 54 LYS A 55 0.994 0.994 0.749 0.994 0.496 0.584 55 55 HIS A 56 0.997 0.997 0.925 0.060 56 56 VAL A 57 0.998 0.998 1.000 57 57 ARG A 58 0.999 0.998 1.000 0.936 0.847 0.619 1.000 58 58 ILE A 59 0.998 0.999 1.000 1.000 59 59 GLU A 60 0.997 0.993 1.000 0.929 0.999 60 60 ARG A 61 0.995 0.996 0.526 0.989 0.457 0.931 1.000 61 61 LEU A 62 0.997 0.997 0.999 0.948 62 62 VAL A 63 0.998 0.997 1.000 63 63 ILE A 64 0.997 0.998 0.999 0.471 64 64 GLN A 65 0.998 0.992 0.561 0.995 0.231 65 65 SER A 66 0.999 0.992 0.911 66 66 TYR A 67 0.972 0.989 0.591 0.768 67 67 PHE A 68 0.991 0.523 0.995 0.812 VAL A 69 0.428 0.858 0.641 GLN A 70 0.814 0.977 0.781 0.987 0.716 70 THR A 71 0.988 0.996 1.000 71 71 LEU A 72 0.999 0.995 0.914 0.923 72 72 LYS A 73 0.997 0.998 0.775 0.916 0.798 0.999 73 73 ILE A 74 0.999 0.999 1.000 0.956 74 74 GLU A 75 0.998 0.998 0.997 0.730 0.766 75 75 LYS A 76 0.999 0.997 0.848 0.996 0.505 0.305 76 76 SER A 77 0.999 0.999 0.995 77 77 THR A 78 0.996 0.993 1.000 78 78 SER A 79 0.998 0.891 1.000 79 LYS A 80 0.890 0.991 0.904 1.000 1.000 0.999 80 GLU A 81 0.997 0.999 1.000 1.000 1.000 81 81 PRO A 82 0.999 0.973 1.000 1.000 82 82 VAL A 83 0.996 0.998 1.000 83 83 ASP A 84 0.995 0.898 0.941 0.995 84 PHE A 85 0.890 0.970 0.926 0.881 85 GLU A 86 0.990 0.997 0.573 0.999 1.000 86 86 GLN A 87 0.999 0.998 0.860 0.928 0.984 87 87 TRP A 88 0.996 0.997 0.999 0.996 88 88 ILE A 89 0.995 0.985 0.706 0.753 89 89 GLU A 90 0.992 0.981 0.776 1.000 0.972 90 90 LYS A 91 0.995 0.992 0.646 0.367 0.764 0.983 91 91 ASP A 92 0.996 0.971 0.594 0.884 92 92 LEU A 93 0.984 0.950 0.913 0.631 93 93 VAL A 94 0.983 0.974 0.760 94 94 HIS A 95 0.969 0.978 0.909 0.459 95 95 THR A 96 0.985 0.970 0.921 96 96 GLU A 97 0.989 0.978 0.724 0.636 0.935 97 97 GLY A 98 0.998 0.997 98 98 GLN A 99 0.995 0.975 0.661 0.637 0.826 99 99 LEU A 100 0.996 0.990 0.576 0.569 100 100 GLN A 101 0.982 0.986 0.843 0.777 0.884 101 101 ASN A 102 0.993 0.983 0.671 0.795 102 102 GLU A 103 0.994 0.986 0.624 0.314 0.778 103 103 GLU A 104 0.996 0.994 0.565 0.999 0.932 104 104 ILE A 105 0.998 0.995 0.999 0.887 105 105 VAL A 106 0.996 0.996 1.000 106 106 ALA A 107 0.990 0.994 107 107 HIS A 108 0.991 0.991 0.999 0.997 108 108 GLY A 109 0.990 0.997 109 109 SER A 110 0.993 0.994 0.598 110 110 ALA A 111 0.998 0.998 111 111 THR A 112 0.998 1.000 0.920 112 112 TYR A 113 0.999 1.000 0.999 0.887 113 113 LEU A 114 0.999 0.995 0.928 0.924 114 114 ARG A 115 0.993 0.997 0.999 0.989 0.572 0.976 0.999 115 115 PHE A 116 0.999 0.998 0.999 0.998 116 116 ILE A 117 0.999 0.998 1.000 0.921 117 117 ILE A 118 0.998 0.998 1.000 1.000 118 118 VAL A 119 0.990 0.999 1.000 119 119 SER A 120 0.989 0.986 0.778 120 120 ALA A 121 0.997 0.997 121 121 PHE A 122 0.996 0.998 0.998 0.809 122 122 ASP A 123 0.998 0.997 1.000 0.999 123 123 HIS A 124 0.989 0.981 0.333 0.782 124 124 PHE A 125 0.997 0.998 0.819 0.999 125 125 ALA A 126 0.988 0.995 126 126 SER A 127 0.998 0.995 0.737 127 127 VAL A 128 0.998 0.997 1.000 128 128 HIS A 129 0.983 0.991 0.680 0.263 129 129 SER A 130 0.992 0.994 0.385 130 130 VAL A 131 0.994 0.998 1.000 131 131 SER A 132 0.997 0.997 0.735 132 132 ALA A 133 0.996 0.993 133 133 GLU A 134 0.997 0.990 0.783 0.996 0.906 134 134 GLY A 135 0.987 0.998 135 135 THR A 136 0.997 0.999 0.830 136 136 VAL A 137 0.999 0.999 1.000 137 137 VAL A 138 0.996 0.998 1.000 138 138 SER A 139 0.946 0.941 0.728 139 139 ASN A 140 0.992 0.672 0.235 0.944 LEU A 141 0.916 0.379 0.587 0.610 SER A 142 0.836 0.318 0.473 SER A 143 0.782 0.920 Ranges: 6 from: A 4 to A 16 from: A 22 to A 30 from: A 33 to A 67 from: A 71 to A 78 from: A 81 to A 83 from: A 86 to A 139 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..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 1 is: 0.855 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 2 is: 0.507 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 3 is: 0.564 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 4 is: 0.459 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 5 is: 0.740 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 6 is: 0.698 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 7 is: 0.631 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 8 is: 0.725 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 9 is: 0.576 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 10 is: 0.524 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 11 is: 0.533 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 12 is: 0.603 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 13 is: 0.734 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 14 is: 0.430 (*) > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 15 is: 0.486 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 16 is: 0.557 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 17 is: 0.737 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 18 is: 0.623 > > Kabsch RMSD statistics for 18 structures: > Mean RMSD using as refer. str. `average' for res.[4..16],[22..30],[33..67],[71..78],[81..83],[86..139], is: 0.610 > Range of RMSD values to reference struct. is 0.430 to 0.855 > 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..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 1 is: 1.441 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 2 is: 0.820 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 3 is: 0.830 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 4 is: 0.772 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 5 is: 0.964 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 6 is: 1.157 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 7 is: 0.962 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 8 is: 1.010 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 9 is: 0.845 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 10 is: 0.797 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 11 is: 0.941 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 12 is: 0.909 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 13 is: 1.043 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 14 is: 0.795 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 15 is: 0.757 (*) > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 16 is: 0.942 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 17 is: 1.191 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 18 is: 0.988 > > Kabsch RMSD statistics for 18 structures: > Mean RMSD using as refer. str. `average' for res.[4..16],[22..30],[33..67],[71..78],[81..83],[86..139], is: 0.954 > Range of RMSD values to reference struct. is 0.757 to 1.441 PdbStat> PdbStat> *END* of program detected, BYE! ...