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_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 09-OCT-04 1XPW > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF HUMAN PROTEIN HSPCO34. NORTHEAST > ReadCoordsPdb(): >> TITLE 2 STRUCTURAL GENOMICS TARGET HR1958 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): >> COMPND 2 MOLECULE: LOC51668 PROTEIN; 1 > ReadCoordsPdb(): Counting models in file `HR1958_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 HR1958_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 44980 ATOM records read from file > ReadCoordsPdb(): --> 44980 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 0.265 0.167 0.283 0.782 ARG A 2 0.519 0.340 0.270 0.931 0.221 0.683 0.999 LYS A 3 0.258 0.900 0.205 0.892 0.302 0.270 ILE A 4 0.916 0.988 0.998 0.999 4 4 ASP A 5 0.998 0.992 0.707 0.550 5 5 LEU A 6 0.994 0.988 0.999 0.997 6 6 CYS A 7 0.999 0.993 0.463 7 7 LEU A 8 0.988 0.992 0.962 0.930 8 8 SER A 9 0.998 0.998 0.130 9 9 SER A 10 0.991 0.995 0.474 10 10 GLU A 11 0.995 0.981 0.892 0.991 0.989 11 11 GLY A 12 0.971 0.990 12 12 SER A 13 0.965 0.975 0.861 13 13 GLU A 14 0.978 0.970 0.537 0.552 0.392 14 14 VAL A 15 0.986 0.967 0.589 15 15 ILE A 16 0.974 0.968 0.941 0.998 16 16 LEU A 17 0.998 0.106 0.876 0.691 ALA A 18 0.170 0.955 THR A 19 0.993 0.957 0.689 19 19 SER A 20 0.927 0.907 0.309 20 20 SER A 21 0.908 0.957 0.199 21 21 ASP A 22 0.970 0.995 0.877 0.363 22 22 GLU A 23 0.983 0.984 0.541 0.322 0.468 23 23 LYS A 24 0.989 0.978 0.730 0.725 0.363 0.062 24 24 HIS A 25 0.988 0.995 0.935 0.058 25 25 PRO A 26 0.986 0.978 0.964 0.915 26 26 PRO A 27 0.995 0.987 0.975 0.951 27 27 GLU A 28 0.989 0.990 0.510 0.221 0.487 28 28 ASN A 29 0.982 0.974 0.593 0.137 29 29 ILE A 30 0.993 0.983 0.629 0.997 30 30 ILE A 31 0.960 0.746 0.855 0.998 ASP A 32 0.412 0.958 0.862 0.719 GLY A 33 0.963 0.907 33 33 ASN A 34 0.953 0.981 0.786 0.561 34 34 PRO A 35 0.991 0.940 0.948 0.878 35 35 GLU A 36 0.977 0.944 0.534 0.414 0.206 36 36 THR A 37 0.925 0.906 0.412 37 37 PHE A 38 0.935 0.975 0.979 0.127 38 38 TRP A 39 0.982 0.983 0.993 0.995 39 39 THR A 40 0.980 0.985 0.835 40 40 THR A 41 0.982 0.977 0.409 41 41 THR A 42 0.997 0.941 0.895 42 42 GLY A 43 0.974 0.943 43 43 MET A 44 0.964 0.978 0.565 0.516 0.515 44 44 PHE A 45 0.980 0.989 0.996 0.232 45 45 PRO A 46 0.996 0.987 0.960 0.906 46 46 GLN A 47 0.987 0.952 0.390 0.550 0.122 47 47 GLU A 48 0.967 0.975 0.857 0.921 0.530 48 48 PHE A 49 0.992 0.993 0.999 0.900 49 49 ILE A 50 0.996 0.988 0.998 1.000 50 50 ILE A 51 0.991 0.996 0.998 0.999 51 51 CYS A 52 0.994 0.992 0.349 52 52 PHE A 53 0.996 0.996 0.997 0.998 53 53 HIS A 54 0.999 0.981 0.785 0.830 54 54 LYS A 55 0.980 0.987 0.851 0.995 0.848 0.671 55 55 HIS A 56 0.992 0.996 0.681 0.391 56 56 VAL A 57 0.994 0.983 0.996 57 57 ARG A 58 0.971 0.991 0.721 0.768 0.072 0.589 0.998 58 58 ILE A 59 0.998 0.994 0.998 1.000 59 59 GLU A 60 0.987 0.970 0.545 0.439 0.433 60 60 ARG A 61 0.985 0.990 0.438 0.843 0.212 0.628 0.996 61 61 LEU A 62 0.990 0.983 0.994 0.764 62 62 VAL A 63 0.987 0.996 0.999 63 63 ILE A 64 0.992 0.983 0.997 0.545 64 64 GLN A 65 0.989 0.999 0.584 0.941 0.538 65 65 SER A 66 0.986 0.976 0.538 66 66 TYR A 67 0.980 0.980 0.708 0.425 67 67 PHE A 68 0.996 0.619 0.988 0.988 VAL A 69 0.452 0.847 0.987 GLN A 70 0.831 0.982 0.857 0.848 0.184 70 THR A 71 0.978 0.996 0.783 71 71 LEU A 72 0.995 0.997 0.998 0.998 72 72 LYS A 73 0.996 0.985 0.562 0.914 0.641 0.116 73 73 ILE A 74 0.990 0.992 0.999 0.997 74 74 GLU A 75 0.994 0.994 0.852 0.692 0.596 75 75 LYS A 76 0.992 0.983 0.561 0.959 0.447 0.393 76 76 SER A 77 0.983 0.991 0.558 77 77 THR A 78 0.989 0.991 0.774 78 78 SER A 79 0.996 0.888 0.369 79 LYS A 80 0.886 0.974 0.178 0.786 0.228 0.444 80 GLU A 81 0.977 0.990 0.856 0.318 0.322 81 81 PRO A 82 0.997 0.989 0.944 0.875 82 82 VAL A 83 0.995 0.973 1.000 83 83 ASP A 84 0.996 0.878 0.892 0.636 84 PHE A 85 0.888 0.931 0.903 0.273 85 GLU A 86 0.949 0.982 0.323 0.593 0.363 86 86 GLN A 87 0.990 0.977 0.125 0.576 0.256 87 87 TRP A 88 0.963 0.992 0.998 0.994 88 88 ILE A 89 0.996 0.949 0.741 0.997 89 89 GLU A 90 0.959 0.975 0.404 0.745 0.450 90 90 LYS A 91 0.969 0.953 0.698 0.410 0.667 0.225 91 91 ASP A 92 0.975 0.969 0.840 0.708 92 92 LEU A 93 0.961 0.927 0.411 0.688 93 93 VAL A 94 0.964 0.952 0.854 94 94 HIS A 95 0.969 0.968 0.704 0.715 95 95 THR A 96 0.942 0.985 0.975 96 96 GLU A 97 0.973 0.983 0.168 0.304 0.364 97 97 GLY A 98 0.979 0.913 98 98 GLN A 99 0.941 0.980 0.462 0.583 0.182 99 99 LEU A 100 0.989 0.982 0.783 0.738 100 100 GLN A 101 0.969 0.926 0.571 0.227 0.177 101 101 ASN A 102 0.972 0.971 0.864 0.637 102 102 GLU A 103 0.995 0.974 0.777 0.080 0.356 103 103 GLU A 104 0.988 0.993 0.439 0.565 0.336 104 104 ILE A 105 0.984 0.985 0.998 0.787 105 105 VAL A 106 0.991 0.991 0.135 106 106 ALA A 107 0.978 0.980 107 107 HIS A 108 0.994 0.994 0.595 0.555 108 108 GLY A 109 0.999 0.959 109 109 SER A 110 0.956 0.988 0.892 110 110 ALA A 111 0.993 0.988 111 111 THR A 112 0.987 0.998 0.916 112 112 TYR A 113 0.998 0.995 0.996 0.802 113 113 LEU A 114 0.996 0.996 0.952 0.937 114 114 ARG A 115 0.999 0.994 0.980 0.938 0.408 0.637 0.998 115 115 PHE A 116 0.997 0.992 0.997 0.096 116 116 ILE A 117 0.990 0.997 0.998 0.953 117 117 ILE A 118 0.998 0.994 0.999 1.000 118 118 VAL A 119 0.993 0.993 1.000 119 119 SER A 120 0.986 0.985 0.364 120 120 ALA A 121 0.995 0.994 121 121 PHE A 122 0.993 0.986 0.996 0.932 122 122 ASP A 123 0.987 0.984 0.858 0.146 123 123 HIS A 124 0.985 0.982 0.353 0.211 124 124 PHE A 125 0.974 0.971 0.623 0.887 125 125 ALA A 126 0.969 0.951 126 126 SER A 127 0.976 0.985 0.427 127 127 VAL A 128 0.964 0.985 0.996 128 128 HIS A 129 0.969 0.980 0.868 0.278 129 129 SER A 130 0.963 0.973 0.303 130 130 VAL A 131 0.986 0.913 0.931 131 131 SER A 132 0.925 0.991 0.651 132 132 ALA A 133 0.991 0.987 133 133 GLU A 134 0.998 0.964 0.930 0.962 0.639 134 134 GLY A 135 0.953 0.985 135 135 THR A 136 0.996 0.982 0.935 136 136 VAL A 137 0.985 0.979 0.194 137 137 VAL A 138 0.971 0.983 0.922 138 138 SER A 139 0.949 0.946 0.298 139 139 ASN A 140 0.970 0.716 0.695 0.494 LEU A 141 0.909 0.463 0.423 0.310 SER A 142 0.832 0.543 0.344 SER A 143 0.854 0.579 Ranges: 6 from: A 4 to A 16 from: A 19 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[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 1 is: 0.569 (*) > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 2 is: 0.775 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 3 is: 0.696 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 4 is: 0.673 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 5 is: 0.800 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 6 is: 0.602 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 7 is: 0.826 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 8 is: 0.618 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 9 is: 0.753 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 10 is: 0.724 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 11 is: 0.800 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 12 is: 0.746 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 13 is: 0.706 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 14 is: 0.822 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 15 is: 0.649 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 16 is: 0.762 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 17 is: 0.837 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 18 is: 0.801 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 19 is: 0.621 > Kabsch RMSD of backbone atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 20 is: 0.629 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..16],[19..30],[33..67],[71..78],[81..83],[86..139], is: 0.720 > Range of RMSD values to reference struct. is 0.569 to 0.837 > 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[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 1 is: 1.057 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 2 is: 1.162 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 3 is: 1.195 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 4 is: 1.202 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 5 is: 1.218 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 6 is: 1.103 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 7 is: 1.212 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 8 is: 1.047 (*) > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 9 is: 1.190 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 10 is: 1.201 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 11 is: 1.251 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 12 is: 1.177 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 13 is: 1.232 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 14 is: 1.225 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 15 is: 1.115 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 16 is: 1.143 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 17 is: 1.219 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 18 is: 1.500 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 19 is: 1.174 > Kabsch RMSD of heavy atoms in res. A[4..16],A[19..30],A[33..67],A[71..78],A[81..83],A[86..139],for model 20 is: 1.071 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..16],[19..30],[33..67],[71..78],[81..83],[86..139], is: 1.185 > Range of RMSD values to reference struct. is 1.047 to 1.500 PdbStat> PdbStat> *END* of program detected, BYE! ...