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 `STR65_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 109 VAL ASN PHE LYS ASP LYS SER MET PRO THR ALA ILE GLU 1 > ReadCoordsPdb(): Counting models in file `STR65_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 STR65_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 34000 ATOM records read from file > ReadCoordsPdb(): --> 34000 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 ----------------------------------------------------------------------------------- VAL A 1 0.572 0.595 ASN A 2 0.809 0.347 0.498 0.836 PHE A 3 0.457 0.205 0.849 0.992 LYS A 4 0.375 0.750 0.446 0.998 0.999 0.930 ASP A 5 0.506 0.684 0.569 0.936 LYS A 6 0.679 0.360 0.633 0.999 0.999 0.998 SER A 7 0.360 0.794 0.361 MET A 8 0.678 0.787 0.431 0.253 0.199 PRO A 9 0.982 0.543 0.884 0.817 THR A 10 0.736 0.337 0.530 ALA A 11 0.994 0.991 11 11 ILE A 12 0.998 0.997 0.945 0.934 12 12 GLU A 13 0.997 0.994 0.633 0.783 0.919 13 13 LYS A 14 0.999 0.999 0.998 0.798 1.000 1.000 14 14 ALA A 15 0.999 0.999 15 15 LEU A 16 0.995 0.992 0.999 0.999 16 16 ASP A 17 0.997 0.997 0.939 0.952 17 17 PHE A 18 0.994 0.993 0.861 0.755 18 18 ILE A 19 0.984 0.992 0.999 1.000 19 19 GLY A 20 0.956 0.762 GLY A 21 0.260 0.405 MET A 22 0.441 0.494 0.564 0.443 0.316 ASN A 23 0.206 0.430 0.503 0.858 THR A 24 0.751 0.192 0.461 SER A 25 0.355 0.428 0.158 ALA A 26 0.525 0.671 SER A 27 0.818 0.812 0.302 27 VAL A 28 0.779 0.290 0.581 PRO A 29 0.968 0.518 0.877 0.822 HIS A 30 0.524 0.509 0.688 0.538 SER A 31 0.928 0.895 0.767 31 MET A 32 0.952 0.950 0.307 0.625 0.379 32 32 ASP A 33 0.981 0.970 0.432 0.901 33 33 GLU A 34 0.956 0.978 0.808 0.923 0.911 34 34 SER A 35 0.980 0.980 0.659 35 35 THR A 36 0.968 0.990 0.718 36 36 ALA A 37 0.997 0.994 37 37 LYS A 38 0.996 0.996 0.999 0.997 0.928 0.998 38 38 GLY A 39 0.998 0.996 39 39 ILE A 40 0.999 0.997 0.945 1.000 40 40 LEU A 41 0.996 0.996 0.990 0.837 41 41 LYS A 42 0.996 0.995 0.939 0.864 0.869 0.610 42 42 TYR A 43 0.997 0.998 0.935 0.951 43 43 LEU A 44 0.999 0.999 0.932 0.863 44 44 HIS A 45 0.997 0.998 0.927 0.436 45 45 ASP A 46 0.998 0.999 1.000 1.000 46 46 LEU A 47 0.999 0.998 1.000 0.999 47 47 GLY A 48 0.988 0.990 48 48 VAL A 49 0.990 0.969 0.998 49 49 PRO A 50 0.995 0.923 0.982 0.969 50 50 VAL A 51 0.967 0.994 1.000 51 51 SER A 52 0.993 0.987 0.800 52 52 PRO A 53 0.996 0.998 0.940 0.886 53 53 GLU A 54 0.999 0.997 0.874 1.000 1.000 54 54 VAL A 55 0.997 0.995 0.846 55 55 VAL A 56 0.998 0.999 1.000 56 56 VAL A 57 0.999 0.999 1.000 57 57 ALA A 58 0.999 0.996 58 58 ARG A 59 0.996 0.994 0.694 0.632 0.513 0.802 1.000 59 59 GLY A 60 0.997 0.991 60 60 GLU A 61 0.990 0.996 0.873 1.000 1.000 61 61 GLN A 62 0.994 0.993 0.762 0.856 0.929 62 62 GLU A 63 0.994 0.990 0.929 0.587 0.809 63 63 GLY A 64 0.983 0.729 TRP A 65 0.663 0.632 0.998 0.970 ASN A 66 0.662 0.976 0.514 0.836 PRO A 67 0.988 0.977 0.972 0.969 67 67 GLU A 68 0.982 0.982 0.693 0.376 0.860 68 68 PHE A 69 0.998 0.994 0.944 0.943 69 69 THR A 70 0.998 0.999 1.000 70 70 LYS A 71 0.997 0.996 0.666 1.000 0.936 0.999 71 71 LYS A 72 0.997 0.996 0.999 0.802 0.925 0.829 72 72 VAL A 73 0.999 1.000 1.000 73 73 ALA A 74 1.000 0.999 74 74 GLY A 75 1.000 0.999 75 75 TRP A 76 0.999 0.998 0.997 0.994 76 76 ALA A 77 0.999 0.998 77 77 GLU A 78 0.998 0.998 0.935 1.000 1.000 78 78 LYS A 79 0.996 0.992 0.947 0.612 1.000 1.000 79 79 VAL A 80 0.996 0.987 0.664 80 80 ALA A 81 0.993 0.999 81 81 SER A 82 0.998 0.995 0.756 82 82 GLY A 83 0.987 0.991 83 83 ASN A 84 0.988 0.768 0.821 0.955 ARG A 85 0.734 0.920 0.847 0.999 0.813 0.939 1.000 ILE A 86 0.880 0.802 0.429 0.843 86 LEU A 87 0.901 0.848 0.668 0.693 87 ILE A 88 0.853 0.315 0.564 0.846 LYS A 89 0.364 0.827 0.802 0.858 0.931 0.995 ASN A 90 0.812 0.831 0.608 0.795 90 PRO A 91 0.977 0.683 0.891 0.820 GLU A 92 0.406 0.363 0.630 0.879 0.959 TYR A 93 0.385 0.690 0.923 0.635 PHE A 94 0.654 0.815 0.467 0.963 SER A 95 0.928 0.970 0.772 95 95 THR A 96 0.982 0.988 0.506 96 96 TYR A 97 0.998 0.999 0.999 0.970 97 97 MET A 98 0.998 0.996 1.000 0.725 0.464 98 98 GLN A 99 0.996 0.992 0.534 0.999 0.909 99 99 GLU A 100 0.995 0.998 0.936 0.923 0.983 100 100 GLN A 101 0.998 0.992 0.937 0.845 0.940 101 101 LEU A 102 0.998 0.999 0.999 1.000 102 102 LYS A 103 0.999 0.996 1.000 0.999 1.000 1.000 103 103 GLU A 104 0.995 0.998 0.999 1.000 1.000 104 104 LEU A 105 0.997 0.990 0.874 0.792 105 105 VAL A 106 0.976 0.982 0.691 106 106 LEU A 107 0.988 0.985 0.805 0.808 107 107 GLU A 108 0.966 0.941 0.800 0.528 0.927 108 108 HIS A 109 0.490 0.528 0.234 Ranges: 4 from: A 11 to A 19 from: A 32 to A 63 from: A 67 to A 83 from: A 95 to A 108 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[11..19],A[32..63],A[67..83],A[95..108],for model 1 is: 0.981 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 2 is: 1.081 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 3 is: 1.214 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 4 is: 0.999 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 5 is: 0.892 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 6 is: 0.539 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 7 is: 1.056 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 8 is: 0.582 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 9 is: 0.564 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 10 is: 0.692 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 11 is: 0.618 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 12 is: 0.617 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 13 is: 0.655 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 14 is: 0.839 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 15 is: 0.900 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 16 is: 0.988 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 17 is: 0.657 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 18 is: 0.502 (*) > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 19 is: 0.612 > Kabsch RMSD of backbone atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 20 is: 0.726 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[11..19],[32..63],[67..83],[95..108], is: 0.786 > Range of RMSD values to reference struct. is 0.502 to 1.214 > 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[11..19],A[32..63],A[67..83],A[95..108],for model 1 is: 1.272 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 2 is: 1.217 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 3 is: 1.654 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 4 is: 1.318 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 5 is: 1.328 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 6 is: 0.729 (*) > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 7 is: 1.387 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 8 is: 0.873 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 9 is: 0.814 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 10 is: 1.062 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 11 is: 0.887 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 12 is: 0.940 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 13 is: 0.967 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 14 is: 1.225 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 15 is: 1.302 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 16 is: 1.367 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 17 is: 0.984 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 18 is: 0.756 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 19 is: 0.985 > Kabsch RMSD of heavy atoms in res. A[11..19],A[32..63],A[67..83],A[95..108],for model 20 is: 1.092 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[11..19],[32..63],[67..83],[95..108], is: 1.108 > Range of RMSD values to reference struct. is 0.729 to 1.654 PdbStat> PdbStat> *END* of program detected, BYE! ...