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 `PSR293_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 24-FEB-09 2KFP > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF PSPTO_3016 FROM PSEUDOMONAS > ReadCoordsPdb(): >> TITLE 2 SYRINGAE. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET > ReadCoordsPdb(): >> TITLE 3 PSR293. > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `PSR293_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 PSR293_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 41420 ATOM records read from file > ReadCoordsPdb(): --> 41420 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 0.929 0.839 0.655 0.265 ASN A 2 0.961 0.991 0.596 0.377 2 2 ARG A 3 1.000 0.998 0.717 0.926 0.100 0.699 1.000 3 3 GLN A 4 0.995 0.999 0.989 0.566 0.547 4 4 GLN A 5 1.000 0.999 0.992 0.322 0.555 5 5 PHE A 6 1.000 1.000 0.997 0.701 6 6 ILE A 7 1.000 1.000 0.988 0.193 7 7 ASP A 8 1.000 0.999 0.613 0.941 8 8 TYR A 9 0.999 0.998 0.997 0.506 9 9 ALA A 10 0.998 0.994 10 10 GLN A 11 0.999 0.991 0.322 0.675 0.231 11 11 LYS A 12 0.994 0.993 0.654 0.934 0.805 0.322 12 12 LYS A 13 0.990 0.969 0.668 0.479 0.880 0.266 13 13 TYR A 14 0.964 0.980 0.951 0.732 14 14 ASP A 15 0.988 0.996 0.209 0.743 15 15 THR A 16 0.988 0.986 0.603 16 16 LYS A 17 0.987 0.970 0.666 0.677 0.574 0.101 17 17 PRO A 18 0.989 0.993 0.909 0.856 18 18 ASP A 19 0.986 0.980 0.638 0.973 19 19 HIS A 20 0.966 0.970 0.720 0.305 20 20 PRO A 21 0.978 0.939 0.908 0.877 21 21 TRP A 22 0.993 0.953 0.867 0.791 22 22 GLU A 23 0.986 0.991 0.993 0.786 0.849 23 23 LYS A 24 0.995 0.998 0.997 0.995 0.266 0.504 24 24 PHE A 25 0.991 0.996 0.992 0.317 25 25 PRO A 26 0.997 0.997 0.946 0.900 26 26 ASP A 27 0.996 0.999 0.584 0.957 27 27 TYR A 28 0.994 0.997 0.997 0.985 28 28 ALA A 29 0.995 0.989 29 29 VAL A 30 0.991 0.999 0.984 30 30 PHE A 31 0.998 0.980 0.994 0.798 31 31 ARG A 32 0.991 0.986 0.403 0.940 0.248 0.570 1.000 32 32 HIS A 33 0.993 0.974 0.802 0.210 33 33 SER A 34 0.985 0.976 0.229 34 34 ASP A 35 0.969 0.946 0.652 0.991 35 35 ASN A 36 0.983 0.914 0.398 0.345 36 36 ASP A 37 0.881 0.442 0.507 0.851 LYS A 38 0.475 0.151 0.346 0.732 0.609 0.575 TRP A 39 0.426 0.860 0.322 0.342 TYR A 40 0.934 0.998 0.682 0.320 40 40 ALA A 41 0.998 0.966 41 41 LEU A 42 0.968 0.982 0.080 0.203 42 42 LEU A 43 0.995 0.997 0.999 0.992 43 43 MET A 44 0.996 0.996 0.997 0.665 0.993 44 44 ASP A 45 0.998 0.980 0.373 0.996 45 45 ILE A 46 0.978 1.000 0.999 0.997 46 46 PRO A 47 0.993 0.998 0.932 0.891 47 47 ALA A 48 0.999 0.999 48 48 GLU A 49 0.991 0.989 0.485 0.808 0.917 49 49 LYS A 50 0.986 0.973 0.983 0.485 0.757 0.364 50 50 ILE A 51 0.978 0.994 0.999 0.999 51 51 GLY A 52 0.982 0.964 52 52 ILE A 53 0.987 0.996 0.995 0.999 53 53 ASN A 54 0.788 0.369 0.450 0.544 GLY A 55 0.530 0.541 ASP A 56 0.450 0.975 0.205 0.948 LYS A 57 0.964 0.983 0.329 0.934 0.728 0.372 57 57 ARG A 58 0.989 0.994 0.656 0.948 0.265 0.741 0.991 58 58 VAL A 59 0.999 0.997 0.999 59 59 ASP A 60 0.996 0.998 0.782 0.877 60 60 VAL A 61 1.000 0.999 0.992 61 61 ILE A 62 0.999 0.997 0.998 0.999 62 62 ASP A 63 0.958 0.990 0.617 0.909 63 63 LEU A 64 0.992 0.961 0.407 0.512 64 64 LYS A 65 0.995 0.997 0.546 0.920 0.396 0.424 65 65 VAL A 66 0.999 0.999 0.991 66 66 GLN A 67 0.993 0.996 0.947 0.995 0.172 67 67 PRO A 68 0.991 0.994 0.924 0.880 68 68 GLU A 69 0.993 0.999 0.343 0.448 0.886 69 69 LEU A 70 0.998 0.996 0.998 0.999 70 70 VAL A 71 0.999 0.997 0.997 71 71 GLY A 72 0.993 0.975 72 72 SER A 73 0.998 0.986 0.187 73 73 LEU A 74 0.991 0.991 0.610 0.862 74 74 ARG A 75 0.994 0.978 0.795 0.955 0.497 0.580 1.000 75 75 LYS A 76 0.990 0.979 0.807 0.218 0.777 0.523 76 76 LYS A 77 0.980 0.966 0.982 0.739 0.556 0.195 77 77 PRO A 78 0.989 0.997 0.914 0.865 78 78 GLY A 79 0.991 0.991 79 79 ILE A 80 0.989 0.998 0.995 0.412 80 80 TYR A 81 0.994 0.992 0.988 0.129 81 81 PRO A 82 0.989 0.995 0.922 0.870 82 82 ALA A 83 0.992 0.951 83 83 TYR A 84 0.900 0.456 0.616 0.197 HIS A 85 0.431 0.488 0.251 0.168 MET A 86 0.665 0.196 0.775 0.612 0.306 ASN A 87 0.325 0.083 0.848 0.250 LYS A 88 0.266 0.656 0.991 0.995 0.465 0.460 GLU A 89 0.770 0.943 0.587 0.869 0.967 HIS A 90 0.964 0.965 0.986 0.392 90 90 TRP A 91 0.994 0.990 0.988 0.631 91 91 ILE A 92 0.993 0.987 0.988 0.756 92 92 THR A 93 0.991 0.995 0.635 93 93 VAL A 94 0.998 1.000 0.997 94 94 LEU A 95 0.999 0.996 0.999 1.000 95 95 LEU A 96 0.997 0.995 0.998 0.996 96 96 ASN A 97 0.995 0.993 0.687 0.296 97 97 GLY A 98 0.981 0.982 98 98 PRO A 99 0.993 0.908 0.969 0.949 99 99 LEU A 100 0.909 0.808 0.415 0.074 100 GLY A 101 0.812 0.989 101 ALA A 102 0.999 0.996 102 102 LYS A 103 0.998 0.999 0.573 0.745 0.602 0.286 103 103 GLU A 104 0.999 0.999 0.633 0.197 0.970 104 104 ILE A 105 1.000 1.000 0.997 0.999 105 105 HIS A 106 0.999 1.000 0.898 0.914 106 106 SER A 107 1.000 1.000 0.297 107 107 LEU A 108 1.000 1.000 1.000 0.999 108 108 ILE A 109 1.000 1.000 1.000 1.000 109 109 GLU A 110 0.999 0.999 0.998 0.590 0.920 110 110 ASP A 111 1.000 0.999 0.719 0.989 111 111 SER A 112 0.996 0.997 0.118 112 112 PHE A 113 1.000 1.000 0.999 0.998 113 113 GLN A 114 0.992 0.992 0.775 0.732 0.623 114 114 LEU A 115 0.990 0.983 0.871 0.437 115 115 THR A 116 0.991 0.998 0.993 116 116 ARG A 117 0.979 0.812 0.378 0.892 0.339 0.711 1.000 117 LEU A 118 0.793 0.791 0.721 0.707 GLU A 119 0.302 0.505 0.578 0.584 0.904 HIS A 120 0.445 0.215 0.400 0.267 HIS A 121 0.732 0.630 0.717 0.023 HIS A 122 0.657 0.158 0.365 0.283 HIS A 123 0.606 0.528 0.268 0.366 HIS A 124 0.696 0.191 0.230 0.110 HIS A 125 0.565 0.219 0.143 Ranges: 5 from: A 2 to A 36 from: A 40 to A 53 from: A 57 to A 83 from: A 90 to A 99 from: A 102 to A 116 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[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 1 is: 0.529 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 2 is: 0.518 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 3 is: 0.626 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 4 is: 0.666 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 5 is: 0.678 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 6 is: 0.823 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 7 is: 0.640 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 8 is: 0.704 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 9 is: 0.727 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 10 is: 0.473 (*) > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 11 is: 0.587 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 12 is: 0.548 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 13 is: 0.674 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 14 is: 0.867 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 15 is: 0.718 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 16 is: 0.593 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 17 is: 0.718 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 18 is: 0.706 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 19 is: 0.618 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 20 is: 0.734 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..36],[40..53],[57..83],[90..99],[102..116], is: 0.657 > Range of RMSD values to reference struct. is 0.473 to 0.867 > 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[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 1 is: 0.924 (*) > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 2 is: 1.067 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 3 is: 1.093 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 4 is: 1.132 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 5 is: 1.052 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 6 is: 1.245 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 7 is: 1.136 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 8 is: 1.315 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 9 is: 1.117 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 10 is: 1.038 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 11 is: 1.010 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 12 is: 1.033 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 13 is: 1.160 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 14 is: 1.366 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 15 is: 1.168 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 16 is: 1.082 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 17 is: 1.114 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 18 is: 1.089 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 19 is: 1.048 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 20 is: 1.131 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..36],[40..53],[57..83],[90..99],[102..116], is: 1.116 > Range of RMSD values to reference struct. is 0.924 to 1.366 PdbStat> PdbStat> *END* of program detected, BYE! ...