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 `GMR137_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 78 MET ASN LEU THR VAL ASN GLY LYS PRO SER THR VAL ASP 1 > ReadCoordsPdb(): Counting models in file `GMR137_R3Cons_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 GMR137_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 23480 ATOM records read from file > ReadCoordsPdb(): --> 23480 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 0.964 0.999 0.998 0.695 ASN A 2 0.991 0.996 0.930 0.944 2 2 LEU A 3 0.997 0.991 0.999 0.999 3 3 THR A 4 0.997 0.996 1.000 4 4 VAL A 5 0.997 0.997 1.000 5 5 ASN A 6 0.999 1.000 0.947 0.213 6 6 GLY A 7 0.998 0.999 7 7 LYS A 8 0.997 0.946 1.000 1.000 1.000 1.000 8 8 PRO A 9 0.991 0.996 0.903 0.819 9 9 SER A 10 0.992 0.965 0.674 10 10 THR A 11 0.986 0.998 1.000 11 11 VAL A 12 0.993 0.967 0.659 12 12 ASP A 13 0.888 0.934 0.586 0.964 13 GLY A 14 0.881 0.801 14 ALA A 15 0.703 0.883 GLU A 16 0.954 0.619 0.930 0.999 0.999 SER A 17 0.512 0.941 0.784 LEU A 18 0.964 0.995 0.555 0.587 18 18 ASN A 19 0.995 0.995 0.493 0.957 19 19 VAL A 20 0.998 0.999 1.000 20 20 THR A 21 0.999 0.999 1.000 21 21 GLU A 22 0.998 0.999 1.000 0.465 0.939 22 22 LEU A 23 0.997 0.994 0.815 0.737 23 23 LEU A 24 0.999 0.998 0.894 0.714 24 24 SER A 25 0.999 0.998 0.832 25 25 ALA A 26 0.999 0.999 26 26 LEU A 27 0.998 0.997 0.936 0.926 27 27 LYS A 28 0.999 0.998 0.999 0.928 1.000 0.999 28 28 VAL A 29 0.992 0.992 0.933 29 29 ALA A 30 0.981 0.367 GLN A 31 0.417 0.858 0.999 0.584 0.737 ALA A 32 0.979 0.981 32 32 GLU A 33 0.990 0.986 0.070 0.632 0.885 33 33 TYR A 34 0.991 0.958 0.995 0.102 34 34 VAL A 35 0.947 0.986 0.600 35 35 THR A 36 0.977 0.989 1.000 36 36 VAL A 37 0.993 0.992 0.925 37 37 GLU A 38 0.987 0.973 0.380 0.999 0.975 38 38 LEU A 39 0.998 0.997 0.717 0.743 39 39 ASN A 40 0.999 0.999 0.999 0.874 40 40 GLY A 41 0.999 0.995 41 41 GLU A 42 0.981 0.998 0.808 0.999 1.000 42 42 VAL A 43 0.997 0.999 1.000 43 43 LEU A 44 0.995 0.996 0.923 0.687 44 44 GLU A 45 0.978 0.982 0.866 1.000 0.984 45 45 ARG A 46 0.995 0.993 0.156 0.997 0.719 0.754 1.000 46 46 GLU A 47 0.996 0.997 1.000 1.000 1.000 47 47 ALA A 48 0.994 0.995 48 48 PHE A 49 0.999 0.993 0.998 0.992 49 49 ASP A 50 0.992 0.998 0.939 0.887 50 50 ALA A 51 0.991 0.926 51 51 THR A 52 0.920 0.997 1.000 52 52 THR A 53 0.996 0.999 1.000 53 53 VAL A 54 0.996 0.997 1.000 54 54 LYS A 55 0.987 0.949 0.495 0.998 0.999 0.926 55 55 ASP A 56 0.909 0.963 0.997 0.689 56 56 GLY A 57 0.947 0.967 57 57 ASP A 58 0.959 0.986 0.772 0.944 58 58 ALA A 59 0.984 0.949 59 59 VAL A 60 0.975 0.953 0.926 60 60 GLU A 61 0.970 0.983 0.999 0.748 0.931 61 61 PHE A 62 0.956 0.989 0.717 0.594 62 62 LEU A 63 0.935 0.934 0.597 0.865 63 63 TYR A 64 0.063 0.918 0.919 0.834 PHE A 65 0.594 0.270 0.614 0.989 MET A 66 0.427 0.567 0.242 0.124 0.261 GLY A 67 0.623 0.740 GLY A 68 0.081 0.073 GLY A 69 0.390 0.540 LYS A 70 0.439 0.844 0.574 0.937 0.936 0.930 LEU A 71 0.685 0.604 0.725 0.653 GLU A 72 0.725 0.420 0.577 0.723 0.951 HIS A 73 0.550 0.358 0.309 0.157 HIS A 74 0.561 0.538 0.319 0.553 HIS A 75 0.606 0.828 0.564 0.567 HIS A 76 0.672 0.773 0.579 0.301 HIS A 77 0.974 0.988 0.416 0.816 77 77 HIS A 78 0.989 0.871 0.902 Ranges: 3 from: A 2 to A 12 from: A 18 to A 29 from: A 32 to A 63 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..12],A[18..29],A[32..63],for model 1 is: 0.743 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 2 is: 0.467 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 3 is: 0.677 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 4 is: 0.469 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 5 is: 0.617 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 6 is: 0.577 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 7 is: 0.585 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 8 is: 0.838 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 9 is: 0.782 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 10 is: 0.779 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 11 is: 0.556 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 12 is: 0.531 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 13 is: 0.566 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 14 is: 0.596 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 15 is: 0.667 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 16 is: 0.767 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 17 is: 0.725 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 18 is: 0.407 (*) > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 19 is: 0.450 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..63],for model 20 is: 0.887 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..12],[18..29],[32..63], is: 0.634 > Range of RMSD values to reference struct. is 0.407 to 0.887 > 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..12],A[18..29],A[32..63],for model 1 is: 1.028 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 2 is: 0.715 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 3 is: 0.871 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 4 is: 0.790 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 5 is: 0.888 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 6 is: 0.894 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 7 is: 1.177 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 8 is: 1.289 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 9 is: 1.176 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 10 is: 1.107 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 11 is: 0.901 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 12 is: 0.852 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 13 is: 0.850 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 14 is: 0.945 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 15 is: 0.895 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 16 is: 1.153 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 17 is: 0.980 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 18 is: 0.701 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 19 is: 0.691 (*) > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..63],for model 20 is: 1.130 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..12],[18..29],[32..63], is: 0.952 > Range of RMSD values to reference struct. is 0.691 to 1.289 PdbStat> PdbStat> *END* of program detected, BYE! ...