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 `UUR17A_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 121 MET LEU SER GLN ALA ASN GLU ASP PHE LYS LYS ILE VAL 1 > ReadCoordsPdb(): Counting models in file `UUR17A_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 UUR17A_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 40120 ATOM records read from file > ReadCoordsPdb(): --> 40120 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 0.236 0.687 0.424 0.369 LEU A 2 0.755 0.539 0.617 0.639 SER A 3 0.783 0.654 0.397 GLN A 4 0.845 0.806 0.747 0.797 0.699 4 ALA A 5 0.790 0.981 ASN A 6 0.998 0.997 1.000 1.000 6 6 GLU A 7 0.990 0.997 1.000 0.535 0.921 7 7 ASP A 8 0.994 0.993 0.999 0.983 8 8 PHE A 9 0.995 0.995 0.584 0.650 9 9 LYS A 10 0.996 0.998 0.934 0.999 0.939 0.998 10 10 LYS A 11 0.996 0.998 0.999 0.999 0.997 0.995 11 11 ILE A 12 0.999 0.995 1.000 0.762 12 12 VAL A 13 0.990 0.988 0.756 13 13 ASN A 14 0.993 0.994 0.946 0.960 14 14 ASN A 15 0.987 0.949 0.999 0.965 15 15 ILE A 16 0.976 0.997 0.999 0.770 16 16 ARG A 17 0.968 0.994 0.999 0.644 0.999 0.715 1.000 17 17 LEU A 18 0.991 0.964 0.923 0.779 18 18 LYS A 19 0.968 0.975 0.530 0.930 0.998 0.788 19 19 ASP A 20 0.974 0.996 0.934 0.947 20 20 THR A 21 0.985 0.997 0.927 21 21 PHE A 22 0.975 0.980 0.743 0.993 22 22 ASP A 23 0.960 0.989 1.000 0.985 23 23 PHE A 24 0.979 0.971 0.591 0.202 24 24 LYS A 25 0.971 0.958 0.842 0.870 0.998 0.998 25 25 LEU A 26 0.978 0.972 0.992 0.937 26 26 ALA A 27 0.996 0.994 27 27 ALA A 28 0.996 0.989 28 28 PHE A 29 0.997 0.997 0.999 0.799 29 29 PRO A 30 0.986 0.971 0.906 0.842 30 30 ASN A 31 0.965 0.865 0.211 0.879 31 GLN A 32 0.949 0.938 0.745 0.756 0.888 32 32 ASN A 33 0.904 0.933 0.702 0.929 33 33 TYR A 34 0.976 0.970 0.581 0.894 34 34 ASP A 35 0.941 0.960 0.393 0.940 35 35 GLN A 36 0.977 0.926 0.998 0.570 0.819 36 36 LEU A 37 0.941 0.969 0.542 0.493 37 37 LEU A 38 0.971 0.974 0.655 0.582 38 38 PRO A 39 0.995 0.993 0.965 0.936 39 39 SER A 40 0.992 0.987 0.282 40 40 GLN A 41 0.981 0.989 0.873 0.551 0.842 41 41 ILE A 42 0.985 0.989 0.890 1.000 42 42 TYR A 43 0.996 0.992 0.924 0.893 43 43 LYS A 44 0.970 0.971 0.590 0.999 0.998 0.927 44 44 ASN A 45 0.938 0.959 0.699 0.398 45 45 TYR A 46 0.987 0.983 0.695 0.989 46 46 TYR A 47 0.959 0.956 0.413 0.915 47 47 GLN A 48 0.967 0.926 0.998 0.729 0.832 48 48 GLY A 49 0.961 0.983 49 49 ILE A 50 0.985 0.993 0.862 0.840 50 50 GLU A 51 0.968 0.976 0.683 0.999 0.999 51 51 ILE A 52 0.986 0.995 0.999 0.389 52 52 GLN A 53 0.980 0.969 0.574 0.104 0.534 53 53 GLN A 54 0.988 0.988 0.463 0.815 0.635 54 54 HIS A 55 0.984 0.937 0.932 0.568 55 55 LYS A 56 0.963 0.900 0.935 0.571 0.996 0.763 56 TYR A 57 0.550 0.743 0.606 0.854 GLN A 58 0.884 0.765 0.212 0.429 0.574 ASN A 59 0.788 0.974 0.740 0.924 GLU A 60 0.967 0.965 0.789 0.273 0.917 60 60 LEU A 61 0.985 0.955 0.506 0.592 61 61 ASP A 62 0.970 0.993 0.938 0.999 62 62 ILE A 63 0.989 0.995 0.939 0.742 63 63 LYS A 64 0.981 0.958 0.660 0.933 0.999 0.999 64 64 ILE A 65 0.961 0.997 0.808 0.918 65 65 ILE A 66 0.991 0.995 0.999 0.456 66 66 ASN A 67 0.993 0.979 0.285 0.648 67 67 PHE A 68 0.981 0.905 0.996 0.992 68 68 LEU A 69 0.897 0.981 0.477 0.660 69 TYR A 70 0.975 0.991 0.993 0.551 70 70 PRO A 71 0.984 0.425 0.909 0.859 ASP A 72 0.339 0.841 0.415 0.906 GLY A 73 0.797 0.636 ASP A 74 0.926 0.949 0.936 0.715 74 74 PHE A 75 0.996 0.982 0.490 0.946 75 75 GLY A 76 0.992 0.992 76 76 SER A 77 0.995 0.988 0.230 77 77 ALA A 78 0.991 0.996 78 78 ASN A 79 0.996 0.984 0.778 0.816 79 79 LYS A 80 0.973 0.990 0.781 0.994 0.613 0.990 80 80 ASN A 81 0.966 0.966 0.846 0.928 81 81 GLY A 82 0.979 0.959 82 82 THR A 83 0.981 0.970 0.445 83 83 LEU A 84 0.983 0.990 0.638 0.674 84 84 LYS A 85 0.992 0.961 0.999 0.995 0.998 0.988 85 85 LEU A 86 0.950 0.992 0.742 0.998 86 86 SER A 87 0.996 0.992 0.616 87 87 LEU A 88 0.988 0.992 0.787 0.810 88 88 MET A 89 0.986 0.997 0.999 0.931 0.254 89 89 LEU A 90 0.994 0.990 0.905 0.778 90 90 THR A 91 0.990 0.996 1.000 91 91 ASP A 92 0.992 0.993 0.996 0.968 92 92 LYS A 93 0.994 0.989 0.932 0.928 0.937 0.866 93 93 LYS A 94 0.976 0.991 0.602 0.624 0.998 0.990 94 94 ASN A 95 0.986 0.997 0.999 0.998 95 95 ASN A 96 0.999 0.996 0.943 0.948 96 96 GLN A 97 0.996 0.990 0.917 0.920 0.934 97 97 VAL A 98 0.989 0.996 1.000 98 98 TYR A 99 0.993 0.943 0.997 0.997 99 99 TYR A 100 0.957 0.961 0.619 0.992 100 100 LYS A 101 0.978 0.969 0.492 0.338 1.000 0.997 101 101 LEU A 102 0.987 0.984 0.691 0.679 102 102 LEU A 103 0.988 0.964 0.531 0.454 103 103 GLU A 104 0.977 0.983 0.930 0.999 0.999 104 104 VAL A 105 0.988 0.965 0.493 105 105 SER A 106 0.956 0.980 0.304 106 106 GLY A 107 0.983 0.989 107 107 PHE A 108 0.992 0.892 0.900 0.921 108 LYS A 109 0.896 0.902 0.793 0.442 0.794 0.872 109 SER A 110 0.900 0.965 0.853 110 110 ASN A 111 0.987 0.980 0.880 0.907 111 111 PRO A 112 0.992 0.979 0.904 0.820 112 112 TYR A 113 0.906 0.959 0.513 0.992 113 113 LEU A 114 0.951 0.904 0.854 0.863 114 114 GLU A 115 0.929 0.520 0.529 0.379 0.904 HIS A 116 0.648 0.638 0.727 0.676 HIS A 117 0.829 0.380 0.483 0.441 HIS A 118 0.754 0.566 0.386 0.556 HIS A 119 0.531 0.371 0.526 0.716 HIS A 120 0.637 0.313 0.344 0.658 HIS A 121 0.899 0.803 0.809 Ranges: 5 from: A 6 to A 30 from: A 32 to A 55 from: A 60 to A 68 from: A 74 to A 107 from: A 110 to A 114 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[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 1 is: 1.265 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 2 is: 1.291 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 3 is: 1.068 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 4 is: 1.677 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 5 is: 1.387 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 6 is: 0.808 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 7 is: 1.236 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 8 is: 1.023 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 9 is: 0.989 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 10 is: 0.866 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 11 is: 1.732 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 12 is: 0.862 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 13 is: 1.069 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 14 is: 1.001 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 15 is: 0.648 (*) > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 16 is: 0.836 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 17 is: 1.430 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 18 is: 1.430 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 19 is: 1.096 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 20 is: 1.613 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[6..30],[32..55],[60..68],[74..107],[110..114], is: 1.166 > Range of RMSD values to reference struct. is 0.648 to 1.732 > 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[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 1 is: 1.746 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 2 is: 1.713 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 3 is: 1.545 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 4 is: 2.062 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 5 is: 1.879 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 6 is: 1.235 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 7 is: 1.672 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 8 is: 1.571 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 9 is: 1.578 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 10 is: 1.371 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 11 is: 2.301 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 12 is: 1.350 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 13 is: 1.627 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 14 is: 1.478 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 15 is: 1.190 (*) > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 16 is: 1.452 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 17 is: 1.834 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 18 is: 2.028 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 19 is: 1.473 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..55],A[60..68],A[74..107],A[110..114],for model 20 is: 2.359 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[6..30],[32..55],[60..68],[74..107],[110..114], is: 1.673 > Range of RMSD values to reference struct. is 1.190 to 2.359 PdbStat> PdbStat> *END* of program detected, BYE! ...