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_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 143 MET ARG LYS ILE ASP LEU CYS LEU SER SER GLU GLY SER 1 > ReadCoordsPdb(): Counting models in file `HR1958_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 HR1958_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 45020 ATOM records read from file > ReadCoordsPdb(): --> 45020 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 0.286 0.746 0.702 0.338 ARG A 2 0.530 0.369 0.565 0.999 0.588 0.887 1.000 LYS A 3 0.204 0.960 0.865 0.928 0.999 0.860 ILE A 4 0.989 0.973 0.552 1.000 4 4 ASP A 5 0.997 0.986 0.777 0.968 5 5 LEU A 6 0.995 0.990 0.999 0.999 6 6 CYS A 7 0.997 0.994 0.998 7 7 LEU A 8 0.999 0.998 0.999 0.998 8 8 SER A 9 0.999 0.999 0.831 9 9 SER A 10 1.000 1.000 1.000 10 10 GLU A 11 0.995 0.997 0.993 0.989 0.990 11 11 GLY A 12 0.999 0.999 12 12 SER A 13 0.999 0.996 0.925 13 13 GLU A 14 0.996 0.991 0.741 0.999 0.983 14 14 VAL A 15 0.997 0.999 1.000 15 15 ILE A 16 0.999 0.989 1.000 1.000 16 16 LEU A 17 0.991 0.281 0.524 0.574 ALA A 18 0.279 0.893 THR A 19 0.988 0.986 0.550 19 19 SER A 20 0.987 0.849 0.529 20 SER A 21 0.831 0.968 0.314 21 ASP A 22 0.981 0.990 0.996 0.726 22 22 GLU A 23 0.998 0.999 0.935 1.000 1.000 23 23 LYS A 24 0.999 0.998 1.000 1.000 1.000 1.000 24 24 HIS A 25 0.999 0.999 0.995 0.799 25 25 PRO A 26 0.994 0.989 0.948 0.910 26 26 PRO A 27 0.993 0.995 0.933 0.870 27 27 GLU A 28 0.999 0.999 0.651 0.338 0.940 28 28 ASN A 29 0.997 0.996 0.854 0.781 29 29 ILE A 30 0.994 0.987 0.826 1.000 30 30 ILE A 31 0.964 0.653 0.563 0.952 ASP A 32 0.407 0.966 0.596 0.827 GLY A 33 0.985 0.976 33 33 ASN A 34 0.960 0.983 0.554 0.813 34 34 PRO A 35 0.984 0.987 0.897 0.832 35 35 GLU A 36 0.992 0.983 0.934 0.999 0.999 36 36 THR A 37 0.981 0.984 0.705 37 37 PHE A 38 0.992 0.994 0.863 0.902 38 38 TRP A 39 0.990 0.994 0.998 0.998 39 39 THR A 40 0.995 0.997 0.594 40 40 THR A 41 0.995 0.990 0.844 41 41 THR A 42 0.993 0.992 0.999 42 42 GLY A 43 0.994 0.990 43 43 MET A 44 0.988 0.995 1.000 0.601 0.496 44 44 PHE A 45 0.995 0.999 0.998 0.992 45 45 PRO A 46 0.999 0.997 1.000 1.000 46 46 GLN A 47 0.991 0.989 0.907 0.464 0.476 47 47 GLU A 48 0.994 0.994 0.636 0.998 0.760 48 48 PHE A 49 0.999 0.997 1.000 0.999 49 49 ILE A 50 0.998 0.999 0.998 0.841 50 50 ILE A 51 0.999 0.999 1.000 0.999 51 51 CYS A 52 0.999 0.999 0.712 52 52 PHE A 53 0.998 0.998 0.997 0.897 53 53 HIS A 54 0.999 0.997 0.997 0.339 54 54 LYS A 55 0.994 0.999 0.838 0.997 0.727 0.561 55 55 HIS A 56 0.997 0.994 0.932 0.523 56 56 VAL A 57 0.999 0.999 1.000 57 57 ARG A 58 0.999 0.998 0.999 0.943 0.794 0.510 1.000 58 58 ILE A 59 0.998 0.999 1.000 1.000 59 59 GLU A 60 0.997 0.996 1.000 0.938 0.999 60 60 ARG A 61 0.994 0.996 0.347 0.984 0.174 0.805 1.000 61 61 LEU A 62 0.999 0.998 0.999 1.000 62 62 VAL A 63 0.998 0.999 1.000 63 63 ILE A 64 0.996 0.998 0.999 0.580 64 64 GLN A 65 0.996 0.990 0.537 0.989 0.669 65 65 SER A 66 0.999 0.996 1.000 66 66 TYR A 67 0.974 0.985 0.623 0.776 67 67 PHE A 68 0.989 0.479 0.995 0.624 VAL A 69 0.390 0.814 0.615 GLN A 70 0.797 0.977 0.754 0.994 0.821 THR A 71 0.991 0.998 1.000 71 71 LEU A 72 0.999 0.998 1.000 1.000 72 72 LYS A 73 0.997 0.996 0.801 0.871 0.934 0.997 73 73 ILE A 74 0.998 0.999 1.000 1.000 74 74 GLU A 75 0.998 0.998 0.998 0.935 0.868 75 75 LYS A 76 1.000 0.999 0.929 0.997 0.509 0.539 76 76 SER A 77 0.998 0.999 0.995 77 77 THR A 78 0.998 0.997 1.000 78 78 SER A 79 0.998 0.899 0.817 79 LYS A 80 0.901 0.995 0.913 1.000 1.000 1.000 80 80 GLU A 81 0.996 0.999 1.000 1.000 1.000 81 81 PRO A 82 0.998 0.974 1.000 1.000 82 82 VAL A 83 0.997 0.998 1.000 83 83 ASP A 84 0.996 0.906 0.946 0.995 84 84 PHE A 85 0.900 0.969 0.942 0.890 85 85 GLU A 86 0.993 0.997 0.682 1.000 1.000 86 86 GLN A 87 0.999 0.999 1.000 0.816 0.965 87 87 TRP A 88 0.997 0.999 0.999 0.994 88 88 ILE A 89 0.994 0.988 0.683 0.777 89 89 GLU A 90 0.996 0.985 0.688 0.999 0.945 90 90 LYS A 91 0.992 0.995 0.890 0.648 0.865 0.957 91 91 ASP A 92 0.996 0.980 0.586 0.932 92 92 LEU A 93 0.994 0.943 0.979 0.667 93 93 VAL A 94 0.966 0.977 0.776 94 94 HIS A 95 0.966 0.966 0.917 0.486 95 95 THR A 96 0.965 0.980 0.692 96 96 GLU A 97 0.975 0.972 0.611 0.754 0.961 97 97 GLY A 98 0.998 0.994 98 98 GLN A 99 0.994 0.971 0.693 0.596 0.828 99 99 LEU A 100 0.996 0.995 0.670 0.698 100 100 GLN A 101 0.985 0.994 0.998 0.932 0.967 101 101 ASN A 102 0.994 0.984 0.804 0.946 102 102 GLU A 103 0.993 0.992 0.581 0.289 0.706 103 103 GLU A 104 0.997 0.998 0.636 0.999 0.900 104 104 ILE A 105 0.999 0.996 0.999 0.894 105 105 VAL A 106 0.995 0.994 1.000 106 106 ALA A 107 0.991 0.988 107 107 HIS A 108 0.983 0.986 0.584 0.786 108 108 GLY A 109 0.992 0.995 109 109 SER A 110 0.981 0.991 0.546 110 110 ALA A 111 0.998 0.998 111 111 THR A 112 0.998 1.000 1.000 112 112 TYR A 113 0.998 1.000 0.999 0.799 113 113 LEU A 114 0.999 0.995 0.935 0.931 114 114 ARG A 115 0.995 0.997 0.999 0.983 0.558 0.965 0.999 115 115 PHE A 116 0.999 0.999 0.999 0.998 116 116 ILE A 117 1.000 0.998 1.000 0.963 117 117 ILE A 118 0.998 0.999 1.000 1.000 118 118 VAL A 119 0.991 0.999 1.000 119 119 SER A 120 0.992 0.985 0.740 120 120 ALA A 121 0.998 0.996 121 121 PHE A 122 0.994 0.997 0.998 0.925 122 122 ASP A 123 0.998 0.997 1.000 0.999 123 123 HIS A 124 0.988 0.974 0.788 0.815 124 124 PHE A 125 0.998 0.999 0.919 0.999 125 125 ALA A 126 0.993 0.994 126 126 SER A 127 0.997 0.996 0.844 127 127 VAL A 128 0.998 0.997 1.000 128 128 HIS A 129 0.990 0.991 0.823 0.666 129 129 SER A 130 0.994 0.995 0.228 130 130 VAL A 131 0.995 0.998 1.000 131 131 SER A 132 0.998 0.998 0.767 132 132 ALA A 133 0.999 0.996 133 133 GLU A 134 0.995 0.987 0.580 0.993 0.827 134 134 GLY A 135 0.984 0.997 135 135 THR A 136 0.996 0.999 0.714 136 136 VAL A 137 0.998 0.999 0.922 137 137 VAL A 138 0.997 0.998 1.000 138 138 SER A 139 0.948 0.936 0.758 139 139 ASN A 140 0.992 0.670 0.107 0.949 LEU A 141 0.907 0.354 0.584 0.615 SER A 142 0.807 0.311 0.513 SER A 143 0.740 0.927 Ranges: 5 from: A 4 to A 16 from: A 22 to A 30 from: A 33 to A 67 from: A 71 to A 78 from: A 80 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[22..30],A[33..67],A[71..78],A[80..139],for model 1 is: 0.635 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 2 is: 0.529 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 3 is: 0.441 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 4 is: 0.618 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 5 is: 0.384 (*) > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 6 is: 0.617 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 7 is: 0.574 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 8 is: 0.406 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 9 is: 0.572 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 10 is: 0.421 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 11 is: 0.641 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 12 is: 0.643 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 13 is: 0.419 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 14 is: 0.468 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 15 is: 0.480 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 16 is: 0.453 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 17 is: 0.567 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 18 is: 0.516 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 19 is: 0.845 > Kabsch RMSD of backbone atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 20 is: 0.696 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..16],[22..30],[33..67],[71..78],[80..139], is: 0.546 > Range of RMSD values to reference struct. is 0.384 to 0.845 > 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[22..30],A[33..67],A[71..78],A[80..139],for model 1 is: 1.086 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 2 is: 0.851 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 3 is: 0.713 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 4 is: 0.928 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 5 is: 0.682 (*) > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 6 is: 0.942 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 7 is: 0.919 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 8 is: 0.682 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 9 is: 0.992 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 10 is: 0.740 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 11 is: 0.938 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 12 is: 0.969 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 13 is: 0.757 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 14 is: 0.909 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 15 is: 0.890 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 16 is: 0.794 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 17 is: 0.883 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 18 is: 0.785 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 19 is: 1.392 > Kabsch RMSD of heavy atoms in res. A[4..16],A[22..30],A[33..67],A[71..78],A[80..139],for model 20 is: 1.010 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..16],[22..30],[33..67],[71..78],[80..139], is: 0.893 > Range of RMSD values to reference struct. is 0.682 to 1.392 PdbStat> PdbStat> *END* of program detected, BYE! ...