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 `CTR107_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 166 MET ASP PHE GLU CYS GLN PHE VAL CYS GLU LEU LYS GLU 1 > ReadCoordsPdb(): Counting models in file `CTR107_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 CTR107_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 49740 ATOM records read from file > ReadCoordsPdb(): --> 49740 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 0.588 0.509 0.864 0.422 ASP A 2 0.300 0.234 0.564 0.911 PHE A 3 0.571 0.517 0.495 0.907 GLU A 4 0.300 0.503 0.659 0.805 0.936 CYS A 5 0.507 0.527 0.495 GLN A 6 0.537 0.817 0.751 0.792 0.890 PHE A 7 0.543 0.771 0.693 0.912 VAL A 8 0.953 0.993 1.000 8 8 CYS A 9 0.995 0.993 0.796 9 9 GLU A 10 0.991 0.991 0.768 0.999 0.911 10 10 LEU A 11 0.993 0.998 0.997 0.999 11 11 LYS A 12 0.993 0.994 0.866 0.604 0.998 0.869 12 12 GLU A 13 0.999 0.996 0.604 1.000 0.999 13 13 LEU A 14 0.981 0.985 0.536 0.597 14 14 ALA A 15 0.984 0.996 15 15 PRO A 16 0.995 0.977 0.954 0.917 16 16 VAL A 17 0.990 0.990 0.926 17 17 PRO A 18 0.994 0.985 0.924 0.853 18 18 ALA A 19 0.996 0.998 19 19 LEU A 20 0.990 0.993 0.501 0.651 20 20 LEU A 21 0.987 0.994 0.690 0.899 21 21 ILE A 22 0.980 0.994 0.521 0.928 22 22 ARG A 23 0.995 0.995 0.764 0.996 0.502 0.827 1.000 23 23 THR A 24 0.993 0.985 0.399 24 24 GLN A 25 0.985 0.988 0.586 0.999 0.887 25 25 THR A 26 0.927 0.936 0.377 26 26 ALA A 27 0.903 0.995 27 27 MET A 28 0.534 0.284 0.592 0.864 0.566 SER A 29 0.185 0.899 0.383 GLU A 30 0.934 0.922 0.837 0.993 0.905 30 30 LEU A 31 0.999 0.993 0.722 0.491 31 31 GLY A 32 0.987 0.991 32 32 SER A 33 1.000 1.000 1.000 33 33 LEU A 34 1.000 0.996 0.582 0.576 34 34 PHE A 35 0.998 0.995 0.786 0.504 35 35 GLU A 36 0.999 0.999 0.606 0.999 1.000 36 36 ALA A 37 0.998 0.996 37 37 GLY A 38 1.000 0.999 38 38 TYR A 39 0.999 0.996 0.685 0.818 39 39 HIS A 40 1.000 1.000 0.932 0.949 40 40 ASP A 41 0.927 0.514 0.691 0.957 ILE A 42 0.644 0.560 0.110 0.794 LEU A 43 0.648 0.845 0.700 0.631 GLN A 44 0.993 0.978 0.999 0.999 0.995 44 44 LEU A 45 0.993 0.985 0.451 0.615 45 45 LEU A 46 0.958 0.992 0.823 0.819 46 46 ALA A 47 0.997 0.997 47 47 GLY A 48 0.990 0.987 48 48 GLN A 49 0.989 0.994 0.916 0.737 0.757 49 49 GLY A 50 0.996 0.989 50 50 LYS A 51 0.974 0.998 0.904 0.603 0.950 0.929 51 51 SER A 52 0.969 0.969 0.811 52 52 PRO A 53 0.994 0.990 0.902 0.823 53 53 SER A 54 0.969 0.984 0.918 54 54 GLY A 55 0.980 0.986 55 55 PRO A 56 0.998 0.999 0.984 0.969 56 56 PRO A 57 0.989 0.988 0.919 0.840 57 57 PHE A 58 0.989 0.933 0.497 0.787 58 58 ALA A 59 0.959 0.998 59 59 ARG A 60 0.988 0.992 0.395 0.982 0.433 0.678 1.000 60 60 TYR A 61 0.984 0.972 0.577 0.893 61 61 PHE A 62 0.988 0.966 0.467 0.994 62 62 GLY A 63 0.546 0.479 MET A 64 0.587 0.598 0.868 0.633 0.401 SER A 65 0.773 0.196 0.254 ALA A 66 0.595 0.238 GLY A 67 0.194 0.887 THR A 68 0.962 0.980 0.583 68 68 PHE A 69 0.900 0.963 0.462 0.927 69 69 GLU A 70 0.982 0.979 0.580 0.992 0.770 70 70 VAL A 71 0.998 0.995 0.790 71 71 GLU A 72 0.988 0.963 0.665 0.944 0.835 72 72 PHE A 73 0.997 0.904 0.344 0.889 73 73 GLY A 74 0.671 0.761 PHE A 75 0.929 0.997 0.525 0.927 75 75 PRO A 76 0.994 0.989 0.921 0.836 76 76 VAL A 77 0.999 0.995 1.000 77 77 GLU A 78 0.962 0.977 0.391 0.994 0.754 78 78 GLY A 79 0.842 0.149 GLY A 80 0.217 0.967 VAL A 81 0.987 1.000 1.000 81 81 GLU A 82 0.986 0.993 1.000 1.000 1.000 82 82 GLY A 83 0.947 0.946 83 83 SER A 84 0.896 0.493 0.627 GLY A 85 0.847 0.572 ARG A 86 0.673 0.952 0.911 0.997 0.795 0.886 1.000 VAL A 87 0.948 0.990 0.864 87 87 VAL A 88 0.997 0.997 1.000 88 88 THR A 89 0.973 0.999 0.797 89 89 GLY A 90 0.972 0.985 90 90 LEU A 91 0.990 0.989 0.897 0.742 91 91 THR A 92 0.979 0.968 0.783 92 92 PRO A 93 0.990 0.995 0.908 0.826 93 93 SER A 94 0.957 0.987 0.700 94 94 GLY A 95 0.858 0.945 95 LYS A 96 0.961 0.990 0.878 0.891 0.999 0.930 96 96 ALA A 97 0.997 0.998 97 97 ALA A 98 0.983 0.993 98 98 SER A 99 0.994 0.997 0.365 99 99 SER A 100 0.990 0.986 0.998 100 100 LEU A 101 0.993 0.990 0.676 0.656 101 101 TYR A 102 0.961 0.983 0.751 0.883 102 102 ILE A 103 0.998 0.998 1.000 0.882 103 103 GLY A 104 0.956 0.979 104 104 PRO A 105 0.994 0.888 0.942 0.893 105 TYR A 106 0.963 0.992 0.691 0.763 106 106 GLY A 107 0.856 0.740 GLU A 108 0.865 0.850 0.728 0.944 0.923 108 ILE A 109 1.000 0.998 0.948 0.644 109 109 GLU A 110 0.999 0.998 0.999 0.808 0.975 110 110 ALA A 111 0.999 0.996 111 111 VAL A 112 0.998 0.998 0.613 112 112 TYR A 113 1.000 0.997 0.616 0.721 113 113 ASP A 114 1.000 0.999 0.784 0.847 114 114 ALA A 115 0.999 0.999 115 115 LEU A 116 1.000 0.999 0.829 0.805 116 116 MET A 117 1.000 0.999 0.627 0.750 0.206 117 117 LYS A 118 1.000 0.999 0.611 0.870 0.947 0.729 118 118 TRP A 119 1.000 1.000 0.996 0.997 119 119 VAL A 120 1.000 0.999 0.901 120 120 ASP A 121 1.000 0.999 0.790 0.872 121 121 ASP A 122 1.000 0.998 1.000 1.000 122 122 ASN A 123 0.999 0.991 0.997 0.816 123 123 GLY A 124 0.999 0.981 124 124 PHE A 125 0.953 0.999 0.917 0.808 125 125 ASP A 126 0.917 0.976 0.697 0.882 126 126 LEU A 127 0.808 0.988 0.599 0.599 127 SER A 128 0.908 0.752 0.311 GLY A 129 0.203 0.348 GLU A 130 0.947 0.959 0.296 0.864 0.807 130 130 ALA A 131 0.961 0.995 131 131 TYR A 132 0.990 0.990 0.249 0.985 132 132 GLU A 133 0.992 0.994 0.528 0.996 0.903 133 133 ILE A 134 0.984 0.993 0.788 0.959 134 134 TYR A 135 0.959 0.820 0.927 0.380 135 LEU A 136 0.814 0.037 0.697 0.684 ASP A 137 0.346 0.916 0.586 0.934 ASN A 138 0.875 0.936 0.813 0.910 138 PRO A 139 0.990 0.991 0.905 0.827 139 139 ALA A 140 0.887 0.850 140 GLU A 141 0.842 0.929 0.999 0.921 0.984 141 THR A 142 0.919 0.118 0.115 ALA A 143 0.244 0.889 PRO A 144 0.989 0.479 0.918 0.858 ASP A 145 0.529 0.930 0.857 0.939 GLN A 146 0.963 0.958 0.999 0.686 0.879 146 146 LEU A 147 0.950 0.903 0.628 0.738 147 147 ARG A 148 0.951 0.990 0.860 0.938 0.609 0.892 1.000 148 148 THR A 149 0.994 0.992 0.998 149 149 ARG A 150 0.987 0.997 0.928 0.999 0.476 0.720 1.000 150 150 VAL A 151 0.998 0.998 0.849 151 151 SER A 152 0.991 0.987 0.517 152 152 LEU A 153 0.990 0.981 0.869 0.876 153 153 MET A 154 0.973 0.650 0.476 0.674 0.094 LEU A 155 0.684 0.218 0.547 0.594 HIS A 156 0.255 0.219 0.793 0.414 GLU A 157 0.019 0.178 0.486 0.851 0.937 SER A 158 0.445 0.493 0.361 LEU A 159 0.527 0.245 0.713 0.720 GLU A 160 0.530 0.749 0.526 0.394 0.782 HIS A 161 0.602 0.417 0.551 0.385 HIS A 162 0.540 0.442 0.581 0.809 HIS A 163 0.547 0.580 0.448 0.166 HIS A 164 0.396 0.655 0.410 0.200 HIS A 165 0.765 0.529 0.406 0.624 HIS A 166 0.866 0.547 0.464 Ranges: 11 from: A 8 to A 27 from: A 30 to A 40 from: A 44 to A 62 from: A 68 to A 73 from: A 75 to A 78 from: A 81 to A 83 from: A 87 to A 94 from: A 96 to A 104 from: A 109 to A 126 from: A 130 to A 134 from: A 146 to A 153 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[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 1 is: 1.597 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 2 is: 0.962 (*) > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 3 is: 1.266 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 4 is: 1.128 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 5 is: 1.263 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 6 is: 1.442 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 7 is: 1.187 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 8 is: 1.089 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 9 is: 1.271 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 10 is: 1.410 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 11 is: 1.106 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 12 is: 1.616 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 13 is: 2.289 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 14 is: 1.208 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 15 is: 1.443 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 16 is: 1.299 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 17 is: 1.122 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 18 is: 1.397 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 19 is: 1.074 > Kabsch RMSD of backbone atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 20 is: 1.425 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[8..27],[30..40],[44..62],[68..73],[75..78],[81..83],[87..94],[96..104],[109..126],[130..134],[146..153], is: 1.330 > Range of RMSD values to reference struct. is 0.962 to 2.289 > 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[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 1 is: 1.822 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 2 is: 1.408 (*) > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 3 is: 1.661 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 4 is: 1.487 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 5 is: 1.650 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 6 is: 1.755 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 7 is: 1.518 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 8 is: 1.463 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 9 is: 1.740 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 10 is: 1.790 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 11 is: 1.512 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 12 is: 1.882 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 13 is: 2.750 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 14 is: 1.662 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 15 is: 1.757 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 16 is: 1.626 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 17 is: 1.436 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 18 is: 1.853 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 19 is: 1.433 > Kabsch RMSD of heavy atoms in res. A[8..27],A[30..40],A[44..62],A[68..73],A[75..78],A[81..83],A[87..94],A[96..104],A[109..126],A[130..134],A[146..153],for model 20 is: 1.829 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[8..27],[30..40],[44..62],[68..73],[75..78],[81..83],[87..94],[96..104],[109..126],[130..134],[146..153], is: 1.702 > Range of RMSD values to reference struct. is 1.408 to 2.750 PdbStat> PdbStat> *END* of program detected, BYE! ...