Running PDBSTAT from Linux Ayuda is on: /farm/software/PdbStat/PdbStat-5.9 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2013 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.9-exp mar may 14 00:20:00 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 ...) 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 `SPR104_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 82 MET LYS LYS MET ALA GLU PHE THR PHE GLU ILE GLU GLU > ReadCoordsPdb(): Counting models in file `SPR104_R3Cons_em_bcr3.pdb'; Model: > 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 SPR104_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 52640 ATOM records read from file > ReadCoordsPdb(): --> 52640 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 M 1 0.336 0.693 0.506 0.216 LYS M 2 0.627 0.601 0.607 0.927 0.999 0.999 LYS M 3 0.752 0.410 0.695 0.998 0.928 0.999 MET M 4 0.552 0.052 0.481 0.618 0.347 ALA M 5 0.237 0.282 GLU M 6 0.582 0.379 0.695 0.924 0.978 PHE M 7 0.707 0.594 0.490 0.792 THR M 8 0.975 0.992 0.612 8 8 PHE M 9 0.957 0.991 0.639 0.717 9 9 GLU M 10 0.994 0.998 0.564 0.998 1.000 10 10 ILE M 11 0.999 1.000 1.000 1.000 11 11 GLU M 12 0.997 0.996 1.000 0.996 0.973 12 12 GLU M 13 0.999 0.998 0.933 1.000 0.972 13 13 HIS M 14 0.999 0.995 0.559 0.626 14 14 LEU M 15 0.995 0.995 0.998 0.907 15 15 LEU M 16 0.995 0.981 0.464 0.842 16 16 THR M 17 0.998 0.996 1.000 17 17 LEU M 18 0.996 0.998 0.998 0.998 18 18 SER M 19 0.997 0.997 0.706 19 19 GLU M 20 0.988 0.996 1.000 1.000 0.979 20 20 ASN M 21 0.994 0.981 0.826 0.891 21 21 GLU M 22 0.751 0.468 0.687 0.875 0.902 LYS M 23 0.398 0.741 0.800 0.999 0.999 1.000 GLY M 24 0.773 0.910 TRP M 25 0.977 0.908 0.996 0.903 25 25 THR M 26 0.985 0.988 0.571 26 26 LYS M 27 0.985 0.998 0.907 0.864 0.596 0.759 27 27 GLU M 28 0.992 0.997 0.665 0.998 0.756 28 28 ILE M 29 0.999 0.998 1.000 0.967 29 29 ASN M 30 0.989 0.999 0.794 0.846 30 30 ARG M 31 0.995 0.995 0.948 0.996 0.940 0.994 1.000 31 31 VAL M 32 0.998 0.999 1.000 32 32 SER M 33 0.996 0.997 0.494 33 33 PHE M 34 0.995 0.974 0.998 0.535 34 34 ASN M 35 0.902 0.555 0.642 0.745 GLY M 36 0.519 0.159 ALA M 37 0.657 0.138 PRO M 38 0.979 0.686 0.885 0.822 ALA M 39 0.560 0.947 LYS M 40 0.993 0.999 0.998 0.598 0.869 0.999 40 40 PHE M 41 0.995 0.998 0.998 0.990 41 41 ASP M 42 0.996 0.998 0.723 0.756 42 42 ILE M 43 0.997 0.998 0.998 0.795 43 43 ARG M 44 0.988 0.986 0.180 0.851 0.339 0.643 1.000 44 44 ALA M 45 0.983 0.988 45 45 TRP M 46 0.986 0.989 0.581 0.407 46 46 SER M 47 0.849 0.819 0.615 47 PRO M 48 0.987 0.227 0.901 0.833 ASP M 49 0.203 0.282 0.379 0.910 HIS M 50 0.240 0.485 0.704 0.802 THR M 51 0.657 0.364 0.552 LYS M 52 0.836 0.433 0.848 0.873 0.871 0.922 MET M 53 0.741 0.517 0.417 0.511 0.269 GLY M 54 0.485 0.364 LYS M 55 0.530 0.764 0.931 0.804 0.936 0.999 GLY M 56 0.852 0.908 56 ILE M 57 0.996 0.999 1.000 0.948 57 57 THR M 58 0.997 0.999 1.000 58 58 LEU M 59 0.998 0.997 0.999 0.956 59 59 SER M 60 0.986 0.987 0.814 60 60 ASN M 61 1.000 0.999 0.999 0.982 61 61 GLU M 62 0.999 0.999 1.000 0.947 0.999 62 62 GLU M 63 1.000 0.999 0.998 0.908 0.910 63 63 PHE M 64 0.999 0.999 0.976 0.990 64 64 GLN M 65 0.998 0.998 0.994 0.905 0.947 65 65 THR M 66 1.000 0.998 0.999 66 66 MET M 67 0.994 0.990 0.738 0.764 0.699 67 67 VAL M 68 0.999 0.995 1.000 68 68 ASP M 69 0.996 0.996 0.815 0.840 69 69 ALA M 70 0.999 0.999 70 70 PHE M 71 0.996 0.994 0.995 0.600 71 71 LYS M 72 0.995 0.994 0.799 0.900 0.857 0.849 72 72 GLY M 73 0.981 0.905 73 73 ASN M 74 0.929 0.334 0.604 0.862 LEU M 75 0.198 0.317 0.793 0.983 GLU M 76 0.406 0.256 0.721 0.374 0.828 HIS M 77 0.908 0.538 0.625 0.589 HIS M 78 0.755 0.471 0.233 0.254 HIS M 79 0.583 0.359 0.584 0.575 HIS M 80 0.588 0.316 0.584 0.536 HIS M 81 0.611 0.610 0.589 0.717 HIS M 82 0.938 0.240 0.674 0.533 MET M 93 0.277 0.336 0.694 0.506 0.216 LYS M 94 0.627 0.601 0.607 0.927 0.999 0.999 LYS M 95 0.752 0.410 0.694 0.998 0.928 0.999 MET M 96 0.552 0.052 0.481 0.618 0.347 ALA M 97 0.237 0.282 GLU M 98 0.582 0.379 0.695 0.924 0.978 PHE M 99 0.707 0.594 0.491 0.791 THR M 100 0.975 0.992 0.612 100 100 PHE M 101 0.957 0.991 0.639 0.718 101 101 GLU M 102 0.994 0.998 0.564 0.998 1.000 102 102 ILE M 103 0.999 1.000 1.000 1.000 103 103 GLU M 104 0.997 0.996 1.000 0.996 0.974 104 104 GLU M 105 0.999 0.998 0.933 1.000 0.972 105 105 HIS M 106 0.999 0.995 0.559 0.626 106 106 LEU M 107 0.995 0.995 0.998 0.907 107 107 LEU M 108 0.995 0.981 0.464 0.842 108 108 THR M 109 0.998 0.996 1.000 109 109 LEU M 110 0.995 0.998 0.998 0.998 110 110 SER M 111 0.997 0.997 0.706 111 111 GLU M 112 0.988 0.996 1.000 1.000 0.979 112 112 ASN M 113 0.994 0.981 0.826 0.891 113 113 GLU M 114 0.752 0.468 0.687 0.875 0.902 LYS M 115 0.398 0.741 0.800 0.999 0.999 1.000 GLY M 116 0.773 0.910 TRP M 117 0.977 0.908 0.996 0.903 117 117 THR M 118 0.985 0.988 0.571 118 118 LYS M 119 0.985 0.998 0.907 0.864 0.596 0.759 119 119 GLU M 120 0.992 0.997 0.665 0.998 0.756 120 120 ILE M 121 0.999 0.998 1.000 0.967 121 121 ASN M 122 0.989 0.999 0.795 0.846 122 122 ARG M 123 0.995 0.995 0.948 0.996 0.940 0.994 1.000 123 123 VAL M 124 0.998 0.999 1.000 124 124 SER M 125 0.996 0.997 0.494 125 125 PHE M 126 0.995 0.974 0.998 0.535 126 126 ASN M 127 0.902 0.555 0.642 0.745 GLY M 128 0.519 0.159 ALA M 129 0.657 0.138 PRO M 130 0.979 0.686 0.885 0.822 ALA M 131 0.560 0.947 LYS M 132 0.993 0.999 0.998 0.598 0.869 0.999 132 132 PHE M 133 0.995 0.998 0.998 0.990 133 133 ASP M 134 0.996 0.998 0.723 0.756 134 134 ILE M 135 0.997 0.998 0.998 0.795 135 135 ARG M 136 0.988 0.986 0.180 0.851 0.339 0.643 1.000 136 136 ALA M 137 0.983 0.988 137 137 TRP M 138 0.986 0.989 0.581 0.407 138 138 SER M 139 0.849 0.819 0.615 139 PRO M 140 0.987 0.227 0.901 0.833 ASP M 141 0.203 0.282 0.379 0.910 HIS M 142 0.240 0.485 0.704 0.802 THR M 143 0.657 0.364 0.552 LYS M 144 0.836 0.433 0.848 0.873 0.870 0.922 MET M 145 0.741 0.518 0.417 0.511 0.269 GLY M 146 0.485 0.364 LYS M 147 0.530 0.764 0.931 0.804 0.936 0.999 GLY M 148 0.852 0.908 148 ILE M 149 0.996 0.999 1.000 0.948 149 149 THR M 150 0.997 0.999 1.000 150 150 LEU M 151 0.998 0.997 0.999 0.956 151 151 SER M 152 0.986 0.987 0.814 152 152 ASN M 153 1.000 0.999 0.999 0.982 153 153 GLU M 154 0.999 0.999 1.000 0.947 0.999 154 154 GLU M 155 1.000 0.999 0.998 0.907 0.910 155 155 PHE M 156 0.999 0.999 0.976 0.990 156 156 GLN M 157 0.998 0.998 0.994 0.905 0.947 157 157 THR M 158 1.000 0.998 0.999 158 158 MET M 159 0.994 0.990 0.738 0.764 0.699 159 159 VAL M 160 0.999 0.995 1.000 160 160 ASP M 161 0.996 0.996 0.815 0.839 161 161 ALA M 162 0.999 0.999 162 162 PHE M 163 0.996 0.994 0.995 0.600 163 163 LYS M 164 0.995 0.994 0.799 0.900 0.857 0.849 164 164 GLY M 165 0.981 0.905 165 165 ASN M 166 0.929 0.334 0.604 0.862 LEU M 167 0.198 0.317 0.793 0.983 GLU M 168 0.406 0.256 0.721 0.374 0.828 HIS M 169 0.908 0.538 0.625 0.589 HIS M 170 0.756 0.471 0.233 0.253 HIS M 171 0.583 0.359 0.584 0.575 HIS M 172 0.588 0.316 0.584 0.536 HIS M 173 0.611 0.610 0.589 0.717 HIS M 174 0.938 0.674 0.533 Ranges: 8 from: M 8 to M 21 from: M 25 to M 34 from: M 40 to M 46 from: M 57 to M 73 from: M 100 to M 113 from: M 117 to M 126 from: M 132 to M 138 from: M 149 to M 165 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. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 1 is: 0.906 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 2 is: 0.901 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 3 is: 0.441 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 4 is: 0.410 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 5 is: 0.861 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 6 is: 0.452 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 7 is: 0.467 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 8 is: 0.391 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 9 is: 0.598 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 10 is: 0.638 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 11 is: 0.730 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 12 is: 0.629 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 13 is: 0.484 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 14 is: 0.779 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 15 is: 0.719 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 16 is: 0.552 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 17 is: 0.313 (*) > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 18 is: 0.345 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 19 is: 0.989 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 20 is: 1.408 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[8..21],[25..34],[40..46],[57..73],[100..113],[117..126],[132..138],[149..165], is: 0.651 > Range of RMSD values to reference struct. is 0.313 to 1.408 > 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. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 1 is: 1.309 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 2 is: 1.289 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 3 is: 0.726 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 4 is: 0.881 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 5 is: 1.310 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 6 is: 0.892 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 7 is: 0.794 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 8 is: 0.688 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 9 is: 0.983 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 10 is: 1.030 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 11 is: 1.009 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 12 is: 0.858 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 13 is: 0.895 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 14 is: 1.091 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 15 is: 1.419 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 16 is: 0.846 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 17 is: 0.844 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 18 is: 0.647 (*) > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 19 is: 1.157 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..73],M[100..113],M[117..126],M[132..138],M[149..165],for model 20 is: 1.586 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[8..21],[25..34],[40..46],[57..73],[100..113],[117..126],[132..138],[149..165], is: 1.013 > Range of RMSD values to reference struct. is 0.647 to 1.586 PdbStat> PdbStat> *END* of program detected, BYE! ...