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 `SOR77_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 19 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 18 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 80 MET ALA ILE GLN SER LYS TYR SER ASN THR GLN VAL GLU > ReadCoordsPdb(): Counting models in file `SOR77_R3Cons_em_bcr3.pdb'; Model: > ReadCoordsPdb(): After scanning there is(are) 18 model(s) > ReadCoordsPdb(): what model do you want [(1 to 18) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file SOR77_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (18) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 45468 ATOM records read from file > ReadCoordsPdb(): --> 45468 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 0.715 0.677 0.581 0.656 ALA M 2 0.768 0.372 ILE M 3 0.835 0.156 0.554 0.909 GLN M 4 0.492 0.388 0.489 0.402 0.797 SER M 5 0.560 0.419 0.476 LYS M 6 0.518 0.655 0.696 0.755 0.859 0.997 TYR M 7 0.512 0.832 0.642 0.323 SER M 8 0.832 0.965 0.632 8 ASN M 9 0.999 0.999 0.874 0.907 9 9 THR M 10 0.998 0.996 0.835 10 10 GLN M 11 0.999 0.999 0.998 0.850 0.981 11 11 VAL M 12 0.998 0.999 1.000 12 12 GLU M 13 0.999 0.998 0.605 0.999 1.000 13 13 SER M 14 0.999 0.999 0.907 14 14 LEU M 15 0.998 0.994 0.843 0.990 15 15 ILE M 16 0.999 0.999 1.000 1.000 16 16 ALA M 17 1.000 0.999 17 17 GLU M 18 0.998 0.998 0.873 0.526 0.911 18 18 ILE M 19 1.000 1.000 1.000 1.000 19 19 LEU M 20 1.000 1.000 1.000 1.000 20 20 VAL M 21 1.000 1.000 1.000 21 21 VAL M 22 0.999 0.998 1.000 22 22 LEU M 23 0.999 0.997 0.999 0.999 23 23 GLU M 24 0.999 0.997 0.696 0.925 0.998 24 24 LYS M 25 0.999 0.997 0.656 0.995 0.638 0.998 25 25 HIS M 26 0.998 0.996 0.999 0.992 26 26 LYS M 27 0.996 0.946 1.000 1.000 1.000 1.000 27 27 ALA M 28 0.918 0.988 28 28 PRO M 29 0.999 0.998 0.984 0.966 29 29 THR M 30 1.000 1.000 0.999 30 30 ASP M 31 0.999 0.999 1.000 1.000 31 31 LEU M 32 0.999 1.000 0.999 0.999 32 32 SER M 33 0.999 0.999 1.000 33 33 LEU M 34 0.999 0.998 0.999 0.999 34 34 MET M 35 0.999 0.998 0.865 0.634 0.389 35 35 ALA M 36 1.000 0.998 36 36 LEU M 37 1.000 1.000 0.990 0.811 37 37 GLY M 38 1.000 1.000 38 38 ASN M 39 1.000 1.000 0.999 0.969 39 39 CYS M 40 0.999 0.999 0.882 40 40 VAL M 41 0.999 0.998 1.000 41 41 THR M 42 0.997 0.995 0.722 42 42 HIS M 43 0.999 0.996 0.999 0.999 43 43 LEU M 44 0.999 0.997 0.999 0.999 44 44 LEU M 45 0.997 0.987 0.740 0.918 45 45 GLU M 46 0.997 0.996 0.700 0.920 0.975 46 46 ARG M 47 0.994 0.977 0.840 0.825 0.685 0.993 1.000 47 47 LYS M 48 0.995 0.988 0.999 0.924 1.000 0.999 48 48 VAL M 49 0.989 0.999 1.000 49 49 PRO M 50 0.996 0.998 0.913 0.820 50 50 SER M 51 0.999 0.998 1.000 51 51 GLU M 52 0.999 0.999 1.000 1.000 1.000 52 52 SER M 53 0.999 0.999 1.000 53 53 ARG M 54 0.999 0.996 0.752 0.987 0.640 0.976 0.998 54 54 GLN M 55 1.000 0.998 0.795 0.998 0.994 55 55 ALA M 56 0.999 1.000 56 56 VAL M 57 1.000 1.000 1.000 57 57 ALA M 58 0.999 0.999 58 58 GLU M 59 1.000 0.999 0.923 0.997 1.000 59 59 GLN M 60 1.000 0.999 1.000 0.915 0.987 60 60 PHE M 61 1.000 1.000 0.999 0.994 61 61 ALA M 62 1.000 0.999 62 62 LYS M 63 1.000 0.997 1.000 1.000 0.999 1.000 63 63 ALA M 64 1.000 0.998 64 64 LEU M 65 0.999 0.995 0.796 0.979 65 65 ALA M 66 0.999 0.998 66 66 GLN M 67 0.999 0.999 0.866 0.839 0.921 67 67 SER M 68 0.999 0.997 0.402 68 68 VAL M 69 0.997 0.999 1.000 69 69 LYS M 70 0.999 0.998 0.809 0.999 1.000 1.000 70 70 SER M 71 0.998 0.994 0.475 71 71 ASN M 72 0.998 0.997 1.000 0.999 72 72 LEU M 73 0.997 0.988 0.925 0.919 73 73 GLU M 74 0.393 0.264 0.635 0.930 0.976 HIS M 75 0.465 0.521 0.534 0.432 HIS M 76 0.445 0.458 0.549 0.276 HIS M 77 0.473 0.412 0.511 0.618 HIS M 78 0.545 0.035 0.371 0.493 HIS M 79 0.615 0.093 0.547 0.691 HIS M 80 0.868 0.473 0.601 0.311 MET M 91 0.249 0.715 0.677 0.581 0.656 ALA M 92 0.768 0.372 ILE M 93 0.835 0.156 0.553 0.909 GLN M 94 0.492 0.388 0.490 0.402 0.797 SER M 95 0.560 0.419 0.476 LYS M 96 0.518 0.655 0.696 0.755 0.859 0.997 TYR M 97 0.512 0.832 0.642 0.323 SER M 98 0.832 0.965 0.632 98 ASN M 99 0.999 0.999 0.874 0.907 99 99 THR M 100 0.998 0.997 0.835 100 100 GLN M 101 0.999 0.999 0.998 0.850 0.981 101 101 VAL M 102 0.998 0.999 1.000 102 102 GLU M 103 0.999 0.998 0.606 0.999 1.000 103 103 SER M 104 0.999 0.999 0.907 104 104 LEU M 105 0.998 0.994 0.843 0.990 105 105 ILE M 106 1.000 0.999 1.000 1.000 106 106 ALA M 107 1.000 0.999 107 107 GLU M 108 0.998 0.998 0.873 0.526 0.911 108 108 ILE M 109 1.000 1.000 1.000 1.000 109 109 LEU M 110 1.000 1.000 1.000 1.000 110 110 VAL M 111 1.000 1.000 1.000 111 111 VAL M 112 0.999 0.998 1.000 112 112 LEU M 113 0.999 0.997 0.999 0.999 113 113 GLU M 114 0.999 0.997 0.696 0.925 0.998 114 114 LYS M 115 0.999 0.997 0.656 0.995 0.638 0.998 115 115 HIS M 116 0.998 0.996 0.999 0.992 116 116 LYS M 117 0.996 0.946 1.000 1.000 1.000 1.000 117 117 ALA M 118 0.918 0.988 118 118 PRO M 119 0.999 0.998 0.984 0.966 119 119 THR M 120 1.000 1.000 0.999 120 120 ASP M 121 0.999 0.999 1.000 1.000 121 121 LEU M 122 0.999 1.000 0.999 0.999 122 122 SER M 123 0.999 0.999 1.000 123 123 LEU M 124 0.999 0.998 0.999 0.999 124 124 MET M 125 0.999 0.998 0.865 0.634 0.389 125 125 ALA M 126 1.000 0.998 126 126 LEU M 127 1.000 1.000 0.990 0.811 127 127 GLY M 128 1.000 1.000 128 128 ASN M 129 1.000 1.000 0.999 0.969 129 129 CYS M 130 0.999 0.999 0.882 130 130 VAL M 131 0.999 0.998 1.000 131 131 THR M 132 0.997 0.995 0.722 132 132 HIS M 133 0.999 0.996 0.999 0.999 133 133 LEU M 134 0.999 0.997 0.999 0.999 134 134 LEU M 135 0.997 0.987 0.740 0.918 135 135 GLU M 136 0.997 0.996 0.700 0.920 0.975 136 136 ARG M 137 0.994 0.977 0.840 0.825 0.685 0.993 1.000 137 137 LYS M 138 0.995 0.987 0.999 0.924 1.000 0.999 138 138 VAL M 139 0.989 0.999 1.000 139 139 PRO M 140 0.996 0.998 0.913 0.819 140 140 SER M 141 0.999 0.998 1.000 141 141 GLU M 142 0.999 0.999 1.000 1.000 1.000 142 142 SER M 143 0.999 0.999 1.000 143 143 ARG M 144 0.999 0.996 0.752 0.987 0.640 0.976 0.998 144 144 GLN M 145 1.000 0.998 0.794 0.998 0.994 145 145 ALA M 146 0.999 1.000 146 146 VAL M 147 1.000 1.000 1.000 147 147 ALA M 148 0.999 0.999 148 148 GLU M 149 1.000 0.999 0.923 0.997 1.000 149 149 GLN M 150 1.000 0.999 1.000 0.915 0.987 150 150 PHE M 151 1.000 1.000 0.999 0.994 151 151 ALA M 152 1.000 0.999 152 152 LYS M 153 1.000 0.997 1.000 1.000 0.999 1.000 153 153 ALA M 154 1.000 0.998 154 154 LEU M 155 0.999 0.995 0.796 0.979 155 155 ALA M 156 0.999 0.998 156 156 GLN M 157 0.999 0.999 0.866 0.839 0.921 157 157 SER M 158 0.999 0.997 0.401 158 158 VAL M 159 0.997 0.999 1.000 159 159 LYS M 160 0.999 0.998 0.809 0.999 1.000 1.000 160 160 SER M 161 0.998 0.994 0.475 161 161 ASN M 162 0.998 0.997 1.000 0.999 162 162 LEU M 163 0.997 0.988 0.925 0.919 163 163 GLU M 164 0.393 0.264 0.635 0.930 0.976 HIS M 165 0.465 0.521 0.534 0.432 HIS M 166 0.445 0.458 0.549 0.276 HIS M 167 0.473 0.412 0.511 0.618 HIS M 168 0.545 0.035 0.371 0.493 HIS M 169 0.615 0.093 0.548 0.691 HIS M 170 0.868 0.600 0.311 Ranges: 2 from: M 9 to M 73 from: M 99 to M 163 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[9..73],M[99..163],for model 1 is: 0.324 (*) > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 2 is: 0.664 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 3 is: 0.519 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 4 is: 0.416 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 5 is: 0.521 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 6 is: 0.346 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 7 is: 0.759 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 8 is: 0.416 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 9 is: 0.485 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 10 is: 0.494 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 11 is: 0.371 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 12 is: 0.695 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 13 is: 0.897 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 14 is: 0.603 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 15 is: 0.484 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 16 is: 0.657 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 17 is: 0.403 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 18 is: 0.549 > > Kabsch RMSD statistics for 18 structures: > Mean RMSD using as refer. str. `average' for res.[9..73],[99..163], is: 0.533 > Range of RMSD values to reference struct. is 0.324 to 0.897 > 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[9..73],M[99..163],for model 1 is: 0.939 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 2 is: 0.747 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 3 is: 0.767 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 4 is: 0.545 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 5 is: 0.657 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 6 is: 0.578 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 7 is: 1.016 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 8 is: 0.727 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 9 is: 0.760 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 10 is: 0.723 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 11 is: 0.507 (*) > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 12 is: 0.830 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 13 is: 1.087 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 14 is: 0.733 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 15 is: 0.694 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 16 is: 0.913 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 17 is: 0.562 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 18 is: 0.748 > > Kabsch RMSD statistics for 18 structures: > Mean RMSD using as refer. str. `average' for res.[9..73],[99..163], is: 0.752 > Range of RMSD values to reference struct. is 0.507 to 1.087 PdbStat> PdbStat> *END* of program detected, BYE! ...