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 `CSR4_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 19-JUN-07 2JR2 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF HOMODIMER CPS_2611 FROM COLWELLIA > ReadCoordsPdb(): >> TITLE 2 PSYCHRERYTHRAEA. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET > ReadCoordsPdb(): >> TITLE 3 CSR4. > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `CSR4_NMR_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 CSR4_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 49200 ATOM records read from file > ReadCoordsPdb(): --> 49200 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 0.679 0.532 0.167 0.672 PRO M 2 0.990 0.599 0.940 0.872 ILE M 3 0.710 0.714 0.232 0.572 VAL M 4 0.765 0.368 0.521 SER M 5 0.365 0.220 0.607 LYS M 6 0.345 0.728 0.566 0.775 0.377 0.247 TYR M 7 0.138 0.820 0.721 0.435 SER M 8 0.901 0.956 0.155 8 8 ASN M 9 0.999 0.995 0.405 0.331 9 9 GLU M 10 0.998 0.993 0.478 0.405 0.317 10 10 ARG M 11 0.995 0.997 0.994 0.931 0.990 0.648 0.998 11 11 VAL M 12 0.999 0.998 0.999 12 12 GLU M 13 0.994 0.991 0.643 0.740 0.288 13 13 LYS M 14 0.995 0.990 0.826 0.894 0.920 0.085 14 14 ILE M 15 0.999 0.999 0.999 0.999 15 15 ILE M 16 1.000 0.999 1.000 0.999 16 16 GLN M 17 0.999 0.998 0.997 0.999 0.762 17 17 ASP M 18 0.996 0.998 0.836 0.585 18 18 LEU M 19 0.999 0.998 0.999 0.999 19 19 LEU M 20 1.000 0.997 0.999 1.000 20 20 ASP M 21 0.998 0.998 0.738 0.476 21 21 VAL M 22 0.999 0.999 0.999 22 22 LEU M 23 0.998 0.997 0.999 1.000 23 23 VAL M 24 0.996 0.996 0.772 24 24 LYS M 25 0.996 0.989 0.751 0.919 0.378 0.293 25 25 GLU M 26 0.993 0.993 0.995 0.997 0.711 26 26 GLU M 27 0.996 0.988 0.908 0.621 0.353 27 27 VAL M 28 0.989 0.982 0.999 28 28 THR M 29 0.993 0.993 0.762 29 29 PRO M 30 0.996 0.995 0.967 0.923 30 30 ASP M 31 0.997 0.996 0.336 0.426 31 31 LEU M 32 0.999 0.999 0.999 0.999 32 32 ALA M 33 1.000 0.997 33 33 LEU M 34 0.999 0.998 0.999 1.000 34 34 MET M 35 0.999 0.996 0.999 1.000 0.999 35 35 CYS M 36 0.997 0.999 0.999 36 36 LEU M 37 1.000 0.997 1.000 1.000 37 37 GLY M 38 0.999 0.996 38 38 ASN M 39 0.999 0.998 0.786 0.908 39 39 ALA M 40 1.000 0.998 40 40 VAL M 41 0.999 0.998 1.000 41 41 THR M 42 0.997 0.991 0.813 42 42 ASN M 43 0.993 0.993 0.799 0.787 43 43 ILE M 44 0.991 0.990 0.768 0.694 44 44 ILE M 45 0.999 0.996 0.998 0.999 45 45 ALA M 46 0.996 0.995 46 46 GLN M 47 0.996 0.985 0.999 0.999 1.000 47 47 VAL M 48 0.984 0.982 0.746 48 48 PRO M 49 0.995 0.993 0.942 0.872 49 49 GLU M 50 0.988 0.985 0.576 0.425 0.325 50 50 SER M 51 0.996 0.992 0.657 51 51 LYS M 52 0.968 0.978 0.771 0.927 0.281 0.372 52 52 ARG M 53 0.991 0.996 0.882 0.974 0.511 0.842 0.995 53 53 VAL M 54 0.996 0.997 0.999 54 54 ALA M 55 0.998 0.998 55 55 VAL M 56 0.999 0.998 0.852 56 56 VAL M 57 0.999 0.999 0.999 57 57 ASP M 58 0.998 0.996 0.842 0.421 58 58 ASN M 59 0.997 0.998 0.939 0.831 59 59 PHE M 60 0.999 0.999 0.998 0.994 60 60 THR M 61 0.999 0.999 0.998 61 61 LYS M 62 0.999 0.997 0.987 0.782 0.472 0.254 62 62 ALA M 63 0.998 0.997 63 63 LEU M 64 0.998 0.994 0.903 0.993 64 64 LYS M 65 0.998 0.994 0.992 0.930 0.375 0.497 65 65 GLN M 66 0.997 0.984 0.358 0.582 0.367 66 66 SER M 67 0.991 0.977 0.393 67 67 VAL M 68 0.981 0.994 0.999 68 68 LEU M 69 0.992 0.961 0.893 0.673 69 69 GLU M 70 0.950 0.468 0.433 0.265 0.272 HIS M 71 0.673 0.509 0.805 0.350 HIS M 72 0.506 0.077 0.317 0.262 HIS M 73 0.568 0.438 0.570 0.402 HIS M 74 0.705 0.455 0.311 0.235 HIS M 75 0.667 0.179 0.439 0.438 HIS M 76 0.796 0.688 0.562 0.340 MET M 87 0.428 0.580 0.633 0.567 0.431 PRO M 88 0.986 0.290 0.951 0.886 ILE M 89 0.819 0.608 0.267 0.583 VAL M 90 0.694 0.421 0.056 SER M 91 0.696 0.307 0.305 LYS M 92 0.838 0.740 0.455 0.643 0.500 0.226 TYR M 93 0.261 0.893 0.831 0.506 SER M 94 0.906 0.962 0.268 94 94 ASN M 95 0.998 0.990 0.195 0.195 95 95 GLU M 96 0.997 0.991 0.427 0.386 0.431 96 96 ARG M 97 0.995 0.996 0.989 0.991 0.930 0.687 0.998 97 97 VAL M 98 0.999 0.997 0.999 98 98 GLU M 99 0.996 0.992 0.594 0.615 0.388 99 99 LYS M 100 0.995 0.992 0.926 0.807 0.653 0.186 100 100 ILE M 101 0.998 0.999 0.999 1.000 101 101 ILE M 102 1.000 0.999 0.999 0.999 102 102 GLN M 103 0.999 0.996 0.993 0.834 0.721 103 103 ASP M 104 0.998 0.997 0.809 0.515 104 104 LEU M 105 0.999 0.999 0.999 0.999 105 105 LEU M 106 0.999 0.997 0.999 0.999 106 106 ASP M 107 0.998 0.996 0.689 0.357 107 107 VAL M 108 0.997 0.998 0.999 108 108 LEU M 109 0.996 0.991 0.849 0.884 109 109 VAL M 110 0.994 0.993 0.627 110 110 LYS M 111 0.994 0.991 0.615 0.959 0.702 0.365 111 111 GLU M 112 0.995 0.996 0.991 0.995 0.876 112 112 GLU M 113 0.998 0.984 0.992 0.991 0.350 113 113 VAL M 114 0.992 0.988 0.999 114 114 THR M 115 0.988 0.992 0.666 115 115 PRO M 116 0.996 0.997 0.979 0.954 116 116 ASP M 117 0.998 0.995 0.424 0.722 117 117 LEU M 118 0.999 0.999 0.998 0.999 118 118 ALA M 119 0.999 0.997 119 119 LEU M 120 1.000 0.998 1.000 1.000 120 120 MET M 121 0.999 0.997 0.999 0.999 0.999 121 121 CYS M 122 0.996 0.999 0.928 122 122 LEU M 123 0.999 0.997 1.000 0.999 123 123 GLY M 124 0.999 0.996 124 124 ASN M 125 0.999 0.995 0.787 0.865 125 125 ALA M 126 0.998 0.996 126 126 VAL M 127 0.996 0.998 1.000 127 127 THR M 128 0.997 0.994 0.729 128 128 ASN M 129 0.993 0.990 0.943 0.579 129 129 ILE M 130 0.988 0.992 0.878 0.698 130 130 ILE M 131 0.999 0.998 0.998 1.000 131 131 ALA M 132 0.997 0.995 132 132 GLN M 133 0.996 0.984 0.998 0.999 1.000 133 133 VAL M 134 0.988 0.984 0.682 134 134 PRO M 135 0.991 0.988 0.936 0.881 135 135 GLU M 136 0.995 0.991 0.636 0.773 0.551 136 136 SER M 137 0.994 0.985 0.719 137 137 LYS M 138 0.983 0.984 0.858 0.871 0.529 0.530 138 138 ARG M 139 0.998 0.995 0.737 0.927 0.556 0.853 0.999 139 139 VAL M 140 0.997 0.999 1.000 140 140 ALA M 141 0.998 0.999 141 141 VAL M 142 0.999 0.997 0.780 142 142 VAL M 143 0.998 0.999 0.999 143 143 ASP M 144 0.999 0.999 0.929 0.716 144 144 ASN M 145 0.997 0.997 0.793 0.487 145 145 PHE M 146 0.999 0.999 0.998 0.995 146 146 THR M 147 0.999 0.999 0.998 147 147 LYS M 148 0.998 0.996 0.953 0.724 0.466 0.272 148 148 ALA M 149 0.999 0.997 149 149 LEU M 150 0.996 0.993 0.837 0.992 150 150 LYS M 151 0.997 0.989 0.971 0.983 0.474 0.293 151 151 GLN M 152 0.995 0.987 0.569 0.338 0.328 152 152 SER M 153 0.991 0.993 0.313 153 153 VAL M 154 0.986 0.996 0.999 154 154 LEU M 155 0.995 0.968 0.832 0.872 155 155 GLU M 156 0.961 0.557 0.659 0.211 0.318 HIS M 157 0.400 0.387 0.675 0.433 HIS M 158 0.572 0.549 0.294 0.335 HIS M 159 0.653 0.588 0.314 0.272 HIS M 160 0.336 0.465 0.231 0.397 HIS M 161 0.610 0.496 0.420 0.162 HIS M 162 0.797 0.204 0.191 Ranges: 2 from: M 8 to M 69 from: M 94 to M 155 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..69],M[94..155],for model 1 is: 0.337 (*) > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 2 is: 0.571 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 3 is: 0.622 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 4 is: 0.430 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 5 is: 0.575 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 6 is: 0.534 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 7 is: 0.399 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 8 is: 0.377 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 9 is: 0.547 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 10 is: 0.477 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 11 is: 0.606 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 12 is: 0.530 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 13 is: 0.550 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 14 is: 0.449 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 15 is: 0.402 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 16 is: 0.408 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 17 is: 0.447 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 18 is: 0.486 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 19 is: 0.631 > Kabsch RMSD of backbone atoms in res. M[8..69],M[94..155],for model 20 is: 0.497 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[8..69],[94..155], is: 0.494 > Range of RMSD values to reference struct. is 0.337 to 0.631 > 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..69],M[94..155],for model 1 is: 0.681 (*) > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 2 is: 0.893 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 3 is: 0.919 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 4 is: 0.801 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 5 is: 0.950 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 6 is: 0.907 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 7 is: 0.737 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 8 is: 0.807 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 9 is: 0.851 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 10 is: 0.826 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 11 is: 0.990 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 12 is: 0.917 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 13 is: 0.803 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 14 is: 0.837 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 15 is: 0.777 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 16 is: 0.801 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 17 is: 0.795 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 18 is: 0.830 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 19 is: 0.971 > Kabsch RMSD of heavy atoms in res. M[8..69],M[94..155],for model 20 is: 0.837 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[8..69],[94..155], is: 0.847 > Range of RMSD values to reference struct. is 0.681 to 0.990 PdbStat> PdbStat> *END* of program detected, BYE! ...