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 `CSR4_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR 2JR2_R3EM.PDB, 20 MODEL/S 2JR2_R3EM.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 76 MET PRO ILE VAL SER LYS TYR SER ASN GLU ARG VAL GLU > ReadCoordsPdb(): Counting models in file `CSR4_R3_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 CSR4_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 48960 ATOM records read from file > ReadCoordsPdb(): --> 48960 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 0.692 0.674 0.520 0.481 PRO M 2 0.990 0.700 0.921 0.869 ILE M 3 0.738 0.688 0.641 0.918 VAL M 4 0.733 0.340 0.394 SER M 5 0.377 0.232 0.128 LYS M 6 0.348 0.747 0.594 0.997 0.999 0.998 TYR M 7 0.111 0.823 0.915 0.825 SER M 8 0.834 0.941 0.651 8 ASN M 9 0.997 0.996 0.938 0.954 9 9 GLU M 10 0.995 0.996 0.571 0.999 1.000 10 10 ARG M 11 0.997 0.995 0.644 0.934 0.731 0.782 1.000 11 11 VAL M 12 0.996 0.998 1.000 12 12 GLU M 13 0.997 0.997 0.598 0.999 1.000 13 13 LYS M 14 0.997 0.995 0.641 0.999 0.996 0.686 14 14 ILE M 15 0.994 0.999 1.000 0.913 15 15 ILE M 16 0.998 0.995 0.918 0.999 16 16 GLN M 17 0.999 0.999 0.938 0.934 0.977 17 17 ASP M 18 1.000 1.000 1.000 1.000 18 18 LEU M 19 0.999 0.999 1.000 1.000 19 19 LEU M 20 0.998 0.997 0.999 1.000 20 20 ASP M 21 0.998 0.994 1.000 1.000 21 21 VAL M 22 0.992 0.999 1.000 22 22 LEU M 23 0.990 0.996 1.000 1.000 23 23 VAL M 24 0.995 0.998 1.000 24 24 LYS M 25 0.997 0.997 0.813 1.000 1.000 1.000 25 25 GLU M 26 0.996 0.983 0.999 0.997 0.997 26 26 GLU M 27 0.997 0.995 1.000 1.000 0.999 27 27 VAL M 28 0.979 0.967 0.539 28 28 THR M 29 0.986 0.989 0.920 29 29 PRO M 30 0.998 0.994 0.982 0.968 30 30 ASP M 31 0.986 0.995 0.998 0.929 31 31 LEU M 32 0.999 0.999 0.999 0.999 32 32 ALA M 33 0.998 0.997 33 33 LEU M 34 0.991 0.995 0.940 0.929 34 34 MET M 35 0.991 0.990 0.818 0.695 0.591 35 35 CYS M 36 0.985 0.994 0.998 36 36 LEU M 37 0.995 0.990 0.999 0.999 37 37 GLY M 38 0.995 0.981 38 38 ASN M 39 0.952 0.999 0.996 0.906 39 39 ALA M 40 0.999 0.997 40 40 VAL M 41 0.998 0.999 1.000 41 41 THR M 42 0.992 0.987 0.779 42 42 ASN M 43 0.994 0.990 0.999 0.961 43 43 ILE M 44 0.981 0.980 0.695 0.537 44 44 ILE M 45 0.992 0.994 0.733 0.945 45 45 ALA M 46 0.994 0.989 46 46 GLN M 47 0.984 0.977 0.929 0.622 0.813 47 47 VAL M 48 0.964 0.982 0.714 48 48 PRO M 49 0.996 0.996 0.954 0.913 49 49 GLU M 50 0.995 0.989 0.537 0.943 0.973 50 50 SER M 51 0.994 0.989 0.835 51 51 LYS M 52 0.971 0.988 0.928 0.857 0.999 1.000 52 52 ARG M 53 0.996 0.986 0.835 0.981 0.464 0.734 1.000 53 53 VAL M 54 0.983 0.975 0.575 54 54 ALA M 55 0.990 0.998 55 55 VAL M 56 0.990 0.987 0.495 56 56 VAL M 57 0.997 0.993 0.721 57 57 ASP M 58 0.997 0.997 0.711 0.839 58 58 ASN M 59 0.999 0.997 1.000 1.000 59 59 PHE M 60 0.999 0.998 0.996 0.989 60 60 THR M 61 0.997 0.996 0.925 61 61 LYS M 62 0.998 0.991 0.817 1.000 0.999 0.999 62 62 ALA M 63 0.999 0.999 63 63 LEU M 64 0.998 0.983 0.558 0.575 64 64 LYS M 65 0.992 0.983 0.713 0.995 0.935 0.993 65 65 GLN M 66 0.967 0.993 0.575 0.429 0.823 66 66 SER M 67 0.989 0.984 0.679 67 67 VAL M 68 0.947 0.982 0.891 68 68 LEU M 69 0.969 0.978 0.751 0.798 69 69 GLU M 70 0.950 0.591 0.749 0.841 0.912 HIS M 71 0.638 0.343 0.441 0.379 HIS M 72 0.519 0.150 0.342 0.202 HIS M 73 0.573 0.378 0.440 0.626 HIS M 74 0.701 0.502 0.395 0.466 HIS M 75 0.674 0.386 0.451 0.579 HIS M 76 0.815 0.425 0.597 0.273 MET M 87 0.333 0.692 0.674 0.520 0.481 PRO M 88 0.990 0.700 0.921 0.869 ILE M 89 0.738 0.688 0.641 0.918 VAL M 90 0.733 0.340 0.394 SER M 91 0.377 0.232 0.128 LYS M 92 0.348 0.747 0.595 0.997 0.999 0.997 TYR M 93 0.111 0.823 0.915 0.825 SER M 94 0.834 0.941 0.651 94 ASN M 95 0.997 0.996 0.938 0.954 95 95 GLU M 96 0.995 0.996 0.570 0.999 1.000 96 96 ARG M 97 0.997 0.995 0.644 0.934 0.731 0.782 1.000 97 97 VAL M 98 0.996 0.998 1.000 98 98 GLU M 99 0.997 0.997 0.598 0.999 1.000 99 99 LYS M 100 0.997 0.995 0.641 0.999 0.996 0.686 100 100 ILE M 101 0.994 0.999 1.000 0.913 101 101 ILE M 102 0.998 0.995 0.918 0.999 102 102 GLN M 103 0.999 0.999 0.938 0.934 0.977 103 103 ASP M 104 1.000 1.000 1.000 1.000 104 104 LEU M 105 0.999 0.999 1.000 1.000 105 105 LEU M 106 0.998 0.997 0.999 1.000 106 106 ASP M 107 0.998 0.994 1.000 1.000 107 107 VAL M 108 0.992 0.999 1.000 108 108 LEU M 109 0.990 0.996 1.000 1.000 109 109 VAL M 110 0.995 0.998 1.000 110 110 LYS M 111 0.997 0.997 0.813 1.000 1.000 1.000 111 111 GLU M 112 0.996 0.983 0.999 0.997 0.997 112 112 GLU M 113 0.997 0.995 1.000 1.000 0.999 113 113 VAL M 114 0.979 0.967 0.539 114 114 THR M 115 0.986 0.989 0.920 115 115 PRO M 116 0.998 0.994 0.982 0.968 116 116 ASP M 117 0.986 0.995 0.998 0.929 117 117 LEU M 118 0.999 0.999 0.999 0.999 118 118 ALA M 119 0.998 0.997 119 119 LEU M 120 0.991 0.995 0.940 0.929 120 120 MET M 121 0.991 0.990 0.818 0.695 0.591 121 121 CYS M 122 0.985 0.994 0.998 122 122 LEU M 123 0.995 0.990 0.999 0.999 123 123 GLY M 124 0.995 0.981 124 124 ASN M 125 0.952 0.999 0.996 0.906 125 125 ALA M 126 0.999 0.997 126 126 VAL M 127 0.998 0.999 1.000 127 127 THR M 128 0.992 0.987 0.779 128 128 ASN M 129 0.994 0.990 0.999 0.961 129 129 ILE M 130 0.981 0.980 0.695 0.537 130 130 ILE M 131 0.992 0.994 0.733 0.945 131 131 ALA M 132 0.994 0.989 132 132 GLN M 133 0.984 0.977 0.929 0.622 0.813 133 133 VAL M 134 0.964 0.982 0.714 134 134 PRO M 135 0.996 0.996 0.954 0.913 135 135 GLU M 136 0.995 0.989 0.537 0.943 0.973 136 136 SER M 137 0.994 0.989 0.836 137 137 LYS M 138 0.971 0.988 0.928 0.857 0.999 1.000 138 138 ARG M 139 0.996 0.986 0.835 0.981 0.464 0.734 1.000 139 139 VAL M 140 0.983 0.975 0.575 140 140 ALA M 141 0.990 0.998 141 141 VAL M 142 0.990 0.987 0.495 142 142 VAL M 143 0.997 0.993 0.721 143 143 ASP M 144 0.997 0.997 0.711 0.839 144 144 ASN M 145 0.999 0.997 1.000 1.000 145 145 PHE M 146 0.999 0.998 0.996 0.989 146 146 THR M 147 0.997 0.996 0.925 147 147 LYS M 148 0.998 0.991 0.817 1.000 0.999 0.999 148 148 ALA M 149 0.999 0.999 149 149 LEU M 150 0.998 0.983 0.558 0.575 150 150 LYS M 151 0.992 0.984 0.713 0.995 0.935 0.993 151 151 GLN M 152 0.967 0.993 0.575 0.429 0.823 152 152 SER M 153 0.989 0.984 0.679 153 153 VAL M 154 0.947 0.982 0.891 154 154 LEU M 155 0.969 0.978 0.751 0.798 155 155 GLU M 156 0.950 0.591 0.749 0.841 0.912 HIS M 157 0.638 0.343 0.441 0.379 HIS M 158 0.519 0.150 0.342 0.202 HIS M 159 0.573 0.378 0.440 0.626 HIS M 160 0.701 0.502 0.395 0.466 HIS M 161 0.674 0.386 0.451 0.579 HIS M 162 0.815 0.597 0.273 Ranges: 2 from: M 9 to M 69 from: M 95 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[9..69],M[95..155],for model 1 is: 0.929 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 2 is: 1.027 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 3 is: 0.407 (*) > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 4 is: 1.488 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 5 is: 0.699 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 6 is: 0.567 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 7 is: 0.889 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 8 is: 0.822 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 9 is: 0.949 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 10 is: 0.711 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 11 is: 1.391 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 12 is: 0.869 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 13 is: 0.517 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 14 is: 0.671 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 15 is: 0.764 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 16 is: 1.394 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 17 is: 0.956 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 18 is: 0.745 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 19 is: 1.375 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 20 is: 0.867 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..69],[95..155], is: 0.902 > Range of RMSD values to reference struct. is 0.407 to 1.488 > 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..69],M[95..155],for model 1 is: 1.285 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 2 is: 1.282 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 3 is: 0.696 (*) > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 4 is: 1.721 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 5 is: 0.947 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 6 is: 0.877 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 7 is: 1.265 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 8 is: 1.122 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 9 is: 1.286 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 10 is: 0.951 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 11 is: 1.697 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 12 is: 1.108 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 13 is: 0.946 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 14 is: 0.992 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 15 is: 1.104 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 16 is: 1.678 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 17 is: 1.219 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 18 is: 1.000 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 19 is: 1.684 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 20 is: 1.346 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..69],[95..155], is: 1.210 > Range of RMSD values to reference struct. is 0.696 to 1.721 PdbStat> PdbStat> *END* of program detected, BYE! ...