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 `SOR77_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP.PDB, 20 MODEL/S TEMP.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 160 MET ALA ILE GLN SER LYS TYR SER ASN THR GLN VAL GLU 1 > ReadCoordsPdb(): Counting models in file `SOR77_R3_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 SOR77_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 50520 ATOM records read from file > ReadCoordsPdb(): --> 50520 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 0.641 0.743 0.518 0.407 ALA M 2 0.587 0.257 ILE M 3 0.840 0.258 0.645 0.918 GLN M 4 0.571 0.342 0.576 0.318 0.698 SER M 5 0.481 0.358 0.214 LYS M 6 0.497 0.758 0.657 0.998 0.997 0.921 TYR M 7 0.594 0.824 0.573 0.988 SER M 8 0.833 0.938 0.653 8 ASN M 9 0.983 0.980 0.888 0.914 9 9 THR M 10 0.969 0.990 0.707 10 10 GLN M 11 0.992 0.993 0.774 0.557 0.751 11 11 VAL M 12 0.983 0.977 0.714 12 12 GLU M 13 0.997 0.993 0.670 1.000 1.000 13 13 SER M 14 0.996 0.989 0.282 14 14 LEU M 15 0.981 0.995 0.796 0.802 15 15 ILE M 16 0.998 0.998 1.000 0.999 16 16 ALA M 17 0.999 0.997 17 17 GLU M 18 0.993 0.996 0.999 0.558 0.765 18 18 ILE M 19 0.999 0.999 1.000 1.000 19 19 LEU M 20 0.999 0.999 0.994 0.918 20 20 VAL M 21 0.999 0.999 1.000 21 21 VAL M 22 0.997 0.997 0.921 22 22 LEU M 23 0.998 0.996 0.999 0.999 23 23 GLU M 24 0.993 0.994 0.999 0.925 0.983 24 24 LYS M 25 0.997 0.996 0.821 0.929 0.999 0.997 25 25 HIS M 26 0.989 0.978 0.886 0.610 26 26 LYS M 27 0.993 0.943 1.000 1.000 1.000 1.000 27 27 ALA M 28 0.918 0.968 28 28 PRO M 29 0.995 0.986 0.939 0.889 29 29 THR M 30 0.998 0.999 0.999 30 30 ASP M 31 0.998 0.996 1.000 1.000 31 31 LEU M 32 0.994 0.991 0.880 0.911 32 32 SER M 33 0.994 0.995 0.826 33 33 LEU M 34 0.994 0.995 0.628 0.638 34 34 MET M 35 0.997 0.990 0.669 0.454 0.204 35 35 ALA M 36 0.998 0.998 36 36 LEU M 37 0.999 0.998 0.999 0.999 37 37 GLY M 38 0.995 0.995 38 38 ASN M 39 0.993 0.994 0.999 0.946 39 39 CYS M 40 0.997 0.998 0.831 40 40 VAL M 41 0.996 0.998 1.000 41 41 THR M 42 0.993 0.983 0.591 42 42 HIS M 43 0.989 0.984 0.568 0.027 43 43 LEU M 44 0.998 0.994 0.606 0.611 44 44 LEU M 45 0.994 0.991 0.931 0.696 45 45 GLU M 46 0.979 0.950 0.280 0.998 0.955 46 46 ARG M 47 0.988 0.940 0.732 0.736 0.989 0.997 1.000 47 47 LYS M 48 0.979 0.945 0.998 0.930 0.998 0.998 48 48 VAL M 49 0.941 0.999 1.000 49 49 PRO M 50 0.990 0.994 0.903 0.819 50 50 SER M 51 0.993 0.978 1.000 51 51 GLU M 52 0.995 0.995 0.786 0.942 0.999 52 52 SER M 53 0.982 0.992 0.773 53 53 ARG M 54 0.998 0.993 0.720 0.996 0.640 0.988 0.998 54 54 GLN M 55 0.998 0.995 0.871 0.676 0.934 55 55 ALA M 56 0.997 0.998 56 56 VAL M 57 0.999 0.999 1.000 57 57 ALA M 58 0.999 0.998 58 58 GLU M 59 0.983 0.992 0.587 0.995 0.962 59 59 GLN M 60 0.997 0.995 0.823 0.647 0.913 60 60 PHE M 61 0.998 0.995 0.809 0.899 61 61 ALA M 62 0.998 0.998 62 62 LYS M 63 0.996 0.992 0.590 0.999 0.998 0.998 63 63 ALA M 64 0.999 0.999 64 64 LEU M 65 0.999 0.993 0.688 0.567 65 65 ALA M 66 0.991 0.993 66 66 GLN M 67 0.980 0.992 0.622 0.173 0.800 67 67 SER M 68 0.997 0.993 0.152 68 68 VAL M 69 0.991 0.991 0.838 69 69 LYS M 70 0.992 0.988 0.596 0.999 0.999 1.000 70 70 SER M 71 0.988 0.989 0.749 71 71 ASN M 72 0.947 0.902 0.996 0.908 72 72 LEU M 73 0.967 0.926 0.549 0.624 73 73 GLU M 74 0.393 0.274 0.541 0.999 0.937 HIS M 75 0.503 0.406 0.384 0.376 HIS M 76 0.395 0.389 0.485 0.300 HIS M 77 0.437 0.452 0.571 0.476 HIS M 78 0.587 0.044 0.413 0.564 HIS M 79 0.667 0.140 0.547 0.660 HIS M 80 0.865 0.299 0.632 0.469 MET M 91 0.275 0.640 0.743 0.518 0.407 ALA M 92 0.587 0.257 ILE M 93 0.840 0.258 0.645 0.918 GLN M 94 0.571 0.342 0.576 0.318 0.698 SER M 95 0.481 0.358 0.213 LYS M 96 0.497 0.758 0.657 0.998 0.997 0.921 TYR M 97 0.595 0.824 0.573 0.988 SER M 98 0.833 0.938 0.652 98 ASN M 99 0.983 0.980 0.888 0.914 99 99 THR M 100 0.969 0.990 0.707 100 100 GLN M 101 0.992 0.993 0.774 0.556 0.751 101 101 VAL M 102 0.983 0.976 0.714 102 102 GLU M 103 0.997 0.993 0.670 1.000 1.000 103 103 SER M 104 0.996 0.989 0.282 104 104 LEU M 105 0.981 0.995 0.796 0.803 105 105 ILE M 106 0.998 0.998 1.000 0.999 106 106 ALA M 107 0.999 0.997 107 107 GLU M 108 0.993 0.996 0.999 0.558 0.765 108 108 ILE M 109 0.999 0.999 1.000 1.000 109 109 LEU M 110 0.999 0.999 0.994 0.918 110 110 VAL M 111 0.999 0.999 1.000 111 111 VAL M 112 0.997 0.997 0.921 112 112 LEU M 113 0.998 0.996 0.999 0.999 113 113 GLU M 114 0.993 0.994 0.999 0.925 0.983 114 114 LYS M 115 0.997 0.996 0.821 0.929 0.999 0.997 115 115 HIS M 116 0.989 0.978 0.886 0.610 116 116 LYS M 117 0.993 0.943 1.000 1.000 1.000 1.000 117 117 ALA M 118 0.918 0.968 118 118 PRO M 119 0.995 0.986 0.939 0.889 119 119 THR M 120 0.998 0.999 0.999 120 120 ASP M 121 0.998 0.996 1.000 1.000 121 121 LEU M 122 0.994 0.991 0.880 0.911 122 122 SER M 123 0.994 0.995 0.826 123 123 LEU M 124 0.994 0.995 0.628 0.638 124 124 MET M 125 0.997 0.990 0.669 0.454 0.204 125 125 ALA M 126 0.998 0.998 126 126 LEU M 127 0.999 0.998 0.999 0.999 127 127 GLY M 128 0.995 0.995 128 128 ASN M 129 0.993 0.994 0.999 0.946 129 129 CYS M 130 0.997 0.998 0.831 130 130 VAL M 131 0.996 0.998 1.000 131 131 THR M 132 0.993 0.983 0.591 132 132 HIS M 133 0.989 0.984 0.567 0.027 133 133 LEU M 134 0.998 0.994 0.607 0.611 134 134 LEU M 135 0.994 0.991 0.931 0.696 135 135 GLU M 136 0.978 0.950 0.279 0.998 0.955 136 136 ARG M 137 0.988 0.940 0.732 0.736 0.989 0.997 1.000 137 137 LYS M 138 0.979 0.945 0.998 0.930 0.998 0.998 138 138 VAL M 139 0.941 0.999 1.000 139 139 PRO M 140 0.990 0.994 0.903 0.819 140 140 SER M 141 0.993 0.978 1.000 141 141 GLU M 142 0.995 0.995 0.786 0.942 0.999 142 142 SER M 143 0.982 0.992 0.773 143 143 ARG M 144 0.998 0.993 0.720 0.996 0.640 0.988 0.998 144 144 GLN M 145 0.998 0.995 0.871 0.676 0.934 145 145 ALA M 146 0.997 0.998 146 146 VAL M 147 0.999 0.999 1.000 147 147 ALA M 148 0.999 0.998 148 148 GLU M 149 0.983 0.992 0.586 0.995 0.962 149 149 GLN M 150 0.997 0.995 0.823 0.647 0.913 150 150 PHE M 151 0.998 0.995 0.809 0.899 151 151 ALA M 152 0.998 0.998 152 152 LYS M 153 0.997 0.992 0.590 1.000 0.998 0.998 153 153 ALA M 154 0.999 0.999 154 154 LEU M 155 0.999 0.993 0.689 0.568 155 155 ALA M 156 0.991 0.993 156 156 GLN M 157 0.980 0.992 0.622 0.173 0.800 157 157 SER M 158 0.997 0.993 0.151 158 158 VAL M 159 0.991 0.991 0.838 159 159 LYS M 160 0.992 0.988 0.596 0.999 0.999 1.000 160 160 SER M 161 0.988 0.989 0.749 161 161 ASN M 162 0.947 0.903 0.996 0.908 162 162 LEU M 163 0.967 0.926 0.549 0.625 163 163 GLU M 164 0.393 0.274 0.541 0.999 0.937 HIS M 165 0.503 0.406 0.384 0.376 HIS M 166 0.395 0.389 0.485 0.300 HIS M 167 0.437 0.452 0.571 0.476 HIS M 168 0.587 0.044 0.413 0.564 HIS M 169 0.667 0.140 0.547 0.660 HIS M 170 0.865 0.632 0.468 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: 0.752 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 2 is: 1.277 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 3 is: 0.677 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 4 is: 1.036 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 5 is: 0.844 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 6 is: 0.512 (*) > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 7 is: 0.869 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 8 is: 0.959 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 9 is: 0.613 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 10 is: 0.860 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 11 is: 0.746 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 12 is: 1.168 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 13 is: 0.884 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 14 is: 0.639 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 15 is: 0.877 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 16 is: 0.760 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 17 is: 0.878 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 18 is: 0.926 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 19 is: 0.906 > Kabsch RMSD of backbone atoms in res. M[9..73],M[99..163],for model 20 is: 0.814 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..73],[99..163], is: 0.850 > Range of RMSD values to reference struct. is 0.512 to 1.277 > 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: 1.173 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 2 is: 1.575 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 3 is: 1.119 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 4 is: 1.505 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 5 is: 1.043 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 6 is: 0.925 (*) > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 7 is: 1.254 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 8 is: 1.322 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 9 is: 1.195 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 10 is: 1.239 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 11 is: 1.042 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 12 is: 1.522 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 13 is: 1.273 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 14 is: 1.200 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 15 is: 1.234 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 16 is: 1.080 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 17 is: 1.444 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 18 is: 1.323 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 19 is: 1.343 > Kabsch RMSD of heavy atoms in res. M[9..73],M[99..163],for model 20 is: 1.274 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..73],[99..163], is: 1.254 > Range of RMSD values to reference struct. is 0.925 to 1.575 PdbStat> PdbStat> *END* of program detected, BYE! ...