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_R3Cons_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 152 MET PRO ILE VAL SER LYS TYR SER ASN GLU ARG VAL GLU 1 > ReadCoordsPdb(): Counting models in file `CSR4_R3Cons_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_R3Cons_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 0.699 0.668 0.550 0.503 PRO M 2 0.990 0.685 0.920 0.868 ILE M 3 0.735 0.713 0.575 0.920 VAL M 4 0.744 0.360 0.435 SER M 5 0.376 0.221 0.139 LYS M 6 0.327 0.806 0.742 0.932 0.870 0.938 TYR M 7 0.073 0.853 0.674 0.494 SER M 8 0.873 0.959 0.653 8 ASN M 9 1.000 0.999 0.943 0.957 9 9 GLU M 10 0.999 0.997 0.759 1.000 1.000 10 10 ARG M 11 0.995 0.995 0.998 0.998 0.929 0.702 1.000 11 11 VAL M 12 0.999 0.999 1.000 12 12 GLU M 13 0.999 0.997 0.674 0.999 1.000 13 13 LYS M 14 1.000 0.999 1.000 0.997 0.997 0.600 14 14 ILE M 15 0.999 0.996 0.926 0.913 15 15 ILE M 16 0.999 1.000 1.000 1.000 16 16 GLN M 17 1.000 1.000 1.000 1.000 1.000 17 17 ASP M 18 1.000 1.000 1.000 1.000 18 18 LEU 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 ASP M 21 1.000 1.000 1.000 1.000 21 21 VAL M 22 1.000 1.000 1.000 22 22 LEU M 23 1.000 0.999 1.000 1.000 23 23 VAL M 24 1.000 0.999 1.000 24 24 LYS M 25 0.998 0.997 0.629 1.000 1.000 1.000 25 25 GLU M 26 0.999 0.999 0.999 0.998 0.990 26 26 GLU M 27 1.000 1.000 1.000 1.000 0.978 27 27 VAL M 28 0.997 0.998 0.999 28 28 THR M 29 0.999 0.999 0.999 29 29 PRO M 30 1.000 0.999 1.000 1.000 30 30 ASP M 31 1.000 0.999 0.870 0.933 31 31 LEU M 32 1.000 0.999 0.999 1.000 32 32 ALA M 33 1.000 1.000 33 33 LEU M 34 0.999 0.998 1.000 1.000 34 34 MET M 35 0.999 0.998 0.999 0.997 0.768 35 35 CYS M 36 0.998 0.997 1.000 36 36 LEU M 37 0.999 0.999 0.999 1.000 37 37 GLY M 38 0.999 1.000 38 38 ASN M 39 0.999 1.000 1.000 0.986 39 39 ALA M 40 1.000 1.000 40 40 VAL M 41 1.000 0.999 1.000 41 41 THR M 42 1.000 0.998 1.000 42 42 ASN M 43 1.000 0.997 1.000 0.989 43 43 ILE M 44 0.997 0.999 0.999 0.393 44 44 ILE M 45 1.000 1.000 1.000 1.000 45 45 ALA M 46 0.999 0.998 46 46 GLN M 47 0.995 0.988 0.999 0.925 0.914 47 47 VAL M 48 0.983 0.988 0.719 48 48 PRO M 49 0.997 0.995 0.983 0.967 49 49 GLU M 50 0.999 0.998 0.883 0.948 0.999 50 50 SER M 51 0.999 0.997 1.000 51 51 LYS M 52 0.972 0.978 0.523 0.996 0.750 0.999 52 52 ARG M 53 0.998 0.993 0.847 0.991 0.771 0.993 1.000 53 53 VAL M 54 0.999 0.999 1.000 54 54 ALA M 55 1.000 0.999 55 55 VAL M 56 0.998 0.994 0.625 56 56 VAL M 57 0.998 1.000 0.999 57 57 ASP M 58 1.000 0.999 0.838 0.911 58 58 ASN M 59 1.000 0.999 1.000 1.000 59 59 PHE M 60 1.000 0.999 0.998 0.991 60 60 THR M 61 1.000 1.000 1.000 61 61 LYS M 62 0.999 0.996 0.937 1.000 1.000 1.000 62 62 ALA M 63 1.000 0.999 63 63 LEU M 64 1.000 0.999 0.826 0.994 64 64 LYS M 65 0.999 0.998 0.686 0.996 0.995 0.997 65 65 GLN M 66 0.998 0.998 0.598 0.174 0.832 66 66 SER M 67 0.998 0.998 0.918 67 67 VAL M 68 0.997 0.998 0.999 68 68 LEU M 69 0.997 0.992 0.815 0.732 69 69 GLU M 70 0.956 0.601 0.937 0.917 0.971 HIS M 71 0.645 0.362 0.576 0.240 HIS M 72 0.541 0.165 0.406 0.155 HIS M 73 0.567 0.388 0.394 0.291 HIS M 74 0.729 0.520 0.448 0.205 HIS M 75 0.682 0.315 0.544 0.713 HIS M 76 0.840 0.646 0.730 0.438 MET M 87 0.136 0.699 0.669 0.550 0.503 PRO M 88 0.990 0.685 0.920 0.868 ILE M 89 0.734 0.713 0.575 0.920 VAL M 90 0.744 0.360 0.435 SER M 91 0.376 0.221 0.139 LYS M 92 0.327 0.806 0.742 0.932 0.870 0.938 TYR M 93 0.073 0.853 0.674 0.494 SER M 94 0.874 0.959 0.653 94 ASN M 95 0.999 0.999 0.943 0.957 95 95 GLU M 96 0.999 0.997 0.759 1.000 1.000 96 96 ARG M 97 0.995 0.995 0.998 0.998 0.929 0.702 1.000 97 97 VAL M 98 0.999 0.999 1.000 98 98 GLU M 99 0.999 0.997 0.673 0.999 1.000 99 99 LYS M 100 1.000 0.999 1.000 0.997 0.997 0.600 100 100 ILE M 101 0.999 0.996 0.926 0.913 101 101 ILE M 102 0.999 1.000 1.000 1.000 102 102 GLN M 103 1.000 1.000 1.000 1.000 1.000 103 103 ASP M 104 1.000 1.000 1.000 1.000 104 104 LEU M 105 1.000 1.000 1.000 1.000 105 105 LEU M 106 1.000 1.000 1.000 1.000 106 106 ASP M 107 1.000 1.000 1.000 1.000 107 107 VAL M 108 1.000 1.000 1.000 108 108 LEU M 109 1.000 0.999 1.000 1.000 109 109 VAL M 110 1.000 0.999 1.000 110 110 LYS M 111 0.998 0.997 0.629 1.000 1.000 1.000 111 111 GLU M 112 0.999 0.999 0.999 0.998 0.990 112 112 GLU M 113 1.000 1.000 1.000 1.000 0.978 113 113 VAL M 114 0.997 0.998 0.999 114 114 THR M 115 0.999 1.000 0.999 115 115 PRO M 116 1.000 0.999 1.000 1.000 116 116 ASP M 117 1.000 0.999 0.870 0.933 117 117 LEU M 118 1.000 0.999 0.999 1.000 118 118 ALA M 119 1.000 1.000 119 119 LEU M 120 0.999 0.998 1.000 1.000 120 120 MET M 121 0.999 0.998 0.999 0.997 0.768 121 121 CYS M 122 0.998 0.997 1.000 122 122 LEU M 123 0.999 0.999 0.999 1.000 123 123 GLY M 124 0.999 1.000 124 124 ASN M 125 0.999 1.000 1.000 0.986 125 125 ALA M 126 1.000 1.000 126 126 VAL M 127 1.000 0.999 1.000 127 127 THR M 128 1.000 0.998 1.000 128 128 ASN M 129 1.000 0.997 1.000 0.989 129 129 ILE M 130 0.997 0.999 0.999 0.393 130 130 ILE M 131 1.000 1.000 1.000 1.000 131 131 ALA M 132 0.999 0.998 132 132 GLN M 133 0.995 0.988 0.999 0.925 0.914 133 133 VAL M 134 0.983 0.988 0.719 134 134 PRO M 135 0.997 0.995 0.983 0.967 135 135 GLU M 136 0.999 0.998 0.883 0.948 0.999 136 136 SER M 137 0.999 0.997 1.000 137 137 LYS M 138 0.972 0.978 0.523 0.996 0.750 0.999 138 138 ARG M 139 0.998 0.993 0.847 0.991 0.771 0.993 1.000 139 139 VAL M 140 0.999 0.999 1.000 140 140 ALA M 141 1.000 0.999 141 141 VAL M 142 0.999 0.994 0.625 142 142 VAL M 143 0.998 1.000 0.999 143 143 ASP M 144 0.999 0.999 0.838 0.911 144 144 ASN M 145 1.000 0.999 1.000 1.000 145 145 PHE M 146 1.000 0.999 0.998 0.991 146 146 THR M 147 1.000 1.000 1.000 147 147 LYS M 148 0.999 0.996 0.937 1.000 1.000 1.000 148 148 ALA M 149 1.000 0.999 149 149 LEU M 150 1.000 0.999 0.826 0.994 150 150 LYS M 151 0.999 0.998 0.686 0.996 0.995 0.997 151 151 GLN M 152 0.998 0.998 0.598 0.174 0.832 152 152 SER M 153 0.998 0.998 0.918 153 153 VAL M 154 0.997 0.998 0.999 154 154 LEU M 155 0.997 0.992 0.815 0.732 155 155 GLU M 156 0.956 0.601 0.937 0.918 0.971 HIS M 157 0.645 0.362 0.576 0.240 HIS M 158 0.541 0.165 0.407 0.155 HIS M 159 0.567 0.388 0.394 0.291 HIS M 160 0.729 0.520 0.448 0.205 HIS M 161 0.682 0.315 0.544 0.713 HIS M 162 0.841 0.730 0.439 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: 0.390 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 2 is: 0.355 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 3 is: 0.372 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 4 is: 0.355 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 5 is: 0.794 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 6 is: 0.478 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 7 is: 0.444 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 8 is: 0.680 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 9 is: 0.725 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 10 is: 0.364 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 11 is: 0.563 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 12 is: 0.296 (*) > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 13 is: 0.442 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 14 is: 0.534 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 15 is: 0.577 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 16 is: 0.427 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 17 is: 0.593 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 18 is: 0.502 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 19 is: 0.560 > Kabsch RMSD of backbone atoms in res. M[9..69],M[95..155],for model 20 is: 0.390 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..69],[95..155], is: 0.492 > Range of RMSD values to reference struct. is 0.296 to 0.794 > 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: 0.628 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 2 is: 0.616 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 3 is: 0.607 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 4 is: 0.578 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 5 is: 0.946 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 6 is: 0.639 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 7 is: 0.633 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 8 is: 0.875 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 9 is: 0.898 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 10 is: 0.554 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 11 is: 0.792 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 12 is: 0.459 (*) > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 13 is: 0.656 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 14 is: 0.771 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 15 is: 0.871 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 16 is: 0.597 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 17 is: 0.761 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 18 is: 0.684 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 19 is: 0.794 > Kabsch RMSD of heavy atoms in res. M[9..69],M[95..155],for model 20 is: 0.650 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..69],[95..155], is: 0.701 > Range of RMSD values to reference struct. is 0.459 to 0.946 PdbStat> PdbStat> *END* of program detected, BYE! ...