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 `SR478_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 80 MET SER GLU LEU PHE SER VAL PRO TYR PHE ILE GLU ASN > ReadCoordsPdb(): Counting models in file `SR478_R3Cons_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 SR478_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 53200 ATOM records read from file > ReadCoordsPdb(): --> 53200 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 0.310 0.604 0.662 0.209 SER M 2 0.250 0.074 0.023 GLU M 3 0.364 0.732 0.609 0.786 0.928 LEU M 4 0.188 0.398 0.539 0.610 PHE M 5 0.615 0.750 0.463 0.662 SER M 6 0.585 0.873 0.499 VAL M 7 0.997 1.000 1.000 7 7 PRO M 8 0.999 0.995 1.000 1.000 8 8 TYR M 9 0.999 0.999 0.990 0.992 9 9 PHE M 10 0.997 0.999 0.992 0.647 10 10 ILE M 11 0.999 1.000 1.000 1.000 11 11 GLU M 12 1.000 0.999 0.999 0.563 0.933 12 12 ASN M 13 1.000 1.000 0.999 0.982 13 13 LEU M 14 1.000 1.000 0.998 0.999 14 14 LYS M 15 1.000 1.000 0.719 0.999 0.931 0.929 15 15 GLN M 16 1.000 1.000 0.999 0.997 0.879 16 16 HIS M 17 0.999 1.000 0.998 0.565 17 17 ILE M 18 1.000 0.999 1.000 1.000 18 18 GLU M 19 0.999 0.998 0.675 0.921 0.983 19 19 MET M 20 0.982 0.772 0.995 0.939 0.670 ASN M 21 0.670 0.978 0.917 0.761 GLN M 22 0.987 0.800 0.811 0.371 0.836 SER M 23 0.721 0.923 0.483 GLU M 24 0.961 0.972 0.907 0.909 0.871 24 24 ASP M 25 0.969 0.979 0.860 0.692 25 25 LYS M 26 0.989 0.997 0.739 0.995 0.695 0.589 26 26 ILE M 27 0.999 0.997 0.671 0.240 27 27 HIS M 28 0.997 0.993 0.949 0.923 28 28 ALA M 29 1.000 0.999 29 29 MET M 30 1.000 0.999 0.736 0.671 0.808 30 30 ASN M 31 0.999 0.999 0.999 0.995 31 31 SER M 32 0.998 0.999 0.402 32 32 TYR M 33 1.000 0.998 0.999 0.202 33 33 TYR M 34 0.999 0.999 0.944 0.459 34 34 ARG M 35 0.999 0.998 0.538 0.762 0.072 0.497 1.000 35 35 SER M 36 0.999 0.999 0.641 36 36 VAL M 37 1.000 0.997 0.939 37 37 VAL M 38 0.999 0.998 0.999 38 38 SER M 39 0.999 0.998 0.214 39 39 THR M 40 0.999 0.999 1.000 40 40 LEU M 41 0.998 0.999 0.779 0.841 41 41 VAL M 42 0.988 0.931 0.718 42 42 GLN M 43 0.909 0.935 0.811 0.536 0.638 43 43 ASP M 44 0.765 0.171 0.935 0.925 GLN M 45 0.203 0.436 0.617 0.647 0.708 LEU M 46 0.360 0.981 0.751 0.908 THR M 47 0.942 0.984 0.726 47 47 LYS M 48 1.000 0.999 0.998 1.000 1.000 1.000 48 48 ASN M 49 1.000 0.999 0.998 0.999 49 49 ALA M 50 1.000 0.999 50 50 VAL M 51 1.000 1.000 1.000 51 51 VAL M 52 1.000 0.999 0.995 52 52 LEU M 53 1.000 0.997 0.928 0.769 53 53 LYS M 54 0.999 1.000 1.000 1.000 1.000 1.000 54 54 ARG M 55 0.999 1.000 0.999 0.726 0.926 0.782 1.000 55 55 ILE M 56 1.000 1.000 1.000 0.830 56 56 GLN M 57 1.000 0.999 1.000 0.998 0.917 57 57 HIS M 58 1.000 1.000 1.000 0.907 58 58 LEU M 59 0.999 0.999 0.998 0.999 59 59 ASP M 60 1.000 0.998 0.998 0.973 60 60 GLU M 61 0.999 0.999 0.981 0.998 0.859 61 61 ALA M 62 1.000 0.999 62 62 TYR M 63 0.998 0.997 0.959 0.496 63 63 ASN M 64 1.000 1.000 0.944 0.931 64 64 LYS M 65 1.000 0.999 0.780 0.622 0.999 1.000 65 65 VAL M 66 0.999 0.996 1.000 66 66 LYS M 67 1.000 0.999 0.865 0.711 0.766 0.904 67 67 ARG M 68 0.994 0.997 0.891 0.997 0.810 0.995 1.000 68 68 GLY M 69 0.990 0.946 69 69 GLU M 70 0.875 0.472 0.833 0.817 0.830 SER M 71 0.369 0.606 0.386 LYS M 72 0.495 0.422 0.644 0.999 1.000 0.931 LEU M 73 0.370 0.531 0.401 0.569 GLU M 74 0.432 0.517 0.846 0.821 0.997 HIS M 75 0.170 0.437 0.467 0.558 HIS M 76 0.206 0.361 0.457 0.507 HIS M 77 0.797 0.232 0.342 0.251 HIS M 78 0.393 0.375 0.510 0.309 HIS M 79 0.590 0.365 0.546 0.388 HIS M 80 0.554 0.205 0.606 0.394 MET M 91 0.356 0.310 0.604 0.662 0.209 SER M 92 0.250 0.074 0.023 GLU M 93 0.364 0.732 0.608 0.786 0.928 LEU M 94 0.188 0.397 0.539 0.610 PHE M 95 0.615 0.751 0.463 0.662 SER M 96 0.585 0.873 0.499 VAL M 97 0.997 1.000 1.000 97 97 PRO M 98 0.999 0.995 1.000 1.000 98 98 TYR M 99 0.999 0.999 0.990 0.992 99 99 PHE M 100 0.997 0.999 0.992 0.647 100 100 ILE M 101 0.999 1.000 1.000 1.000 101 101 GLU M 102 1.000 0.999 0.999 0.563 0.933 102 102 ASN M 103 1.000 1.000 0.999 0.982 103 103 LEU M 104 1.000 1.000 0.998 0.999 104 104 LYS M 105 1.000 1.000 0.719 0.999 0.931 0.929 105 105 GLN M 106 1.000 1.000 0.999 0.997 0.879 106 106 HIS M 107 0.999 1.000 0.998 0.565 107 107 ILE M 108 1.000 0.999 1.000 1.000 108 108 GLU M 109 0.999 0.998 0.674 0.921 0.983 109 109 MET M 110 0.982 0.772 0.995 0.939 0.670 ASN M 111 0.669 0.978 0.917 0.761 GLN M 112 0.987 0.800 0.811 0.371 0.836 SER M 113 0.721 0.923 0.483 GLU M 114 0.961 0.972 0.907 0.909 0.871 114 114 ASP M 115 0.969 0.979 0.860 0.692 115 115 LYS M 116 0.989 0.997 0.740 0.995 0.695 0.589 116 116 ILE M 117 0.999 0.997 0.671 0.240 117 117 HIS M 118 0.997 0.993 0.949 0.923 118 118 ALA M 119 1.000 0.999 119 119 MET M 120 1.000 0.999 0.736 0.671 0.808 120 120 ASN M 121 0.999 0.999 0.999 0.995 121 121 SER M 122 0.998 0.999 0.402 122 122 TYR M 123 1.000 0.998 0.999 0.202 123 123 TYR M 124 0.999 0.999 0.944 0.459 124 124 ARG M 125 0.999 0.998 0.538 0.762 0.072 0.498 1.000 125 125 SER M 126 0.999 0.999 0.641 126 126 VAL M 127 1.000 0.997 0.939 127 127 VAL M 128 0.999 0.998 0.999 128 128 SER M 129 0.999 0.998 0.214 129 129 THR M 130 0.999 0.999 1.000 130 130 LEU M 131 0.998 0.999 0.779 0.841 131 131 VAL M 132 0.988 0.931 0.718 132 132 GLN M 133 0.908 0.935 0.811 0.536 0.638 133 133 ASP M 134 0.765 0.171 0.935 0.926 GLN M 135 0.203 0.436 0.616 0.647 0.708 LEU M 136 0.360 0.981 0.751 0.908 THR M 137 0.942 0.984 0.726 137 137 LYS M 138 1.000 0.999 0.998 1.000 1.000 1.000 138 138 ASN M 139 1.000 0.999 0.998 0.999 139 139 ALA M 140 1.000 0.999 140 140 VAL M 141 1.000 1.000 1.000 141 141 VAL M 142 1.000 0.999 0.995 142 142 LEU M 143 1.000 0.997 0.928 0.769 143 143 LYS M 144 0.999 1.000 1.000 1.000 1.000 1.000 144 144 ARG M 145 0.999 1.000 0.999 0.726 0.926 0.782 1.000 145 145 ILE M 146 1.000 1.000 1.000 0.830 146 146 GLN M 147 1.000 0.999 1.000 0.998 0.917 147 147 HIS M 148 1.000 1.000 1.000 0.907 148 148 LEU M 149 0.999 0.999 0.998 0.999 149 149 ASP M 150 1.000 0.998 0.998 0.973 150 150 GLU M 151 0.999 0.999 0.981 0.998 0.859 151 151 ALA M 152 1.000 0.999 152 152 TYR M 153 0.998 0.997 0.959 0.496 153 153 ASN M 154 1.000 0.999 0.944 0.931 154 154 LYS M 155 1.000 0.999 0.780 0.622 0.999 1.000 155 155 VAL M 156 0.999 0.996 1.000 156 156 LYS M 157 1.000 0.999 0.865 0.711 0.766 0.904 157 157 ARG M 158 0.994 0.997 0.891 0.997 0.810 0.995 1.000 158 158 GLY M 159 0.990 0.946 159 159 GLU M 160 0.875 0.472 0.833 0.817 0.830 SER M 161 0.369 0.606 0.386 LYS M 162 0.495 0.422 0.644 0.999 1.000 0.931 LEU M 163 0.370 0.531 0.401 0.569 GLU M 164 0.432 0.517 0.846 0.821 0.997 HIS M 165 0.170 0.437 0.467 0.558 HIS M 166 0.206 0.361 0.457 0.507 HIS M 167 0.797 0.233 0.342 0.252 HIS M 168 0.393 0.375 0.510 0.309 HIS M 169 0.590 0.365 0.546 0.389 HIS M 170 0.554 0.606 0.394 Ranges: 6 from: M 7 to M 19 from: M 24 to M 43 from: M 47 to M 69 from: M 97 to M 109 from: M 114 to M 133 from: M 137 to M 159 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 >> optimal_rotate(): DET(U) is less than zero for model 2 >> optimal_rotate(): DET(U) is less than zero for model 3 >> optimal_rotate(): DET(U) is less than zero for model 4 >> optimal_rotate(): DET(U) is less than zero for model 5 >> optimal_rotate(): DET(U) is less than zero for model 6 >> optimal_rotate(): DET(U) is less than zero for model 7 >> optimal_rotate(): DET(U) is less than zero for model 8 >> optimal_rotate(): DET(U) is less than zero for model 9 >> optimal_rotate(): DET(U) is less than zero for model 10 >> optimal_rotate(): DET(U) is less than zero for model 11 >> optimal_rotate(): DET(U) is less than zero for model 12 >> optimal_rotate(): DET(U) is less than zero for model 13 >> optimal_rotate(): DET(U) is less than zero for model 15 >> optimal_rotate(): DET(U) is less than zero for model 16 >> optimal_rotate(): DET(U) is less than zero for model 17 >> optimal_rotate(): DET(U) is less than zero for model 19 >> optimal_rotate(): DET(U) is less than zero for model 20 > do_average_coords(): Calc. average coordinates backbone >> optimal_rotate(): DET(U) is less than zero for model 14 >> optimal_rotate(): DET(U) is less than zero for model 18 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 1 is: 8.342 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 2 is: 2.793 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 3 is: 2.278 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 4 is: 1.925 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 5 is: 1.909 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 6 is: 4.801 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 7 is: 2.775 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 8 is: 2.159 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 9 is: 2.657 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 10 is: 5.478 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 11 is: 1.725 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 12 is: 1.805 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 13 is: 2.504 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 14 is: 2.962 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 15 is: 2.239 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 16 is: 2.562 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 17 is: 1.812 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 18 is: 2.781 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 19 is: 1.653 (*) > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 20 is: 2.461 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[7..19],[24..43],[47..69],[97..109],[114..133],[137..159], is: 2.881 > Range of RMSD values to reference struct. is 1.653 to 8.342 > 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 >> optimal_rotate(): DET(U) is less than zero for model 14 >> optimal_rotate(): DET(U) is less than zero for model 18 > do_average_coords(): Calc. average coordinates heavy >> optimal_rotate(): DET(U) is less than zero for model 14 >> optimal_rotate(): DET(U) is less than zero for model 18 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 1 is: 9.223 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 2 is: 2.990 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 3 is: 2.524 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 4 is: 2.209 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 5 is: 2.093 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 6 is: 5.069 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 7 is: 2.968 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 8 is: 2.376 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 9 is: 2.931 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 10 is: 5.762 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 11 is: 2.146 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 12 is: 2.129 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 13 is: 2.682 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 14 is: 3.166 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 15 is: 2.650 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 16 is: 2.808 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 17 is: 2.135 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 18 is: 3.051 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 19 is: 1.912 (*) > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..43],M[47..69],M[97..109],M[114..133],M[137..159],for model 20 is: 2.660 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[7..19],[24..43],[47..69],[97..109],[114..133],[137..159], is: 3.174 > Range of RMSD values to reference struct. is 1.912 to 9.223 PdbStat> PdbStat> *END* of program detected, BYE! ...