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 `SR478_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 SER GLU LEU PHE SER VAL PRO TYR PHE ILE GLU ASN 1 > ReadCoordsPdb(): Counting models in file `SR478_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 SR478_R3_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 0.118 0.686 0.508 0.340 SER M 2 0.268 0.114 0.324 GLU M 3 0.393 0.803 0.574 0.850 0.904 LEU M 4 0.271 0.438 0.684 0.704 PHE M 5 0.641 0.743 0.469 0.744 SER M 6 0.501 0.770 0.772 VAL M 7 0.993 0.998 1.000 7 7 PRO M 8 0.998 0.993 0.969 0.935 8 8 TYR M 9 0.974 0.971 0.518 0.940 9 9 PHE M 10 0.964 0.993 0.866 0.344 10 10 ILE M 11 0.992 0.992 0.897 0.612 11 11 GLU M 12 0.997 0.993 0.676 0.416 0.901 12 12 ASN M 13 0.998 0.996 1.000 0.997 13 13 LEU M 14 0.985 0.984 0.998 0.998 14 14 LYS M 15 0.999 0.985 0.649 1.000 0.999 0.999 15 15 GLN M 16 0.994 0.983 0.935 0.930 0.982 16 16 HIS M 17 0.932 0.981 0.919 0.329 17 17 ILE M 18 0.960 0.991 0.999 0.999 18 18 GLU M 19 0.991 0.990 0.711 0.644 0.961 19 19 MET M 20 0.969 0.537 0.865 0.526 0.298 ASN M 21 0.632 0.912 0.696 0.683 GLN M 22 0.932 0.757 0.696 0.336 0.725 SER M 23 0.657 0.897 0.365 GLU M 24 0.967 0.839 0.320 0.357 0.839 24 ASP M 25 0.915 0.975 0.944 0.906 25 25 LYS M 26 0.963 0.914 0.709 0.932 0.803 0.867 26 26 ILE M 27 0.957 0.974 0.238 0.339 27 27 HIS M 28 0.960 0.948 0.731 0.671 28 28 ALA M 29 0.996 0.992 29 29 MET M 30 0.993 0.990 0.666 0.494 0.330 30 30 ASN M 31 0.993 0.988 0.999 0.997 31 31 SER M 32 0.966 0.993 0.552 32 32 TYR M 33 0.987 0.988 0.997 0.974 33 33 TYR M 34 1.000 0.997 0.994 0.994 34 34 ARG M 35 0.994 0.991 0.591 0.618 0.286 0.779 1.000 35 35 SER M 36 0.992 0.995 0.507 36 36 VAL M 37 0.992 0.996 1.000 37 37 VAL M 38 0.998 0.996 0.942 38 38 SER M 39 0.986 0.985 0.383 39 39 THR M 40 0.974 0.987 0.924 40 40 LEU M 41 0.998 0.993 0.872 0.867 41 41 VAL M 42 0.969 0.940 0.419 42 42 GLN M 43 0.959 0.882 0.927 0.554 0.776 43 ASP M 44 0.814 0.065 0.778 0.896 GLN M 45 0.164 0.477 0.805 0.394 0.667 LEU M 46 0.367 0.964 0.695 0.743 THR M 47 0.907 0.977 0.514 47 47 LYS M 48 0.972 0.979 0.874 0.998 0.999 0.999 48 48 ASN M 49 0.997 0.997 0.922 0.980 49 49 ALA M 50 0.997 0.998 50 50 VAL M 51 0.999 0.999 1.000 51 51 VAL M 52 0.999 0.998 1.000 52 52 LEU M 53 0.998 0.997 0.635 0.602 53 53 LYS M 54 0.996 0.999 0.664 0.934 0.996 0.625 54 54 ARG M 55 0.998 0.996 0.999 0.923 0.928 0.940 1.000 55 55 ILE M 56 0.999 0.998 1.000 1.000 56 56 GLN M 57 0.998 0.998 0.667 0.689 0.882 57 57 HIS M 58 0.994 0.996 0.999 0.380 58 58 LEU M 59 0.998 0.998 0.606 0.628 59 59 ASP M 60 0.997 0.995 0.844 0.822 60 60 GLU M 61 0.999 0.992 0.933 0.591 0.845 61 61 ALA M 62 0.999 0.997 62 62 TYR M 63 0.999 0.997 0.996 0.964 63 63 ASN M 64 0.999 0.998 1.000 1.000 64 64 LYS M 65 0.996 0.994 0.769 0.735 0.998 0.934 65 65 VAL M 66 0.996 0.999 0.999 66 66 LYS M 67 0.994 0.984 0.758 0.817 0.929 0.933 67 67 ARG M 68 0.982 0.994 0.613 0.999 0.931 0.941 1.000 68 68 GLY M 69 0.972 0.899 69 GLU M 70 0.900 0.403 0.499 0.489 0.774 SER M 71 0.338 0.534 0.379 LYS M 72 0.511 0.300 0.550 0.999 0.999 0.999 LEU M 73 0.337 0.514 0.646 0.802 GLU M 74 0.383 0.462 0.702 0.931 0.975 HIS M 75 0.181 0.400 0.269 0.225 HIS M 76 0.223 0.343 0.691 0.552 HIS M 77 0.791 0.223 0.428 0.616 HIS M 78 0.409 0.361 0.429 0.427 HIS M 79 0.670 0.371 0.302 0.623 HIS M 80 0.533 0.313 0.542 0.131 MET M 91 0.334 0.118 0.686 0.508 0.340 SER M 92 0.268 0.114 0.324 GLU M 93 0.393 0.803 0.574 0.850 0.905 LEU M 94 0.271 0.438 0.684 0.704 PHE M 95 0.641 0.743 0.469 0.744 SER M 96 0.502 0.770 0.772 VAL M 97 0.993 0.998 1.000 97 97 PRO M 98 0.998 0.993 0.969 0.935 98 98 TYR M 99 0.974 0.971 0.518 0.940 99 99 PHE M 100 0.964 0.993 0.866 0.344 100 100 ILE M 101 0.992 0.992 0.897 0.612 101 101 GLU M 102 0.997 0.993 0.675 0.416 0.901 102 102 ASN M 103 0.998 0.996 1.000 0.997 103 103 LEU M 104 0.985 0.984 0.998 0.998 104 104 LYS M 105 0.999 0.985 0.649 1.000 0.999 0.999 105 105 GLN M 106 0.994 0.983 0.935 0.930 0.982 106 106 HIS M 107 0.932 0.981 0.919 0.329 107 107 ILE M 108 0.960 0.991 0.999 0.999 108 108 GLU M 109 0.991 0.990 0.712 0.644 0.961 109 109 MET M 110 0.969 0.537 0.865 0.527 0.299 ASN M 111 0.632 0.912 0.696 0.682 GLN M 112 0.932 0.757 0.696 0.336 0.725 SER M 113 0.657 0.897 0.365 GLU M 114 0.967 0.839 0.319 0.357 0.840 114 ASP M 115 0.915 0.974 0.944 0.906 115 115 LYS M 116 0.963 0.914 0.709 0.932 0.803 0.867 116 116 ILE M 117 0.957 0.974 0.238 0.339 117 117 HIS M 118 0.960 0.948 0.731 0.671 118 118 ALA M 119 0.996 0.992 119 119 MET M 120 0.993 0.990 0.665 0.494 0.330 120 120 ASN M 121 0.993 0.988 0.999 0.997 121 121 SER M 122 0.966 0.992 0.552 122 122 TYR M 123 0.987 0.988 0.997 0.974 123 123 TYR M 124 1.000 0.997 0.994 0.994 124 124 ARG M 125 0.994 0.991 0.591 0.618 0.286 0.780 1.000 125 125 SER M 126 0.992 0.995 0.507 126 126 VAL M 127 0.992 0.996 1.000 127 127 VAL M 128 0.998 0.996 0.942 128 128 SER M 129 0.986 0.985 0.383 129 129 THR M 130 0.974 0.987 0.924 130 130 LEU M 131 0.998 0.993 0.872 0.867 131 131 VAL M 132 0.969 0.940 0.419 132 132 GLN M 133 0.959 0.883 0.927 0.554 0.776 133 ASP M 134 0.814 0.065 0.778 0.896 GLN M 135 0.164 0.477 0.805 0.394 0.667 LEU M 136 0.367 0.964 0.695 0.743 THR M 137 0.907 0.977 0.514 137 137 LYS M 138 0.972 0.979 0.874 0.998 0.999 0.999 138 138 ASN M 139 0.997 0.997 0.922 0.980 139 139 ALA M 140 0.997 0.998 140 140 VAL M 141 0.999 0.999 1.000 141 141 VAL M 142 0.999 0.998 1.000 142 142 LEU M 143 0.998 0.997 0.635 0.602 143 143 LYS M 144 0.996 0.999 0.664 0.934 0.996 0.624 144 144 ARG M 145 0.998 0.996 0.999 0.923 0.928 0.940 1.000 145 145 ILE M 146 0.999 0.998 1.000 1.000 146 146 GLN M 147 0.998 0.998 0.667 0.689 0.882 147 147 HIS M 148 0.994 0.996 0.999 0.380 148 148 LEU M 149 0.998 0.998 0.606 0.628 149 149 ASP M 150 0.997 0.995 0.844 0.822 150 150 GLU M 151 0.999 0.992 0.933 0.591 0.845 151 151 ALA M 152 0.999 0.997 152 152 TYR M 153 0.999 0.997 0.996 0.964 153 153 ASN M 154 0.999 0.998 1.000 1.000 154 154 LYS M 155 0.996 0.994 0.769 0.735 0.998 0.934 155 155 VAL M 156 0.996 0.999 0.999 156 156 LYS M 157 0.994 0.984 0.758 0.817 0.929 0.933 157 157 ARG M 158 0.982 0.994 0.613 0.999 0.931 0.941 1.000 158 158 GLY M 159 0.972 0.899 159 GLU M 160 0.900 0.403 0.498 0.489 0.774 SER M 161 0.338 0.534 0.379 LYS M 162 0.511 0.300 0.550 0.999 0.999 0.999 LEU M 163 0.336 0.514 0.646 0.801 GLU M 164 0.383 0.462 0.702 0.931 0.975 HIS M 165 0.181 0.401 0.268 0.225 HIS M 166 0.223 0.343 0.691 0.553 HIS M 167 0.791 0.224 0.428 0.616 HIS M 168 0.409 0.361 0.429 0.427 HIS M 169 0.670 0.371 0.303 0.623 HIS M 170 0.533 0.542 0.131 Ranges: 6 from: M 7 to M 19 from: M 25 to M 42 from: M 47 to M 68 from: M 97 to M 109 from: M 115 to M 132 from: M 137 to M 158 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[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 1 is: 2.329 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 2 is: 2.217 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 3 is: 8.810 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 4 is: 5.133 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 5 is: 4.555 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 6 is: 7.463 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 7 is: 2.570 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 8 is: 2.355 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 9 is: 2.538 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 10 is: 2.788 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 11 is: 2.162 (*) > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 12 is: 9.904 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 13 is: 2.558 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 14 is: 2.180 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 15 is: 2.310 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 16 is: 2.287 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 17 is: 2.476 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 18 is: 2.618 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 19 is: 5.510 > Kabsch RMSD of backbone atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 20 is: 2.285 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[7..19],[25..42],[47..68],[97..109],[115..132],[137..158], is: 3.752 > Range of RMSD values to reference struct. is 2.162 to 9.904 > 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[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 1 is: 2.502 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 2 is: 2.481 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 3 is: 9.020 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 4 is: 5.667 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 5 is: 5.112 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 6 is: 7.542 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 7 is: 2.697 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 8 is: 2.572 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 9 is: 2.811 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 10 is: 3.239 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 11 is: 2.422 (*) > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 12 is: 10.024 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 13 is: 2.799 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 14 is: 2.458 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 15 is: 2.689 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 16 is: 2.582 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 17 is: 2.603 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 18 is: 2.912 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 19 is: 5.691 > Kabsch RMSD of heavy atoms in res. M[7..19],M[25..42],M[47..68],M[97..109],M[115..132],M[137..158],for model 20 is: 2.558 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[7..19],[25..42],[47..68],[97..109],[115..132],[137..158], is: 4.019 > Range of RMSD values to reference struct. is 2.422 to 10.024 PdbStat> PdbStat> *END* of program detected, BYE! ...