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_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 29-JUN-07 2JS1 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE HOMODIMER PROTEIN YVFG FROM > ReadCoordsPdb(): >> TITLE 2 BACILLUS SUBTILIS, NORTHEAST STRUCTURAL GENOMICS > ReadCoordsPdb(): >> TITLE 3 CONSORTIUM TARGET SR478 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `SR478_NMR_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_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 53520 ATOM records read from file > ReadCoordsPdb(): --> 53520 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 0.245 0.499 0.406 0.604 SER M 2 0.230 0.163 0.061 GLU M 3 0.340 0.737 0.518 0.527 0.886 LEU M 4 0.125 0.475 0.435 0.607 PHE M 5 0.755 0.735 0.519 0.132 SER M 6 0.686 0.857 0.064 VAL M 7 0.988 0.995 0.918 7 7 PRO M 8 0.993 0.998 0.973 0.926 8 8 TYR M 9 0.997 0.997 0.996 0.605 9 9 PHE M 10 0.991 0.997 0.987 0.911 10 10 ILE M 11 0.997 0.998 0.994 0.991 11 11 GLU M 12 1.000 0.997 0.692 0.520 0.913 12 12 ASN M 13 0.996 0.998 0.566 0.843 13 13 LEU M 14 0.998 0.999 0.987 0.794 14 14 LYS M 15 0.999 0.998 0.651 0.739 0.565 0.344 15 15 GLN M 16 0.998 0.998 0.999 0.999 0.851 16 16 HIS M 17 0.995 0.999 0.924 0.054 17 17 ILE M 18 0.996 0.999 0.992 0.998 18 18 GLU M 19 0.997 0.994 0.818 0.286 0.937 19 19 MET M 20 0.986 0.820 0.717 0.888 0.454 20 ASN M 21 0.720 0.990 0.728 0.449 GLN M 22 0.991 0.843 0.934 0.295 0.362 22 SER M 23 0.796 0.978 0.425 GLU M 24 0.989 0.982 0.973 0.997 0.891 24 24 ASP M 25 0.985 0.980 0.997 0.998 25 25 LYS M 26 0.989 0.997 0.937 0.999 0.728 0.194 26 26 ILE M 27 0.999 0.997 0.660 0.507 27 27 HIS M 28 0.992 0.980 0.747 0.293 28 28 ALA M 29 0.985 0.998 29 29 MET M 30 0.999 0.996 0.823 0.472 0.633 30 30 ASN M 31 0.999 0.996 0.639 0.299 31 31 SER M 32 0.992 1.000 0.188 32 32 TYR M 33 0.999 0.984 0.990 0.503 33 33 TYR M 34 0.990 0.995 0.996 0.234 34 34 ARG M 35 0.996 0.996 0.501 0.666 0.334 0.370 1.000 35 35 SER M 36 0.998 0.999 0.326 36 36 VAL M 37 0.999 0.994 0.830 37 37 VAL M 38 0.998 0.998 0.544 38 38 SER M 39 0.997 0.978 0.263 39 39 THR M 40 0.986 0.997 0.997 40 40 LEU M 41 0.996 0.993 0.763 0.547 41 41 VAL M 42 0.984 0.885 0.836 42 GLN M 43 0.814 0.899 0.711 0.823 0.693 43 ASP M 44 0.617 0.211 0.576 0.828 GLN M 45 0.105 0.416 0.550 0.761 0.421 LEU M 46 0.394 0.960 0.814 0.905 THR M 47 0.908 0.994 0.706 47 47 LYS M 48 0.995 0.995 0.992 0.765 0.730 0.524 48 48 ASN M 49 0.997 0.986 0.646 0.144 49 49 ALA M 50 0.996 0.999 50 50 VAL M 51 0.998 0.989 0.752 51 51 VAL M 52 0.981 0.996 0.929 52 52 LEU M 53 0.997 0.991 0.897 0.294 53 53 LYS M 54 0.997 0.998 0.306 0.858 0.100 0.250 54 54 ARG M 55 0.999 0.999 0.672 0.349 0.163 0.580 1.000 55 55 ILE M 56 0.999 0.999 0.994 0.444 56 56 GLN M 57 0.999 0.998 0.997 0.573 0.410 57 57 HIS M 58 0.998 0.995 0.458 0.339 58 58 LEU M 59 0.996 0.996 0.982 0.618 59 59 ASP M 60 0.998 0.992 0.244 0.810 60 60 GLU M 61 0.998 0.996 0.995 0.999 0.585 61 61 ALA M 62 0.999 0.996 62 62 TYR M 63 0.999 0.999 0.979 0.419 63 63 ASN M 64 0.999 0.995 0.800 0.444 64 64 LYS M 65 0.997 0.998 0.798 0.228 0.865 0.224 65 65 VAL M 66 0.998 0.996 0.950 66 66 LYS M 67 0.999 0.999 0.999 0.938 0.847 0.673 67 67 ARG M 68 0.983 0.987 0.763 0.696 0.459 0.568 1.000 68 68 GLY M 69 0.986 0.957 69 69 GLU M 70 0.890 0.569 0.503 0.338 0.838 SER M 71 0.335 0.510 0.247 LYS M 72 0.440 0.294 0.561 0.707 0.572 0.044 LEU M 73 0.326 0.426 0.481 0.577 GLU M 74 0.367 0.492 0.630 0.786 0.872 HIS M 75 0.143 0.501 0.335 0.156 HIS M 76 0.211 0.375 0.392 0.119 HIS M 77 0.756 0.196 0.468 0.573 HIS M 78 0.390 0.492 0.423 0.043 HIS M 79 0.565 0.443 0.400 0.126 HIS M 80 0.559 0.290 0.399 0.204 MET M 91 0.327 0.375 0.852 0.351 0.674 SER M 92 0.484 0.186 0.223 GLU M 93 0.430 0.710 0.317 0.474 0.893 LEU M 94 0.232 0.478 0.585 0.418 PHE M 95 0.754 0.577 0.542 0.417 SER M 96 0.505 0.850 0.216 VAL M 97 0.987 0.995 0.918 97 97 PRO M 98 0.992 0.996 0.955 0.879 98 98 TYR M 99 0.995 0.997 0.997 0.595 99 99 PHE M 100 0.994 0.999 0.970 0.834 100 100 ILE M 101 0.998 0.999 0.993 0.997 101 101 GLU M 102 0.999 0.998 0.635 0.602 0.917 102 102 ASN M 103 0.997 0.998 0.542 0.177 103 103 LEU M 104 0.998 0.999 0.983 0.672 104 104 LYS M 105 0.999 0.996 0.711 0.838 0.477 0.625 105 105 GLN M 106 0.997 0.998 0.955 0.996 0.710 106 106 HIS M 107 0.996 0.999 0.927 0.135 107 107 ILE M 108 0.996 0.998 0.995 0.999 108 108 GLU M 109 0.995 0.991 0.830 0.417 0.888 109 109 MET M 110 0.967 0.748 0.682 0.523 0.397 ASN M 111 0.536 0.990 0.203 0.518 GLN M 112 0.990 0.985 0.604 0.599 0.599 112 112 SER M 113 0.981 0.923 0.274 113 113 GLU M 114 0.904 0.995 0.997 1.000 0.933 114 114 ASP M 115 0.994 0.962 0.997 0.983 115 115 LYS M 116 0.957 0.999 1.000 0.998 0.417 0.277 116 116 ILE M 117 1.000 0.998 0.645 0.495 117 117 HIS M 118 0.996 0.979 0.872 0.190 118 118 ALA M 119 0.978 0.996 119 119 MET M 120 0.998 0.997 0.883 0.491 0.800 120 120 ASN M 121 0.999 0.996 0.557 0.320 121 121 SER M 122 0.995 0.998 0.481 122 122 TYR M 123 0.995 0.982 1.000 0.311 123 123 TYR M 124 0.991 0.997 0.998 0.603 124 124 ARG M 125 0.998 0.995 0.588 0.705 0.271 0.520 1.000 125 125 SER M 126 0.998 0.998 0.302 126 126 VAL M 127 0.999 0.990 0.834 127 127 VAL M 128 0.998 0.998 0.358 128 128 SER M 129 0.997 0.982 0.213 129 129 THR M 130 0.993 0.999 0.996 130 130 LEU M 131 0.996 0.995 0.786 0.425 131 131 VAL M 132 0.985 0.940 0.943 132 132 GLN M 133 0.865 0.813 0.693 0.702 0.812 133 ASP M 134 0.723 0.413 0.549 0.837 GLN M 135 0.186 0.145 0.406 0.803 0.415 LEU M 136 0.178 0.963 0.735 0.869 THR M 137 0.923 0.992 0.915 137 137 LYS M 138 0.989 0.992 0.993 0.753 0.944 0.598 138 138 ASN M 139 0.996 0.986 0.591 0.231 139 139 ALA M 140 0.992 0.996 140 140 VAL M 141 0.997 0.990 0.750 141 141 VAL M 142 0.988 0.997 0.813 142 142 LEU M 143 0.998 0.986 0.895 0.427 143 143 LYS M 144 0.998 0.998 0.336 0.825 0.272 0.251 144 144 ARG M 145 0.999 0.998 0.836 0.258 0.471 0.605 1.000 145 145 ILE M 146 0.999 0.999 0.992 0.506 146 146 GLN M 147 0.998 0.995 0.997 0.661 0.585 147 147 HIS M 148 0.998 0.994 0.806 0.199 148 148 LEU M 149 0.991 0.995 0.891 0.354 149 149 ASP M 150 0.998 0.991 0.500 0.682 150 150 GLU M 151 0.998 0.998 0.992 0.998 0.540 151 151 ALA M 152 0.999 0.997 152 152 TYR M 153 0.999 0.999 0.994 0.526 153 153 ASN M 154 0.999 0.999 0.824 0.403 154 154 LYS M 155 0.999 0.999 0.759 0.254 0.999 0.236 155 155 VAL M 156 0.999 0.995 0.999 156 156 LYS M 157 0.998 0.993 0.996 0.915 0.991 0.599 157 157 ARG M 158 0.974 0.982 0.689 0.487 0.249 0.523 1.000 158 158 GLY M 159 0.814 0.877 159 GLU M 160 0.928 0.437 0.410 0.239 0.774 SER M 161 0.146 0.270 0.330 LYS M 162 0.151 0.462 0.862 0.807 0.526 0.230 LEU M 163 0.528 0.137 0.336 0.442 GLU M 164 0.295 0.344 0.822 0.642 0.927 HIS M 165 0.248 0.308 0.619 0.341 HIS M 166 0.507 0.359 0.551 0.257 HIS M 167 0.317 0.293 0.403 0.167 HIS M 168 0.390 0.608 0.562 0.565 HIS M 169 0.505 0.024 0.569 0.280 HIS M 170 0.525 0.405 0.361 Ranges: 6 from: M 7 to M 19 from: M 24 to M 41 from: M 47 to M 69 from: M 97 to M 109 from: M 112 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[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 1 is: 0.813 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 2 is: 0.761 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 3 is: 0.825 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 4 is: 0.723 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 5 is: 0.710 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 6 is: 0.352 (*) > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 7 is: 0.442 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 8 is: 0.747 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 9 is: 0.620 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 10 is: 0.531 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 11 is: 0.893 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 12 is: 1.129 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 13 is: 0.987 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 14 is: 0.662 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 15 is: 0.873 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 16 is: 0.892 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 17 is: 0.885 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 18 is: 0.784 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 19 is: 0.577 > Kabsch RMSD of backbone atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 20 is: 0.626 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[7..19],[24..41],[47..69],[97..109],[112..132],[137..158], is: 0.742 > Range of RMSD values to reference struct. is 0.352 to 1.129 > 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[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 1 is: 1.155 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 2 is: 1.276 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 3 is: 1.191 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 4 is: 1.115 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 5 is: 1.141 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 6 is: 0.982 (*) > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 7 is: 1.072 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 8 is: 1.124 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 9 is: 1.035 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 10 is: 1.043 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 11 is: 1.232 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 12 is: 1.402 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 13 is: 1.448 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 14 is: 1.163 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 15 is: 1.305 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 16 is: 1.269 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 17 is: 1.329 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 18 is: 1.170 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 19 is: 1.020 > Kabsch RMSD of heavy atoms in res. M[7..19],M[24..41],M[47..69],M[97..109],M[112..132],M[137..158],for model 20 is: 1.111 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[7..19],[24..41],[47..69],[97..109],[112..132],[137..158], is: 1.179 > Range of RMSD values to reference struct. is 0.982 to 1.448 PdbStat> PdbStat> *END* of program detected, BYE! ...