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_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 03-SEP-07 2JUW > ReadCoordsPdb(): >> TITLE NMR SOLUTION STRUCTURE OF HOMODIMER PROTEIN SO_2176 FROM SHEWANELLA > ReadCoordsPdb(): >> TITLE 2 ONEIDENSIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SOR77 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): >> COMPND 2 MOLECULE: UPF0352 PROTEIN SO_2176; 1 > ReadCoordsPdb(): Counting models in file `SOR77_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 SOR77_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 50840 ATOM records read from file > ReadCoordsPdb(): --> 50840 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 0.668 0.167 0.603 0.636 ALA M 2 0.618 0.297 ILE M 3 0.845 0.273 0.430 0.603 GLN M 4 0.491 0.443 0.121 0.495 0.130 SER M 5 0.511 0.338 0.663 LYS M 6 0.438 0.680 0.087 0.789 0.139 0.391 TYR M 7 0.501 0.765 0.657 0.537 SER M 8 0.835 0.955 0.161 8 ASN M 9 0.997 0.989 0.202 0.229 9 9 THR M 10 0.993 0.992 0.667 10 10 GLN M 11 0.997 0.993 0.995 0.479 0.482 11 11 VAL M 12 0.997 0.998 0.999 12 12 GLU M 13 0.997 0.993 0.867 0.741 0.260 13 13 SER M 14 0.997 0.997 0.086 14 14 LEU M 15 0.998 0.997 0.771 0.934 15 15 ILE M 16 0.999 0.999 0.998 0.915 16 16 ALA M 17 0.999 0.996 17 17 GLU M 18 0.995 0.995 0.618 0.587 0.332 18 18 ILE M 19 0.998 0.995 0.786 0.690 19 19 LEU M 20 0.999 0.998 0.937 0.937 20 20 VAL M 21 0.999 0.997 0.999 21 21 VAL M 22 0.999 0.996 0.997 22 22 LEU M 23 0.998 0.995 0.998 0.999 23 23 GLU M 24 0.996 0.992 0.623 0.091 0.224 24 24 LYS M 25 0.995 0.994 0.668 0.852 0.200 0.359 25 25 HIS M 26 0.982 0.980 0.842 0.662 26 26 LYS M 27 0.988 0.903 0.443 0.570 0.507 0.247 27 27 ALA M 28 0.894 0.981 28 PRO M 29 0.998 0.995 0.939 0.860 29 29 THR M 30 0.998 0.997 0.978 30 30 ASP M 31 0.996 0.993 0.337 0.433 31 31 LEU M 32 0.997 0.997 0.998 1.000 32 32 SER M 33 0.999 0.998 0.320 33 33 LEU M 34 0.999 0.999 0.999 0.999 34 34 MET M 35 0.999 0.996 0.651 0.653 0.548 35 35 ALA M 36 0.999 0.997 36 36 LEU M 37 0.997 0.996 0.856 0.782 37 37 GLY M 38 0.999 0.992 38 38 ASN M 39 0.991 0.992 0.953 0.660 39 39 CYS M 40 0.998 0.990 0.371 40 40 VAL M 41 0.997 0.998 0.999 41 41 THR M 42 0.996 0.995 0.884 42 42 HIS M 43 0.992 0.991 0.842 0.393 43 43 LEU M 44 0.992 0.990 0.925 0.937 44 44 LEU M 45 0.996 0.979 0.762 0.914 45 45 GLU M 46 0.990 0.948 0.469 0.376 0.655 46 46 ARG M 47 0.989 0.927 0.461 0.115 0.340 0.678 0.999 47 47 LYS M 48 0.972 0.953 0.781 0.352 0.643 0.404 48 48 VAL M 49 0.982 0.997 0.999 49 49 PRO M 50 0.998 0.998 0.944 0.863 50 50 SER M 51 0.999 0.990 0.770 51 51 GLU M 52 0.994 0.981 0.350 0.160 0.293 52 52 SER M 53 0.986 0.993 0.680 53 53 ARG M 54 0.999 0.997 0.626 0.998 0.564 0.990 0.998 54 54 GLN M 55 0.996 0.994 0.661 0.688 0.213 55 55 ALA M 56 0.995 0.997 56 56 VAL M 57 0.999 0.996 0.921 57 57 ALA M 58 0.999 0.997 58 58 GLU M 59 0.997 0.998 0.604 0.336 0.583 59 59 GLN M 60 0.995 0.994 0.773 0.759 0.225 60 60 PHE M 61 0.999 0.998 0.998 0.702 61 61 ALA M 62 0.998 0.998 62 62 LYS M 63 0.995 0.992 0.670 0.762 0.417 0.375 63 63 ALA M 64 0.998 0.997 64 64 LEU M 65 0.999 0.998 0.815 0.853 65 65 ALA M 66 0.999 0.997 66 66 GLN M 67 0.996 0.993 0.681 0.277 0.093 67 67 SER M 68 0.998 0.992 0.535 68 68 VAL M 69 0.993 0.995 0.998 69 69 LYS M 70 0.987 0.974 0.540 0.880 0.527 0.166 70 70 SER M 71 0.980 0.973 0.183 71 71 ASN M 72 0.991 0.983 0.522 0.333 72 72 LEU M 73 0.979 0.931 0.808 0.313 73 73 GLU M 74 0.363 0.247 0.457 0.161 0.346 HIS M 75 0.526 0.359 0.251 0.325 HIS M 76 0.390 0.380 0.329 0.473 HIS M 77 0.464 0.338 0.551 0.347 HIS M 78 0.558 0.089 0.543 0.311 HIS M 79 0.619 0.131 0.509 0.189 HIS M 80 0.849 0.499 0.659 0.305 MET M 91 0.549 0.218 0.256 0.524 0.410 ALA M 92 0.506 0.334 ILE M 93 0.705 0.726 0.209 0.443 GLN M 94 0.521 0.254 0.339 0.708 0.181 SER M 95 0.384 0.765 0.584 LYS M 96 0.928 0.614 0.447 0.605 0.543 0.471 TYR M 97 0.412 0.759 0.873 0.607 SER M 98 0.803 0.974 0.595 98 ASN M 99 0.999 0.991 0.164 0.285 99 99 THR M 100 0.996 0.994 0.752 100 100 GLN M 101 0.995 0.997 0.996 0.553 0.085 101 101 VAL M 102 0.997 0.998 0.999 102 102 GLU M 103 0.996 0.986 0.808 0.484 0.294 103 103 SER M 104 0.996 0.993 0.448 104 104 LEU M 105 0.997 0.995 0.748 0.878 105 105 ILE M 106 0.998 0.999 0.998 0.916 106 106 ALA M 107 0.999 0.995 107 107 GLU M 108 0.994 0.993 0.592 0.528 0.289 108 108 ILE M 109 0.998 0.998 0.936 0.861 109 109 LEU M 110 0.998 0.998 0.959 0.701 110 110 VAL M 111 0.999 0.998 0.999 111 111 VAL M 112 0.998 0.996 0.997 112 112 LEU M 113 0.993 0.992 0.999 0.998 113 113 GLU M 114 0.992 0.974 0.674 0.359 0.272 114 114 LYS M 115 0.995 0.983 0.508 0.923 0.314 0.368 115 115 HIS M 116 0.983 0.982 0.782 0.445 116 116 LYS M 117 0.996 0.973 0.732 0.782 0.345 0.186 117 117 ALA M 118 0.967 0.991 118 118 PRO M 119 0.997 0.995 0.936 0.855 119 119 THR M 120 0.998 0.996 0.994 120 120 ASP M 121 0.996 0.991 0.378 0.268 121 121 LEU M 122 0.994 0.997 0.985 0.928 122 122 SER M 123 0.999 0.997 0.454 123 123 LEU M 124 0.999 0.999 0.999 1.000 124 124 MET M 125 0.999 0.997 0.748 0.745 0.503 125 125 ALA M 126 0.998 0.997 126 126 LEU M 127 0.998 0.997 0.969 0.754 127 127 GLY M 128 1.000 0.998 128 128 ASN M 129 0.996 0.997 0.901 0.562 129 129 CYS M 130 0.998 0.995 0.564 130 130 VAL M 131 0.998 0.999 0.999 131 131 THR M 132 0.998 0.995 0.842 132 132 HIS M 133 0.996 0.996 0.931 0.781 133 133 LEU M 134 0.991 0.994 0.996 0.998 134 134 LEU M 135 0.999 0.992 0.878 0.993 135 135 GLU M 136 0.993 0.951 0.669 0.661 0.399 136 136 ARG M 137 0.994 0.952 0.532 0.344 0.232 0.728 0.998 137 137 LYS M 138 0.973 0.948 0.721 0.136 0.628 0.189 138 138 VAL M 139 0.967 0.993 0.999 139 139 PRO M 140 0.997 0.997 0.951 0.880 140 140 SER M 141 0.998 0.993 0.771 141 141 GLU M 142 0.993 0.984 0.165 0.336 0.394 142 142 SER M 143 0.979 0.990 0.719 143 143 ARG M 144 0.997 0.993 0.606 0.942 0.458 0.939 0.998 144 144 GLN M 145 0.995 0.993 0.681 0.587 0.085 145 145 ALA M 146 0.996 0.995 146 146 VAL M 147 0.999 0.996 0.850 147 147 ALA M 148 0.999 0.998 148 148 GLU M 149 0.997 0.994 0.609 0.438 0.638 149 149 GLN M 150 0.997 0.997 0.570 0.672 0.258 150 150 PHE M 151 1.000 0.999 0.997 0.800 151 151 ALA M 152 0.999 0.999 152 152 LYS M 153 0.996 0.992 0.634 0.567 0.310 0.184 153 153 ALA M 154 0.998 0.997 154 154 LEU M 155 0.999 0.996 0.709 0.784 155 155 ALA M 156 0.999 0.996 156 156 GLN M 157 0.996 0.994 0.557 0.437 0.260 157 157 SER M 158 0.998 0.993 0.351 158 158 VAL M 159 0.986 0.997 0.999 159 159 LYS M 160 0.996 0.977 0.546 0.874 0.614 0.066 160 160 SER M 161 0.993 0.990 0.272 161 161 ASN M 162 0.990 0.987 0.623 0.438 162 162 LEU M 163 0.984 0.909 0.875 0.569 163 163 GLU M 164 0.735 0.712 0.587 0.491 0.314 HIS M 165 0.682 0.286 0.339 0.310 HIS M 166 0.393 0.424 0.480 0.189 HIS M 167 0.672 0.392 0.523 0.225 HIS M 168 0.661 0.426 0.098 0.328 HIS M 169 0.539 0.373 0.452 0.194 HIS M 170 0.667 0.486 0.373 Ranges: 3 from: M 9 to M 27 from: M 29 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..27],M[29..73],M[99..163],for model 1 is: 0.506 (*) > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 2 is: 0.659 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 3 is: 0.688 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 4 is: 0.594 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 5 is: 0.677 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 6 is: 0.581 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 7 is: 0.833 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 8 is: 0.532 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 9 is: 0.821 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 10 is: 0.709 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 11 is: 0.752 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 12 is: 0.767 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 13 is: 0.847 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 14 is: 0.665 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 15 is: 0.557 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 16 is: 0.955 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 17 is: 0.607 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 18 is: 0.666 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 19 is: 0.626 > Kabsch RMSD of backbone atoms in res. M[9..27],M[29..73],M[99..163],for model 20 is: 0.728 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..27],[29..73],[99..163], is: 0.688 > Range of RMSD values to reference struct. is 0.506 to 0.955 > 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..27],M[29..73],M[99..163],for model 1 is: 0.983 (*) > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 2 is: 1.134 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 3 is: 1.132 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 4 is: 1.145 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 5 is: 1.129 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 6 is: 1.095 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 7 is: 1.277 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 8 is: 1.030 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 9 is: 1.174 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 10 is: 1.129 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 11 is: 1.158 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 12 is: 1.185 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 13 is: 1.248 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 14 is: 1.125 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 15 is: 1.079 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 16 is: 1.410 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 17 is: 1.129 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 18 is: 1.107 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 19 is: 1.167 > Kabsch RMSD of heavy atoms in res. M[9..27],M[29..73],M[99..163],for model 20 is: 1.220 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..27],[29..73],[99..163], is: 1.153 > Range of RMSD values to reference struct. is 0.983 to 1.410 PdbStat> PdbStat> *END* of program detected, BYE! ...