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 `SPR104_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 10-SEP-10 2L3A > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF HOMODIMER PROTEIN SP_0782 (7-79) FROM > ReadCoordsPdb(): >> TITLE 2 STREPTOCOCCUS PNEUMONIAE NORTHEAST STRUCTURAL GENOMICS CONSORTIUM > ReadCoordsPdb(): >> TITLE 3 TARGET SPR104 . > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `SPR104_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 SPR104_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 52960 ATOM records read from file > ReadCoordsPdb(): --> 52960 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 0.299 0.430 0.208 0.637 LYS M 2 0.597 0.694 0.314 0.861 0.578 0.211 LYS M 3 0.664 0.436 0.156 0.637 0.584 0.053 MET M 4 0.580 0.056 0.527 0.577 0.412 ALA M 5 0.281 0.196 GLU M 6 0.561 0.308 0.529 0.566 0.369 PHE M 7 0.729 0.584 0.713 0.808 THR M 8 0.943 0.964 0.118 8 8 PHE M 9 0.958 0.985 0.932 0.899 9 9 GLU M 10 0.969 0.975 0.359 0.538 0.263 10 10 ILE M 11 0.993 0.983 0.997 0.756 11 11 GLU M 12 0.988 0.972 0.572 0.533 0.371 12 12 GLU M 13 0.977 0.982 0.990 0.466 0.449 13 13 HIS M 14 0.978 0.973 0.222 0.223 14 14 LEU M 15 0.980 0.988 0.998 0.906 15 15 LEU M 16 0.979 0.962 0.381 0.948 16 16 THR M 17 0.987 0.981 0.998 17 17 LEU M 18 0.983 0.990 0.997 0.996 18 18 SER M 19 0.990 0.986 0.310 19 19 GLU M 20 0.970 0.970 0.721 0.770 0.209 20 20 ASN M 21 0.980 0.960 0.538 0.334 21 21 GLU M 22 0.745 0.527 0.580 0.206 0.192 LYS M 23 0.398 0.722 0.461 0.660 0.534 0.039 GLY M 24 0.771 0.818 TRP M 25 0.954 0.971 0.992 0.940 25 25 THR M 26 0.994 1.000 0.753 26 26 LYS M 27 0.992 0.997 0.915 0.872 0.516 0.378 27 27 GLU M 28 0.992 0.984 0.510 0.907 0.386 28 28 ILE M 29 0.990 0.995 0.999 1.000 29 29 ASN M 30 0.987 0.993 0.781 0.226 30 30 ARG M 31 0.984 0.981 0.927 0.976 0.495 0.693 0.998 31 31 VAL M 32 0.984 0.996 0.998 32 32 SER M 33 0.989 0.975 0.165 33 33 PHE M 34 0.977 0.963 0.996 0.800 34 34 ASN M 35 0.911 0.610 0.436 0.194 GLY M 36 0.589 0.153 ALA M 37 0.647 0.196 PRO M 38 0.961 0.706 0.937 0.885 ALA M 39 0.543 0.935 LYS M 40 0.972 0.985 0.591 0.481 0.433 0.500 40 40 PHE M 41 0.988 0.986 0.908 0.795 41 41 ASP M 42 0.985 0.993 0.796 0.262 42 42 ILE M 43 0.993 0.994 0.999 0.925 43 43 ARG M 44 0.983 0.967 0.406 0.840 0.299 0.667 0.998 44 44 ALA M 45 0.984 0.963 45 45 TRP M 46 0.969 0.977 0.552 0.214 46 46 SER M 47 0.875 0.800 0.133 47 PRO M 48 0.988 0.170 0.943 0.884 ASP M 49 0.216 0.176 0.514 0.333 HIS M 50 0.287 0.401 0.271 0.336 THR M 51 0.652 0.390 0.406 LYS M 52 0.775 0.433 0.563 0.931 0.565 0.197 MET M 53 0.726 0.487 0.537 0.382 0.703 GLY M 54 0.458 0.497 LYS M 55 0.592 0.751 0.639 0.571 0.706 0.209 GLY M 56 0.826 0.889 56 ILE M 57 0.976 0.996 0.999 0.872 57 57 THR M 58 0.998 0.993 0.704 58 58 LEU M 59 0.994 0.985 0.994 0.769 59 59 SER M 60 0.982 0.989 0.222 60 60 ASN M 61 0.997 0.993 0.114 0.415 61 61 GLU M 62 0.996 0.996 0.335 0.246 0.389 62 62 GLU M 63 0.999 0.997 0.995 0.793 0.885 63 63 PHE M 64 0.999 0.998 0.981 0.971 64 64 GLN M 65 0.999 0.998 0.821 0.389 0.275 65 65 THR M 66 0.999 0.999 0.999 66 66 MET M 67 0.996 0.995 0.854 0.773 0.842 67 67 VAL M 68 0.999 0.996 0.997 68 68 ASP M 69 0.996 0.995 0.691 0.688 69 69 ALA M 70 0.999 0.995 70 70 PHE M 71 0.995 0.986 0.997 0.980 71 71 LYS M 72 0.990 0.986 0.589 0.799 0.584 0.485 72 72 GLY M 73 0.969 0.846 73 ASN M 74 0.902 0.398 0.590 0.064 LEU M 75 0.195 0.356 0.927 0.985 GLU M 76 0.432 0.327 0.611 0.241 0.298 HIS M 77 0.846 0.512 0.193 0.143 HIS M 78 0.763 0.492 0.376 0.263 HIS M 79 0.582 0.307 0.433 0.334 HIS M 80 0.639 0.351 0.349 0.318 HIS M 81 0.589 0.430 0.307 0.100 HIS M 82 0.886 0.199 0.314 0.144 MET M 93 0.189 0.203 0.252 0.574 0.627 LYS M 94 0.585 0.290 0.593 0.741 0.437 0.141 LYS M 95 0.738 0.132 0.346 0.444 0.709 0.073 MET M 96 0.469 0.365 0.437 0.416 0.645 ALA M 97 0.507 0.444 GLU M 98 0.604 0.244 0.329 0.406 0.333 PHE M 99 0.564 0.503 0.623 0.528 THR M 100 0.942 0.974 0.237 100 100 PHE M 101 0.957 0.985 0.992 0.898 101 101 GLU M 102 0.960 0.972 0.482 0.291 0.225 102 102 ILE M 103 0.994 0.987 0.995 0.537 103 103 GLU M 104 0.988 0.977 0.647 0.612 0.406 104 104 GLU M 105 0.972 0.979 0.845 0.591 0.292 105 105 HIS M 106 0.980 0.972 0.283 0.280 106 106 LEU M 107 0.968 0.991 0.995 0.824 107 107 LEU M 108 0.973 0.963 0.454 0.477 108 108 THR M 109 0.987 0.977 0.998 109 109 LEU M 110 0.991 0.991 0.998 0.999 110 110 SER M 111 0.990 0.986 0.107 111 111 GLU M 112 0.971 0.967 0.549 0.731 0.353 112 112 ASN M 113 0.974 0.960 0.382 0.327 113 113 GLU M 114 0.676 0.421 0.561 0.224 0.512 LYS M 115 0.183 0.775 0.377 0.576 0.650 0.224 GLY M 116 0.790 0.886 TRP M 117 0.981 0.929 0.993 0.931 117 117 THR M 118 0.976 0.991 0.916 118 118 LYS M 119 0.985 0.998 0.953 0.786 0.703 0.380 119 119 GLU M 120 0.987 0.981 0.321 0.876 0.469 120 120 ILE M 121 0.989 0.990 0.997 0.999 121 121 ASN M 122 0.984 0.991 0.927 0.453 122 122 ARG M 123 0.981 0.992 0.827 0.978 0.385 0.720 0.999 123 123 VAL M 124 0.988 0.996 0.997 124 124 SER M 125 0.987 0.970 0.247 125 125 PHE M 126 0.981 0.974 0.998 0.898 126 126 ASN M 127 0.932 0.534 0.214 0.400 GLY M 128 0.539 0.192 ALA M 129 0.400 0.434 PRO M 130 0.973 0.675 0.946 0.897 ALA M 131 0.728 0.962 LYS M 132 0.983 0.990 0.831 0.569 0.800 0.431 132 132 PHE M 133 0.982 0.987 0.809 0.151 133 133 ASP M 134 0.981 0.984 0.572 0.340 134 134 ILE M 135 0.991 0.993 0.998 0.855 135 135 ARG M 136 0.975 0.965 0.283 0.779 0.199 0.734 0.998 136 136 ALA M 137 0.986 0.955 137 137 TRP M 138 0.994 0.975 0.572 0.102 138 138 SER M 139 0.883 0.987 0.391 139 PRO M 140 0.987 0.296 0.942 0.872 ASP M 141 0.506 0.268 0.475 0.263 HIS M 142 0.265 0.415 0.518 0.372 THR M 143 0.232 0.281 0.475 LYS M 144 0.555 0.264 0.842 0.734 0.845 0.083 MET M 145 0.565 0.357 0.482 0.581 0.386 GLY M 146 0.309 0.410 LYS M 147 0.514 0.661 0.702 0.668 0.778 0.355 GLY M 148 0.746 0.879 ILE M 149 0.983 0.997 0.997 0.997 149 149 THR M 150 0.996 0.993 0.761 150 150 LEU M 151 0.984 0.981 0.853 0.685 151 151 SER M 152 0.994 0.994 0.378 152 152 ASN M 153 0.996 0.986 0.112 0.413 153 153 GLU M 154 0.997 0.991 0.436 0.366 0.436 154 154 GLU M 155 0.998 0.994 0.813 0.750 0.560 155 155 PHE M 156 0.998 0.997 0.988 0.965 156 156 GLN M 157 0.998 0.996 0.796 0.399 0.119 157 157 THR M 158 0.999 0.998 0.998 158 158 MET M 159 0.996 0.994 0.831 0.609 0.795 159 159 VAL M 160 0.998 0.993 0.998 160 160 ASP M 161 0.995 0.996 0.771 0.412 161 161 ALA M 162 0.999 0.993 162 162 PHE M 163 0.994 0.982 0.995 0.994 163 163 LYS M 164 0.987 0.991 0.526 0.632 0.220 0.396 164 164 GLY M 165 0.979 0.851 165 ASN M 166 0.808 0.451 0.650 0.114 LEU M 167 0.381 0.175 0.650 0.939 GLU M 168 0.180 0.241 0.705 0.242 0.366 HIS M 169 0.384 0.514 0.285 0.163 HIS M 170 0.502 0.211 0.443 0.238 HIS M 171 0.571 0.396 0.492 0.316 HIS M 172 0.765 0.203 0.235 0.403 HIS M 173 0.452 0.378 0.273 0.365 HIS M 174 0.685 0.133 0.145 Ranges: 8 from: M 8 to M 21 from: M 25 to M 34 from: M 40 to M 46 from: M 57 to M 72 from: M 100 to M 113 from: M 117 to M 126 from: M 132 to M 138 from: M 149 to M 164 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[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 1 is: 0.505 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 2 is: 0.664 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 3 is: 0.605 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 4 is: 0.710 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 5 is: 0.517 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 6 is: 0.649 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 7 is: 0.503 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 8 is: 0.523 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 9 is: 0.581 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 10 is: 0.632 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 11 is: 0.720 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 12 is: 0.494 (*) > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 13 is: 0.553 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 14 is: 0.660 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 15 is: 0.580 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 16 is: 0.658 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 17 is: 0.817 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 18 is: 0.579 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 19 is: 0.612 > Kabsch RMSD of backbone atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 20 is: 0.682 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[8..21],[25..34],[40..46],[57..72],[100..113],[117..126],[132..138],[149..164], is: 0.612 > Range of RMSD values to reference struct. is 0.494 to 0.817 > 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[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 1 is: 1.080 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 2 is: 1.111 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 3 is: 1.140 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 4 is: 1.115 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 5 is: 1.010 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 6 is: 1.167 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 7 is: 0.939 (*) > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 8 is: 0.992 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 9 is: 1.162 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 10 is: 1.119 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 11 is: 1.164 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 12 is: 1.000 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 13 is: 1.099 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 14 is: 1.085 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 15 is: 1.089 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 16 is: 1.258 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 17 is: 1.367 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 18 is: 1.046 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 19 is: 1.223 > Kabsch RMSD of heavy atoms in res. M[8..21],M[25..34],M[40..46],M[57..72],M[100..113],M[117..126],M[132..138],M[149..164],for model 20 is: 1.161 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[8..21],[25..34],[40..46],[57..72],[100..113],[117..126],[132..138],[149..164], is: 1.116 > Range of RMSD values to reference struct. is 0.939 to 1.367 PdbStat> PdbStat> *END* of program detected, BYE! ...