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 `DRR147D_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 31-DEC-08 2KCZ > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE C-TERMINAL DOMAIN OF PROTEIN > ReadCoordsPdb(): >> TITLE 2 DR_A0006 FROM DEINOCOCCUS RADIODURANS. NORTHEAST > ReadCoordsPdb(): >> TITLE 3 STRUCTURAL GENOMICS CONSORTIUM TARGET DRR147D > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `DRR147D_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 DRR147D_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 48920 ATOM records read from file > ReadCoordsPdb(): --> 48920 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 A 1 0.307 0.464 0.226 0.564 GLY A 2 0.520 0.437 GLU A 3 0.572 0.771 0.340 0.196 0.300 THR A 4 0.915 0.996 0.996 4 4 VAL A 5 0.976 0.969 0.521 5 5 VAL A 6 0.955 0.980 0.303 6 6 ARG A 7 0.969 0.988 0.400 0.567 0.661 0.752 0.999 7 7 ASP A 8 0.986 0.989 0.951 0.395 8 8 ALA A 9 0.995 0.988 9 9 VAL A 10 0.990 0.995 0.997 10 10 THR A 11 0.987 0.990 0.592 11 11 ILE A 12 0.988 0.996 0.937 0.350 12 12 GLY A 13 0.997 0.973 13 13 LYS A 14 0.954 0.995 0.953 0.593 0.391 0.519 14 14 PRO A 15 0.997 1.000 0.950 0.892 15 15 ALA A 16 0.999 0.993 16 16 GLU A 17 0.996 0.993 0.806 0.706 0.349 17 17 GLN A 18 0.985 0.991 0.765 0.140 0.366 18 18 LEU A 19 0.995 0.982 0.995 0.998 19 19 TYR A 20 0.999 0.997 0.354 0.477 20 20 ALA A 21 0.998 0.996 21 21 VAL A 22 0.997 0.999 0.997 22 22 TRP A 23 0.993 0.985 0.518 0.287 23 23 ARG A 24 0.966 0.207 0.706 0.049 0.402 0.888 0.998 ASP A 25 0.064 0.548 0.976 0.882 LEU A 26 0.416 0.850 0.597 0.582 PRO A 27 0.970 0.417 0.939 0.895 GLY A 28 0.270 0.541 LEU A 29 0.529 0.730 0.553 0.249 PRO A 30 0.988 0.818 0.948 0.903 30 LEU A 31 0.220 0.731 0.788 0.613 LEU A 32 0.329 0.644 0.383 0.175 MET A 33 0.217 0.115 0.238 0.822 0.266 THR A 34 0.546 0.033 0.277 HIS A 35 0.355 0.054 0.681 0.489 LEU A 36 0.523 0.403 0.387 0.574 ARG A 37 0.230 0.234 0.078 0.736 0.150 0.827 0.998 SER A 38 0.325 0.191 0.791 VAL A 39 0.691 0.324 0.298 GLU A 40 0.482 0.443 0.482 0.431 0.340 VAL A 41 0.826 0.780 0.539 LEU A 42 0.750 0.977 0.458 0.189 ASP A 43 0.372 0.269 0.629 0.446 ASP A 44 0.616 0.813 0.547 0.542 LYS A 45 0.916 0.712 0.715 0.349 0.226 0.339 ARG A 46 0.469 0.897 0.336 0.522 0.295 0.663 0.997 SER A 47 0.511 0.366 0.626 ARG A 48 0.300 0.298 0.441 0.521 0.450 0.760 0.998 TRP A 49 0.209 0.135 0.229 0.091 THR A 50 0.309 0.140 0.476 VAL A 51 0.252 0.424 0.180 GLU A 52 0.619 0.536 0.648 0.552 0.307 ALA A 53 0.492 0.846 PRO A 54 0.983 0.841 0.940 0.889 54 ALA A 55 0.241 0.875 PRO A 56 0.991 0.964 0.967 0.903 56 56 LEU A 57 0.947 0.961 0.676 0.231 57 57 GLY A 58 0.099 0.331 ALA A 59 0.368 0.600 VAL A 60 0.673 0.230 0.050 SER A 61 0.367 0.186 0.734 TRP A 62 0.621 0.329 0.603 0.104 GLU A 63 0.899 0.989 0.266 0.055 0.369 63 ALA A 64 0.938 0.963 64 64 GLU A 65 0.976 0.973 0.768 0.589 0.334 65 65 LEU A 66 0.969 0.981 0.657 0.608 66 66 THR A 67 0.973 0.988 0.633 67 67 ALA A 68 0.974 0.994 68 68 ASP A 69 0.990 0.832 0.428 0.304 69 GLU A 70 0.899 0.947 0.995 0.559 0.364 70 PRO A 71 0.991 0.396 0.952 0.897 GLY A 72 0.319 0.961 LYS A 73 0.967 0.985 0.582 0.594 0.455 0.581 73 73 ARG A 74 0.974 0.979 0.736 0.947 0.494 0.679 0.998 74 74 ILE A 75 0.989 0.995 0.941 0.500 75 75 ALA A 76 0.977 0.988 76 76 TRP A 77 0.981 0.980 0.516 0.219 77 77 ARG A 78 0.945 0.965 0.338 0.327 0.245 0.748 0.998 78 78 SER A 79 0.949 0.421 0.680 LEU A 80 0.568 0.995 0.974 0.765 PRO A 81 0.991 0.980 0.938 0.884 81 81 GLY A 82 0.979 0.934 82 82 ALA A 83 0.921 0.538 ARG A 84 0.674 0.323 0.439 0.411 0.457 0.852 0.998 ILE A 85 0.662 0.391 0.125 0.519 GLU A 86 0.397 0.292 0.348 0.496 0.635 ASN A 87 0.855 0.967 0.632 0.595 87 SER A 88 0.928 0.995 0.736 88 88 GLY A 89 0.880 0.780 GLU A 90 0.938 0.980 0.579 0.736 0.314 90 90 VAL A 91 0.982 0.992 0.189 91 91 LEU A 92 0.990 0.987 0.865 0.587 92 92 PHE A 93 0.986 0.988 0.996 0.738 93 93 ARG A 94 0.979 0.999 0.558 0.735 0.063 0.749 0.998 94 94 PRO A 95 0.992 0.988 0.955 0.898 95 95 ALA A 96 0.976 0.998 96 96 PRO A 97 0.982 0.954 0.937 0.881 97 97 GLY A 98 0.903 0.799 ALA A 99 0.508 0.993 ARG A 100 0.983 0.946 0.615 0.286 0.368 0.814 0.999 100 100 GLY A 101 0.910 0.958 101 101 THR A 102 0.980 0.995 0.995 102 102 GLU A 103 0.992 0.985 0.817 0.993 0.263 103 103 VAL A 104 0.995 0.981 0.757 104 104 VAL A 105 0.977 0.998 0.505 105 105 VAL A 106 0.992 0.990 0.346 106 106 ARG A 107 0.980 0.990 0.324 0.633 0.103 0.805 0.999 107 107 LEU A 108 0.969 0.977 0.229 0.342 108 108 THR A 109 0.988 0.984 0.276 109 109 TYR A 110 0.941 0.904 0.160 0.617 110 110 ARG A 111 0.928 0.995 0.610 0.926 0.574 0.838 0.998 111 111 PRO A 112 0.984 0.997 0.929 0.871 112 112 PRO A 113 0.979 0.300 0.932 0.876 GLY A 114 0.378 0.179 GLY A 115 0.447 0.131 SER A 116 0.984 0.980 0.532 116 116 ALA A 117 0.995 0.993 117 117 GLY A 118 0.993 0.993 118 118 ALA A 119 0.989 0.986 119 119 VAL A 120 0.996 0.981 0.169 120 120 ILE A 121 0.996 0.990 0.098 0.429 121 121 ALA A 122 0.994 0.984 122 122 ARG A 123 0.985 0.982 0.555 0.699 0.445 0.762 0.998 123 123 MET A 124 0.994 0.983 0.644 0.667 0.332 124 124 PHE A 125 0.424 0.110 0.567 0.388 ASN A 126 0.380 0.143 0.629 0.376 GLN A 127 0.369 0.154 0.222 0.572 0.375 GLU A 128 0.253 0.870 0.611 0.294 0.213 PRO A 129 0.965 0.392 0.945 0.901 SER A 130 0.392 0.434 0.322 GLN A 131 0.398 0.085 0.505 0.413 0.479 GLN A 132 0.332 0.427 0.266 0.606 0.309 LEU A 133 0.454 0.599 0.476 0.379 ARG A 134 0.514 0.639 0.194 0.681 0.184 0.657 0.997 ASP A 135 0.993 0.989 0.189 0.264 135 135 ASP A 136 0.994 0.992 0.757 0.786 136 136 LEU A 137 0.993 0.988 0.910 0.897 137 137 MET A 138 0.997 0.994 0.536 0.085 0.418 138 138 ARG A 139 0.995 0.990 0.455 0.648 0.305 0.676 0.998 139 139 PHE A 140 0.994 0.991 0.841 0.715 140 140 LYS A 141 0.997 0.995 0.872 0.667 0.430 0.241 141 141 ARG A 142 0.996 0.986 0.567 0.343 0.196 0.902 0.999 142 142 GLU A 143 0.994 0.995 0.763 0.516 0.289 143 143 GLN A 144 0.992 0.992 0.563 0.278 0.368 144 144 GLU A 145 0.977 0.980 0.660 0.928 0.489 145 145 LEU A 146 0.968 0.980 0.867 0.394 146 146 GLY A 147 0.137 0.321 LEU A 148 0.405 0.361 0.624 0.464 GLU A 149 0.400 0.211 0.338 0.543 0.298 HIS A 150 0.409 0.461 0.363 0.610 HIS A 151 0.581 0.570 0.416 0.319 HIS A 152 0.674 0.461 0.237 0.345 HIS A 153 0.334 0.367 0.433 0.208 HIS A 154 0.345 0.116 0.386 0.227 HIS A 155 0.887 0.336 0.275 Ranges: 9 from: A 4 to A 23 from: A 56 to A 57 from: A 64 to A 68 from: A 73 to A 78 from: A 81 to A 82 from: A 90 to A 97 from: A 100 to A 112 from: A 116 to A 124 from: A 135 to A 146 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. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 1 is: 3.984 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 2 is: 2.646 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 3 is: 2.158 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 4 is: 3.330 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 5 is: 4.314 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 6 is: 2.343 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 7 is: 1.819 (*) > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 8 is: 4.503 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 9 is: 2.136 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 10 is: 2.411 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 11 is: 2.179 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 12 is: 4.039 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 13 is: 4.281 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 14 is: 3.603 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 15 is: 3.201 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 16 is: 3.767 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 17 is: 3.750 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 18 is: 3.083 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 19 is: 2.638 > Kabsch RMSD of backbone atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 20 is: 3.331 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..23],[56..57],[64..68],[73..78],[81..82],[90..97],[100..112],[116..124],[135..146], is: 3.176 > Range of RMSD values to reference struct. is 1.819 to 4.503 > 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. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 1 is: 4.161 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 2 is: 3.029 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 3 is: 2.679 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 4 is: 3.699 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 5 is: 4.434 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 6 is: 2.664 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 7 is: 2.161 (*) > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 8 is: 4.535 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 9 is: 2.654 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 10 is: 2.898 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 11 is: 2.483 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 12 is: 4.141 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 13 is: 4.479 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 14 is: 3.779 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 15 is: 3.614 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 16 is: 4.097 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 17 is: 4.064 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 18 is: 3.470 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 19 is: 3.058 > Kabsch RMSD of heavy atoms in res. A[4..23],A[56..57],A[64..68],A[73..78],A[81..82],A[90..97],A[100..112],A[116..124],A[135..146],for model 20 is: 3.611 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..23],[56..57],[64..68],[73..78],[81..82],[90..97],[100..112],[116..124],[135..146], is: 3.485 > Range of RMSD values to reference struct. is 2.161 to 4.535 PdbStat> PdbStat> *END* of program detected, BYE! ...