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 `HR41_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 25-JAN-08 2K07 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF HUMAN E2-LIKE UBIQUITIN-FOLD > ReadCoordsPdb(): >> TITLE 2 MODIFIER CONJUGATING ENZYME 1 (UFC1). NORTHEAST STRUCTURAL > ReadCoordsPdb(): >> TITLE 3 GENOMICS CONSORTIUM TARGET HR41 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `HR41_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 HR41_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 57760 ATOM records read from file > ReadCoordsPdb(): --> 57760 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 0.100 0.129 0.240 0.485 ALA A 2 0.869 0.382 ASP A 3 0.380 0.517 0.332 0.323 GLU A 4 0.995 0.989 0.100 0.452 0.491 4 4 ALA A 5 0.997 0.998 5 5 THR A 6 0.998 0.996 0.959 6 6 ARG A 7 0.998 0.991 0.548 0.436 0.236 0.878 0.998 7 7 ARG A 8 0.998 0.995 0.512 0.810 0.226 0.842 0.998 8 8 VAL A 9 0.994 0.998 0.998 9 9 VAL A 10 0.998 0.992 0.999 10 10 SER A 11 0.994 0.983 0.471 11 11 GLU A 12 0.989 0.978 0.996 0.880 0.418 12 12 ILE A 13 0.995 1.000 0.999 0.999 13 13 PRO A 14 0.989 0.979 0.931 0.860 14 14 VAL A 15 0.992 0.986 1.000 15 15 LEU A 16 0.988 0.971 0.998 0.997 16 16 LYS A 17 0.950 0.964 0.291 0.388 0.518 0.152 17 17 THR A 18 0.917 0.760 0.857 ASN A 19 0.757 0.894 0.432 0.294 ALA A 20 0.911 0.600 GLY A 21 0.654 0.987 PRO A 22 0.997 0.992 0.954 0.897 22 22 ARG A 23 0.987 0.970 0.986 0.554 0.572 0.663 0.999 23 23 ASP A 24 0.971 0.977 0.647 0.799 24 24 ARG A 25 0.997 0.988 0.994 0.921 0.043 0.720 0.998 25 25 GLU A 26 0.997 0.991 0.421 0.672 0.252 26 26 LEU A 27 0.996 0.998 0.993 0.937 27 27 TRP A 28 0.998 0.996 0.995 0.996 28 28 VAL A 29 0.999 0.996 0.998 29 29 GLN A 30 0.998 0.994 0.627 0.810 0.662 30 30 ARG A 31 0.998 0.996 0.683 0.669 0.361 0.243 0.996 31 31 LEU A 32 0.998 0.997 0.846 0.537 32 32 LYS A 33 0.997 0.992 0.591 0.992 0.386 0.424 33 33 GLU A 34 0.997 0.993 0.992 0.795 0.479 34 34 GLU A 35 0.995 0.993 0.289 0.251 0.668 35 35 TYR A 36 0.998 0.995 0.950 0.655 36 36 GLN A 37 0.999 0.998 0.987 0.706 0.806 37 37 SER A 38 0.998 0.998 0.475 38 38 LEU A 39 0.999 0.998 0.998 0.998 39 39 ILE A 40 0.999 0.998 0.999 1.000 40 40 ARG A 41 0.998 0.997 0.836 0.516 0.390 0.780 0.998 41 41 TYR A 42 0.998 0.997 0.993 0.986 42 42 VAL A 43 0.999 0.998 1.000 43 43 GLU A 44 0.996 0.989 0.744 0.267 0.258 44 44 ASN A 45 0.998 0.997 0.923 0.889 45 45 ASN A 46 0.995 0.991 0.817 0.663 46 46 LYS A 47 0.998 0.992 0.746 0.727 0.444 0.294 47 47 ASN A 48 0.996 0.986 0.798 0.603 48 48 ALA A 49 0.990 0.996 49 49 ASP A 50 0.997 0.982 0.998 0.983 50 50 ASN A 51 0.973 0.849 0.920 0.627 51 ASP A 52 0.933 0.943 0.692 0.546 52 52 TRP A 53 0.934 0.866 0.420 0.401 53 PHE A 54 0.969 0.973 0.796 0.619 54 54 ARG A 55 0.970 0.999 0.089 0.273 0.171 0.670 0.999 55 55 LEU A 56 0.968 0.996 0.747 0.266 56 56 GLU A 57 0.981 0.991 0.993 0.515 0.424 57 57 SER A 58 0.967 0.987 0.424 58 58 ASN A 59 0.991 0.995 0.599 0.699 59 59 LYS A 60 0.996 0.982 0.476 0.228 0.329 0.441 60 60 GLU A 61 0.991 0.994 0.993 0.407 0.510 61 61 GLY A 62 0.997 0.992 62 62 THR A 63 0.996 0.976 0.998 63 63 ARG A 64 0.964 0.992 0.692 0.885 0.271 0.789 0.998 64 64 TRP A 65 0.994 0.988 0.999 0.994 65 65 PHE A 66 0.989 0.959 0.996 0.700 66 66 GLY A 67 0.914 0.936 67 67 LYS A 68 0.960 0.991 0.224 0.915 0.262 0.099 68 68 CYS A 69 0.989 0.987 0.281 69 69 TRP A 70 0.958 0.979 0.507 0.121 70 70 TYR A 71 0.983 0.987 0.830 0.798 71 71 ILE A 72 0.993 0.997 0.995 0.581 72 72 HIS A 73 0.985 0.989 0.990 0.789 73 73 ASP A 74 0.996 0.653 0.680 0.605 LEU A 75 0.625 0.968 0.943 0.566 LEU A 76 0.958 0.969 0.995 0.943 76 76 LYS A 77 0.981 0.982 0.995 0.926 0.227 0.482 77 77 TYR A 78 0.959 0.969 0.601 0.184 78 78 GLU A 79 0.981 0.996 0.607 0.398 0.310 79 79 PHE A 80 0.995 0.983 0.997 0.897 80 80 ASP A 81 0.984 0.991 0.285 0.284 81 81 ILE A 82 0.992 0.990 0.998 0.999 82 82 GLU A 83 0.977 0.994 0.780 0.857 0.379 83 83 PHE A 84 0.991 0.991 0.841 0.601 84 84 ASP A 85 0.984 0.987 0.794 0.657 85 85 ILE A 86 0.998 1.000 0.999 1.000 86 86 PRO A 87 0.993 0.992 0.956 0.896 87 87 ILE A 88 0.995 0.987 0.989 0.344 88 88 THR A 89 0.993 0.967 0.856 89 89 TYR A 90 0.995 0.999 0.996 0.994 90 90 PRO A 91 1.000 0.997 0.992 0.980 91 91 THR A 92 0.998 0.997 0.997 92 92 THR A 93 0.988 0.988 0.999 93 93 ALA A 94 0.996 1.000 94 94 PRO A 95 0.985 0.939 0.936 0.889 95 95 GLU A 96 0.968 0.895 0.993 0.836 0.606 96 ILE A 97 0.899 0.991 0.999 0.769 97 ALA A 98 0.987 0.605 VAL A 99 0.599 0.998 0.832 PRO A 100 0.996 0.987 0.938 0.851 100 100 GLU A 101 0.985 0.967 0.876 0.793 0.366 101 101 LEU A 102 0.977 0.939 0.999 0.999 102 102 ASP A 103 0.924 0.565 0.853 0.346 GLY A 104 0.552 0.937 LYS A 105 0.960 0.914 0.548 0.399 0.466 0.271 105 105 THR A 106 0.905 0.572 0.771 ALA A 107 0.662 0.145 LYS A 108 0.634 0.536 0.426 0.455 0.241 0.423 MET A 109 0.721 0.764 0.566 0.193 0.714 TYR A 110 0.780 0.327 0.253 0.443 ARG A 111 0.539 0.550 0.466 0.470 0.130 0.741 0.999 GLY A 112 0.548 0.407 GLY A 113 0.255 0.755 LYS A 114 0.815 0.895 0.783 0.564 0.693 0.289 114 ILE A 115 0.970 0.982 0.998 0.955 115 115 CYS A 116 0.977 0.956 0.277 116 116 LEU A 117 0.973 0.853 0.998 0.999 117 THR A 118 0.905 0.990 0.570 118 118 ASP A 119 0.994 0.983 0.159 0.411 119 119 HIS A 120 0.988 0.987 0.611 0.443 120 120 PHE A 121 1.000 0.998 0.964 0.898 121 121 LYS A 122 0.999 0.999 0.667 0.544 0.321 0.367 122 122 PRO A 123 0.997 0.998 0.947 0.882 123 123 LEU A 124 0.998 0.998 0.999 1.000 124 124 TRP A 125 0.999 0.999 0.998 0.996 125 125 ALA A 126 0.998 0.991 126 126 ARG A 127 0.989 0.993 0.784 0.865 0.200 0.930 0.999 127 127 ASN A 128 0.979 0.830 0.994 0.740 128 VAL A 129 0.889 0.997 0.999 129 PRO A 130 0.995 0.982 0.977 0.949 130 130 LYS A 131 0.999 0.949 0.906 0.870 0.453 0.161 131 131 PHE A 132 0.967 0.976 0.906 0.619 132 132 GLY A 133 0.962 0.981 133 133 LEU A 134 0.996 0.998 0.999 0.999 134 134 ALA A 135 0.999 0.996 135 135 HIS A 136 1.000 0.998 0.997 0.977 136 136 LEU A 137 0.999 0.995 0.999 0.999 137 137 MET A 138 0.998 0.994 0.383 0.082 0.401 138 138 ALA A 139 0.999 0.996 139 139 LEU A 140 0.996 0.982 0.999 1.000 140 140 GLY A 141 0.987 0.995 141 141 LEU A 142 0.998 0.996 0.934 0.757 142 142 GLY A 143 1.000 1.000 143 143 PRO A 144 0.997 0.998 0.951 0.890 144 144 TRP A 145 0.999 0.996 0.996 0.990 145 145 LEU A 146 0.999 0.999 0.999 0.999 146 146 ALA A 147 0.998 0.993 147 147 VAL A 148 0.979 0.994 0.999 148 148 GLU A 149 0.933 0.957 0.366 0.154 0.321 149 149 ILE A 150 0.997 0.998 0.986 0.795 150 150 PRO A 151 0.998 0.998 0.946 0.857 151 151 ASP A 152 0.989 0.994 0.877 0.703 152 152 LEU A 153 0.996 0.997 0.765 0.487 153 153 ILE A 154 0.999 0.997 0.999 1.000 154 154 GLN A 155 0.999 0.990 0.387 0.614 0.400 155 155 LYS A 156 0.993 0.991 0.654 0.838 0.203 0.090 156 156 GLY A 157 0.993 0.977 157 157 VAL A 158 0.988 0.967 0.399 158 158 ILE A 159 0.968 0.953 0.936 0.718 159 159 GLN A 160 0.813 0.839 0.521 0.357 0.488 160 HIS A 161 0.847 0.556 0.080 0.110 LYS A 162 0.738 0.391 0.435 0.319 0.523 0.124 GLU A 163 0.280 0.502 0.460 0.220 0.243 LYS A 164 0.933 0.943 0.598 0.536 0.223 0.219 164 164 CYS A 165 0.369 0.471 0.352 ASN A 166 0.837 0.252 0.150 0.483 GLN A 167 0.665 0.661 0.476 0.290 0.367 LEU A 168 0.925 0.649 0.453 0.454 GLU A 169 0.941 0.703 0.107 0.336 0.223 HIS A 170 0.866 0.703 0.179 0.437 HIS A 171 0.839 0.594 0.540 0.414 HIS A 172 0.861 0.448 0.269 0.527 HIS A 173 0.845 0.736 0.413 0.340 HIS A 174 0.846 0.267 0.258 0.180 HIS A 175 0.916 0.161 0.221 Ranges: 8 from: A 4 to A 17 from: A 22 to A 50 from: A 54 to A 73 from: A 76 to A 95 from: A 100 to A 102 from: A 115 to A 116 from: A 118 to A 127 from: A 130 to A 159 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..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 1 is: 0.968 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 2 is: 1.076 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 3 is: 1.070 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 4 is: 0.658 (*) > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 5 is: 0.691 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 6 is: 0.921 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 7 is: 0.786 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 8 is: 0.835 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 9 is: 0.777 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 10 is: 0.802 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 11 is: 0.810 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 12 is: 0.807 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 13 is: 0.846 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 14 is: 0.803 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 15 is: 0.665 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 16 is: 0.697 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 17 is: 0.882 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 18 is: 0.819 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 19 is: 0.797 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 20 is: 0.950 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..17],[22..50],[54..73],[76..95],[100..102],[115..116],[118..127],[130..159], is: 0.833 > Range of RMSD values to reference struct. is 0.658 to 1.076 > 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..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 1 is: 1.393 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 2 is: 1.392 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 3 is: 1.522 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 4 is: 1.236 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 5 is: 1.164 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 6 is: 1.363 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 7 is: 1.314 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 8 is: 1.349 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 9 is: 1.177 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 10 is: 1.227 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 11 is: 1.183 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 12 is: 1.306 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 13 is: 1.273 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 14 is: 1.251 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 15 is: 1.160 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 16 is: 1.132 (*) > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 17 is: 1.339 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 18 is: 1.246 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 19 is: 1.191 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[54..73],A[76..95],A[100..102],A[115..116],A[118..127],A[130..159],for model 20 is: 1.359 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..17],[22..50],[54..73],[76..95],[100..102],[115..116],[118..127],[130..159], is: 1.279 > Range of RMSD values to reference struct. is 1.132 to 1.522 PdbStat> PdbStat> *END* of program detected, BYE! ...