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 `CTR148A_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER TRANSFERASE 08-SEP-09 2KO1 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE ACT DOMAIN FROM GTP > ReadCoordsPdb(): >> TITLE 2 PYROPHOSPHOKINASE OF CHLOROBIUM TEPIDUM. NORTHEAST > ReadCoordsPdb(): >> TITLE 3 STRUCTURAL GENOMICS CONSORTIUM TARGET CTR148A > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `CTR148A_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 CTR148A_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 57160 ATOM records read from file > ReadCoordsPdb(): --> 57160 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 0.518 0.592 0.403 0.194 THR M 2 0.766 0.447 0.329 ASP M 3 0.777 0.960 0.416 0.261 PHE M 4 0.978 0.998 0.999 0.600 4 4 LEU M 5 0.999 1.000 0.999 1.000 5 5 ALA M 6 0.999 0.984 6 6 GLY M 7 0.985 0.998 7 7 ILE M 8 0.999 0.994 0.999 1.000 8 8 ARG M 9 0.991 0.996 0.991 0.917 0.672 0.838 0.998 9 9 ILE M 10 0.995 0.998 0.999 0.999 10 10 VAL M 11 0.998 0.998 0.999 11 11 GLY M 12 0.997 0.997 12 12 GLU M 13 0.998 0.996 0.998 0.995 0.609 13 13 ASP M 14 0.997 0.962 0.904 0.752 14 14 LYS M 15 0.880 0.952 0.517 0.685 0.256 0.257 15 ASN M 16 0.620 0.769 0.528 0.133 GLY M 17 0.504 0.917 MET M 18 0.992 0.995 0.997 0.734 0.708 18 18 THR M 19 0.998 0.998 0.999 19 19 ASN M 20 0.999 0.999 0.763 0.675 20 20 GLN M 21 0.999 0.999 0.999 0.999 0.961 21 21 ILE M 22 0.999 1.000 1.000 0.999 22 22 THR M 23 1.000 1.000 0.998 23 23 GLY M 24 1.000 0.996 24 24 VAL M 25 0.997 0.999 0.999 25 25 ILE M 26 0.998 0.999 0.999 0.853 26 26 SER M 27 0.997 0.996 0.683 27 27 LYS M 28 0.993 0.977 0.877 0.937 0.278 0.471 28 28 PHE M 29 0.988 0.791 0.996 0.996 ASP M 30 0.808 0.923 0.365 0.355 30 THR M 31 0.913 0.989 0.999 31 31 ASN M 32 0.985 0.994 0.634 0.226 32 32 ILE M 33 0.995 0.988 0.998 0.880 33 33 ARG M 34 0.989 0.996 0.709 0.428 0.249 0.596 0.999 34 34 THR M 35 0.999 0.993 0.997 35 35 ILE M 36 0.983 0.996 0.998 0.560 36 36 VAL M 37 0.998 0.969 0.999 37 37 LEU M 38 0.967 0.993 0.999 0.999 38 38 ASN M 39 0.991 0.991 0.982 0.260 39 39 ALA M 40 0.997 0.979 40 40 LYS M 41 0.976 0.851 0.907 0.772 0.816 0.336 41 ASP M 42 0.753 0.889 0.586 0.375 GLY M 43 0.960 0.995 43 43 ILE M 44 0.994 0.988 0.994 0.999 44 44 PHE M 45 0.988 0.998 0.999 0.302 45 45 THR M 46 0.997 0.992 0.999 46 46 CYS M 47 0.989 0.992 1.000 47 47 ASN M 48 0.993 0.998 0.999 0.831 48 48 LEU M 49 1.000 0.996 1.000 1.000 49 49 MET M 50 0.997 0.999 0.999 1.000 1.000 50 50 ILE M 51 1.000 0.997 0.999 0.998 51 51 PHE M 52 0.997 0.996 0.999 0.999 52 52 VAL M 53 0.992 0.996 0.996 53 53 LYS M 54 0.986 0.976 0.565 0.709 0.233 0.449 54 54 ASN M 55 0.968 0.983 0.759 0.386 55 55 THR M 56 0.995 0.996 0.948 56 56 ASP M 57 0.999 0.997 0.622 0.609 57 57 LYS M 58 0.999 0.994 0.972 0.995 0.808 0.616 58 58 LEU M 59 0.996 1.000 0.999 1.000 59 59 THR M 60 0.999 0.999 0.863 60 60 THR M 61 0.999 0.999 0.999 61 61 LEU M 62 0.999 0.995 0.997 0.997 62 62 MET M 63 0.999 0.993 0.996 0.989 0.642 63 63 ASP M 64 0.998 0.998 0.985 0.793 64 64 LYS M 65 0.998 0.996 0.997 0.998 0.938 0.299 65 65 LEU M 66 0.997 0.999 0.999 1.000 66 66 ARG M 67 0.998 0.999 0.662 0.956 0.291 0.785 0.999 67 67 LYS M 68 0.997 0.994 0.995 0.997 0.599 0.629 68 68 VAL M 69 0.994 0.995 0.999 69 69 GLN M 70 0.998 0.993 0.998 0.876 0.311 70 70 GLY M 71 0.991 0.993 71 71 VAL M 72 0.997 0.991 1.000 72 72 PHE M 73 0.992 0.992 0.997 0.301 73 73 THR M 74 0.995 0.999 0.996 74 74 VAL M 75 0.998 1.000 0.999 75 75 GLU M 76 0.995 0.992 0.674 0.557 0.346 76 76 ARG M 77 0.994 0.993 0.994 0.997 0.552 0.626 0.999 77 77 LEU M 78 0.989 0.988 0.999 1.000 78 78 SER M 79 0.988 0.973 0.490 79 79 ASN M 80 0.980 0.987 0.165 0.251 80 80 LEU M 81 0.973 0.964 0.999 0.998 81 81 GLU M 82 0.949 0.982 0.981 0.490 0.257 82 82 HIS M 83 0.984 0.561 0.998 0.998 HIS M 84 0.626 0.608 0.400 0.199 HIS M 85 0.826 0.368 0.231 0.092 HIS M 86 0.625 0.634 0.345 0.207 HIS M 87 0.782 0.399 0.483 0.093 HIS M 88 0.831 0.506 0.278 0.133 MET M 99 0.629 0.086 0.352 0.461 0.363 THR M 100 0.757 0.344 0.474 ASP M 101 0.877 0.958 0.554 0.292 101 PHE M 102 0.966 0.999 1.000 0.500 102 102 LEU M 103 0.999 0.999 1.000 1.000 103 103 ALA M 104 0.997 0.987 104 104 GLY M 105 0.986 0.994 105 105 ILE M 106 0.994 0.990 0.999 1.000 106 106 ARG M 107 0.986 0.996 0.977 0.652 0.494 0.623 0.998 107 107 ILE M 108 0.997 1.000 1.000 1.000 108 108 VAL M 109 0.999 0.999 0.999 109 109 GLY M 110 0.996 0.999 110 110 GLU M 111 0.997 0.990 0.998 0.994 0.600 111 111 ASP M 112 0.996 0.957 0.742 0.690 112 112 LYS M 113 0.950 0.984 0.980 0.595 0.402 0.376 113 113 ASN M 114 0.947 0.678 0.578 0.218 GLY M 115 0.838 0.909 115 MET M 116 0.992 1.000 0.996 0.939 0.927 116 116 THR M 117 0.999 0.998 0.999 117 117 ASN M 118 1.000 0.999 0.602 0.338 118 118 GLN M 119 0.999 0.999 0.999 0.999 1.000 119 119 ILE M 120 0.999 1.000 1.000 1.000 120 120 THR M 121 0.999 1.000 0.997 121 121 GLY M 122 1.000 0.996 122 122 VAL M 123 0.995 0.999 0.999 123 123 ILE M 124 0.999 0.999 0.998 0.711 124 124 SER M 125 0.998 0.997 0.859 125 125 LYS M 126 0.993 0.986 0.788 0.940 0.332 0.198 126 126 PHE M 127 0.993 0.993 0.990 0.991 127 127 ASP M 128 0.979 0.938 0.599 0.578 128 128 THR M 129 0.933 0.994 0.999 129 129 ASN M 130 0.995 0.997 0.629 0.311 130 130 ILE M 131 0.994 0.984 0.998 0.935 131 131 ARG M 132 0.985 0.997 0.637 0.550 0.172 0.772 0.997 132 132 THR M 133 0.999 0.991 0.997 133 133 ILE M 134 0.979 0.996 0.999 0.565 134 134 VAL M 135 0.998 0.946 1.000 135 135 LEU M 136 0.954 0.990 0.999 0.999 136 136 ASN M 137 0.986 0.978 0.848 0.493 137 137 ALA M 138 0.992 0.986 138 138 LYS M 139 0.983 0.919 0.913 0.620 0.921 0.390 139 139 ASP M 140 0.902 0.876 0.618 0.412 140 GLY M 141 0.877 0.989 141 ILE M 142 0.994 0.987 0.995 0.999 142 142 PHE M 143 0.988 0.993 0.999 0.500 143 143 THR M 144 0.993 0.993 0.999 144 144 CYS M 145 0.993 0.987 1.000 145 145 ASN M 146 0.988 0.998 0.931 0.795 146 146 LEU M 147 0.999 0.996 0.999 1.000 147 147 MET M 148 0.996 0.999 0.999 0.983 0.940 148 148 ILE M 149 0.999 0.997 0.999 0.998 149 149 PHE M 150 0.997 0.998 0.999 0.799 150 150 VAL M 151 0.996 0.992 0.998 151 151 LYS M 152 0.984 0.983 0.418 0.775 0.429 0.570 152 152 ASN M 153 0.973 0.987 0.630 0.209 153 153 THR M 154 0.995 0.997 0.999 154 154 ASP M 155 0.998 0.998 0.432 0.329 155 155 LYS M 156 1.000 0.997 0.995 0.999 0.807 0.873 156 156 LEU M 157 0.996 1.000 0.999 1.000 157 157 THR M 158 0.998 0.998 0.925 158 158 THR M 159 0.996 0.999 0.999 159 159 LEU M 160 0.999 0.998 0.999 0.999 160 160 MET M 161 0.998 0.995 0.997 0.993 0.823 161 161 ASP M 162 0.998 0.997 0.900 0.705 162 162 LYS M 163 0.998 0.997 0.996 0.996 0.891 0.337 163 163 LEU M 164 0.998 0.997 0.999 0.999 164 164 ARG M 165 0.997 0.999 0.798 0.994 0.572 0.847 0.999 165 165 LYS M 166 0.999 0.993 0.996 0.995 0.698 0.578 166 166 VAL M 167 0.996 0.994 0.999 167 167 GLN M 168 0.997 0.994 0.998 0.773 0.433 168 168 GLY M 169 0.990 0.994 169 169 VAL M 170 0.996 0.997 0.999 170 170 PHE M 171 0.996 0.994 0.999 0.108 171 171 THR M 172 0.996 0.998 0.998 172 172 VAL M 173 0.998 1.000 0.999 173 173 GLU M 174 0.993 0.995 0.612 0.854 0.316 174 174 ARG M 175 0.995 0.984 0.885 0.997 0.461 0.755 0.998 175 175 LEU M 176 0.975 0.699 0.999 0.999 SER M 177 0.710 0.970 0.351 ASN M 178 0.978 0.978 0.309 0.182 178 178 LEU M 179 0.966 0.885 0.999 0.997 179 GLU M 180 0.878 0.854 0.990 0.647 0.466 180 HIS M 181 0.774 0.667 0.995 0.995 HIS M 182 0.698 0.628 0.283 0.327 HIS M 183 0.824 0.637 0.268 0.183 HIS M 184 0.799 0.764 0.223 0.112 HIS M 185 0.619 0.632 0.293 0.166 HIS M 186 0.765 0.175 0.114 Ranges: 7 from: M 4 to M 14 from: M 18 to M 28 from: M 31 to M 40 from: M 43 to M 82 from: M 102 to M 113 from: M 116 to M 139 from: M 142 to M 175 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[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 1 is: 0.259 (*) > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 2 is: 0.341 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 3 is: 0.449 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 4 is: 0.511 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 5 is: 0.345 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 6 is: 0.385 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 7 is: 0.397 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 8 is: 0.326 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 9 is: 0.372 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 10 is: 0.331 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 11 is: 0.390 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 12 is: 0.365 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 13 is: 0.361 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 14 is: 0.545 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 15 is: 0.418 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 16 is: 0.353 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 17 is: 0.405 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 18 is: 0.424 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 19 is: 0.451 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 20 is: 0.431 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..14],[18..28],[31..40],[43..82],[102..113],[116..139],[142..175], is: 0.393 > Range of RMSD values to reference struct. is 0.259 to 0.545 > 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[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 1 is: 0.595 (*) > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 2 is: 0.642 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 3 is: 0.742 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 4 is: 0.775 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 5 is: 0.703 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 6 is: 0.752 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 7 is: 0.708 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 8 is: 0.667 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 9 is: 0.717 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 10 is: 0.762 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 11 is: 0.767 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 12 is: 0.662 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 13 is: 0.658 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 14 is: 0.853 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 15 is: 0.764 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 16 is: 0.672 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 17 is: 0.789 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 18 is: 0.764 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 19 is: 0.813 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..113],M[116..139],M[142..175],for model 20 is: 0.722 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..14],[18..28],[31..40],[43..82],[102..113],[116..139],[142..175], is: 0.726 > Range of RMSD values to reference struct. is 0.595 to 0.853 PdbStat> PdbStat> *END* of program detected, BYE! ...