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 `SGR145_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 31-MAR-10 2KW5 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE SLR1183 PROTEIN FROM > ReadCoordsPdb(): >> TITLE 2 SYNECHOCYSTIS SP. PCC 6803, NORTHEAST STRUCTURAL GENOMICS > ReadCoordsPdb(): >> TITLE 3 CONSORTIUM TARGET SGR145 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `SGR145_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 SGR145_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 62820 ATOM records read from file > ReadCoordsPdb(): --> 62820 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 0.014 0.584 0.488 0.428 TRP A 2 0.817 0.528 0.072 0.583 ASP A 3 0.808 0.751 0.163 0.294 GLU A 4 0.889 0.698 0.556 0.018 0.251 ARG A 5 0.762 0.845 0.257 0.340 0.212 0.825 0.997 PHE A 6 0.800 0.713 0.221 0.196 SER A 7 0.708 0.610 0.210 GLN A 8 0.700 0.641 0.090 0.161 0.257 SER A 9 0.740 0.724 0.092 GLU A 10 0.871 0.585 0.156 0.461 0.432 TYR A 11 0.761 0.745 0.133 0.346 VAL A 12 0.819 0.721 0.240 TYR A 13 0.709 0.723 0.257 0.374 GLY A 14 0.528 0.562 THR A 15 0.793 0.641 0.112 GLU A 16 0.656 0.897 0.431 0.385 0.473 PRO A 17 0.972 0.631 0.920 0.867 ASN A 18 0.813 0.694 0.095 0.405 ASP A 19 0.659 0.554 0.489 0.361 PHE A 20 0.799 0.984 0.994 0.991 LEU A 21 0.997 0.977 0.995 0.995 21 21 VAL A 22 0.961 0.993 0.993 22 22 SER A 23 0.998 0.998 0.432 23 23 VAL A 24 0.999 0.998 0.989 24 24 ALA A 25 0.999 0.997 25 25 ASN A 26 0.997 0.997 0.755 0.186 26 26 GLN A 27 0.998 0.993 0.994 0.998 0.458 27 27 ILE A 28 0.997 0.998 0.994 0.999 28 28 PRO A 29 0.993 0.988 0.940 0.887 29 29 GLN A 30 0.998 1.000 0.453 0.995 0.353 30 30 GLY A 31 0.999 0.975 31 31 LYS A 32 0.992 0.997 0.535 0.400 0.302 0.301 32 32 ILE A 33 0.999 0.985 0.994 0.997 33 33 LEU A 34 0.987 0.996 0.998 0.997 34 34 CYS A 35 0.994 0.978 0.296 35 35 LEU A 36 0.970 0.923 0.997 0.999 36 36 ALA A 37 0.477 0.725 GLU A 38 0.777 0.325 0.309 0.163 0.397 GLY A 39 0.324 0.523 GLU A 40 0.613 0.302 0.654 0.362 0.312 GLY A 41 0.147 0.775 ARG A 42 0.988 0.991 0.232 0.994 0.144 0.666 0.998 42 42 ASN A 43 0.992 0.990 0.414 0.363 43 43 ALA A 44 0.997 0.995 44 44 CYS A 45 0.997 0.993 0.533 45 45 PHE A 46 0.998 0.993 0.993 0.414 46 46 LEU A 47 0.999 0.999 0.995 0.998 47 47 ALA A 48 0.999 0.999 48 48 SER A 49 0.998 0.995 0.151 49 49 LEU A 50 0.998 0.998 0.999 0.999 50 50 GLY A 51 0.996 0.987 51 51 TYR A 52 0.980 0.992 0.997 0.970 52 52 GLU A 53 0.994 0.999 0.994 0.995 0.284 53 53 VAL A 54 0.997 0.994 0.998 54 54 THR A 55 0.993 0.998 0.026 55 55 ALA A 56 0.997 0.992 56 56 VAL A 57 0.986 0.981 0.996 57 57 ASP A 58 0.982 0.976 0.991 0.533 58 58 GLN A 59 0.991 0.991 0.222 0.929 0.367 59 59 SER A 60 0.989 0.971 0.506 60 60 SER A 61 0.998 0.997 0.321 61 61 VAL A 62 0.998 0.996 0.998 62 62 GLY A 63 0.997 0.997 63 63 LEU A 64 0.998 0.996 0.999 0.999 64 64 ALA A 65 0.999 0.995 65 65 LYS A 66 0.997 0.996 0.581 0.228 0.621 0.176 66 66 ALA A 67 0.999 0.997 67 67 LYS A 68 0.999 0.994 0.927 0.994 0.266 0.283 68 68 GLN A 69 0.998 0.997 0.663 0.343 0.148 69 69 LEU A 70 0.999 0.999 0.998 0.998 70 70 ALA A 71 0.999 0.997 71 71 GLN A 72 0.998 0.995 0.205 0.995 0.580 72 72 GLU A 73 0.997 0.989 0.998 0.937 0.306 73 73 LYS A 74 0.992 0.991 0.997 0.990 0.563 0.169 74 74 GLY A 75 0.997 0.994 75 75 VAL A 76 0.992 0.995 0.999 76 76 LYS A 77 0.985 0.994 0.996 0.997 0.389 0.210 77 77 ILE A 78 0.997 0.998 0.996 0.996 78 78 THR A 79 0.994 0.999 0.998 79 79 THR A 80 0.998 0.992 0.705 80 80 VAL A 81 0.989 0.989 0.999 81 81 GLN A 82 0.987 0.941 0.214 0.996 0.427 82 82 SER A 83 0.814 0.841 0.301 83 ASN A 84 0.998 0.961 0.738 0.470 84 84 LEU A 85 0.978 0.986 0.994 0.997 85 85 ALA A 86 0.974 0.966 86 86 ASP A 87 0.956 0.965 0.994 0.994 87 87 PHE A 88 0.995 0.962 0.990 0.611 88 88 ASP A 89 0.989 0.996 0.991 0.294 89 89 ILE A 90 0.993 0.994 0.997 0.998 90 90 VAL A 91 0.993 0.932 0.998 91 91 ALA A 92 0.982 0.975 92 92 ASP A 93 0.995 0.995 0.776 0.714 93 93 ALA A 94 0.991 0.995 94 94 TRP A 95 0.988 0.907 0.910 0.820 95 95 GLU A 96 0.951 0.950 0.555 0.197 0.313 96 96 GLY A 97 0.947 0.981 97 97 ILE A 98 0.994 0.987 0.996 0.998 98 98 VAL A 99 0.983 0.972 0.999 99 99 SER A 100 0.962 0.991 0.724 100 100 ILE A 101 0.996 0.969 0.994 0.999 101 101 PHE A 102 0.978 0.998 0.599 0.243 102 102 CYS A 103 0.943 0.949 0.359 103 103 HIS A 104 0.945 0.999 0.292 0.302 104 104 LEU A 105 0.973 0.996 0.998 0.998 105 105 PRO A 106 0.994 0.995 0.932 0.869 106 106 SER A 107 0.995 0.993 0.358 107 107 SER A 108 0.997 0.997 0.297 108 108 LEU A 109 0.998 0.997 0.997 0.998 109 109 ARG A 110 0.997 0.995 0.911 0.949 0.088 0.863 0.997 110 110 GLN A 111 0.993 0.985 0.525 0.358 0.354 111 111 GLN A 112 0.995 0.990 0.620 0.090 0.041 112 112 LEU A 113 0.995 0.992 0.999 1.000 113 113 TYR A 114 0.996 0.997 0.997 0.747 114 114 PRO A 115 0.997 0.998 0.912 0.817 115 115 LYS A 116 0.997 0.994 0.567 0.229 0.499 0.509 116 116 VAL A 117 0.997 0.994 0.994 117 117 TYR A 118 0.986 0.997 0.993 0.607 118 118 GLN A 119 0.992 0.993 0.999 0.996 0.264 119 119 GLY A 120 0.992 0.987 120 120 LEU A 121 0.988 0.967 0.996 0.953 121 121 LYS A 122 0.951 0.981 0.611 0.231 0.230 0.058 122 122 PRO A 123 0.995 0.992 0.987 0.975 123 123 GLY A 124 0.998 0.985 124 124 GLY A 125 0.980 0.990 125 125 VAL A 126 0.999 0.998 0.999 126 126 PHE A 127 0.999 0.999 0.996 0.872 127 127 ILE A 128 0.998 0.999 0.997 0.998 128 128 LEU A 129 0.997 0.968 0.992 0.922 129 129 GLU A 130 0.970 0.989 0.999 0.996 0.198 130 130 GLY A 131 0.893 0.911 131 PHE A 132 0.956 0.996 0.993 0.229 132 132 ALA A 133 0.930 0.989 133 133 PRO A 134 0.994 0.945 0.917 0.831 134 134 GLU A 135 0.978 0.970 0.031 0.474 0.304 135 135 GLN A 136 0.991 0.996 0.996 0.999 0.544 136 136 LEU A 137 0.988 0.990 0.954 0.954 137 137 GLN A 138 0.994 0.982 0.995 0.997 0.480 138 138 TYR A 139 0.964 0.923 0.985 0.686 139 139 ASN A 140 0.185 0.499 0.507 0.353 THR A 141 0.968 0.934 0.261 141 141 GLY A 142 0.454 0.580 GLY A 143 0.762 0.701 PRO A 144 0.990 0.463 0.940 0.863 LYS A 145 0.675 0.853 0.408 0.578 0.223 0.308 ASP A 146 0.933 0.636 0.703 0.690 LEU A 147 0.884 0.983 0.995 0.931 147 ASP A 148 0.989 0.997 0.996 0.886 148 148 LEU A 149 0.996 0.986 0.997 0.989 149 149 LEU A 150 0.987 0.996 0.995 0.995 150 150 PRO A 151 0.987 0.981 0.933 0.888 151 151 LYS A 152 0.980 0.989 0.596 0.641 0.246 0.205 152 152 LEU A 153 0.998 0.994 0.998 0.998 153 153 GLU A 154 0.998 0.994 0.435 0.048 0.355 154 154 THR A 155 0.996 0.990 0.488 155 155 LEU A 156 0.993 0.997 0.994 0.993 156 156 GLN A 157 0.998 0.997 0.920 0.749 0.267 157 157 SER A 158 0.995 0.993 0.849 158 158 GLU A 159 0.988 0.976 0.566 0.295 0.371 159 159 LEU A 160 0.990 0.995 0.997 0.998 160 160 PRO A 161 0.993 0.973 0.953 0.918 161 161 SER A 162 0.999 0.994 0.131 162 162 LEU A 163 0.984 0.999 0.999 0.999 163 163 ASN A 164 0.995 0.993 0.778 0.261 164 164 TRP A 165 0.998 0.994 0.999 0.999 165 165 LEU A 166 0.999 0.998 0.999 0.999 166 166 ILE A 167 0.999 0.999 0.999 1.000 167 167 ALA A 168 0.999 0.994 168 168 ASN A 169 0.980 0.995 0.998 0.977 169 169 ASN A 170 0.994 0.991 0.453 0.159 170 170 LEU A 171 0.996 0.988 0.999 0.999 171 171 GLU A 172 0.993 0.985 0.232 0.465 0.243 172 172 ARG A 173 0.954 0.995 0.992 0.996 0.477 0.878 0.998 173 173 ASN A 174 0.990 0.974 0.997 0.506 174 174 LEU A 175 0.981 0.941 0.997 0.997 175 175 ASP A 176 0.854 0.533 0.552 0.348 GLU A 177 0.552 0.416 0.188 0.272 0.242 GLY A 178 0.351 0.431 ALA A 179 0.691 0.231 TYR A 180 0.525 0.768 0.471 0.246 HIS A 181 0.673 0.158 0.427 0.580 GLN A 182 0.530 0.468 0.166 0.624 0.227 GLY A 183 0.477 0.769 LYS A 184 0.951 0.976 0.298 0.505 0.436 0.201 184 184 ALA A 185 0.980 0.984 185 185 ALA A 186 0.979 0.986 186 186 LEU A 187 0.993 0.982 0.999 0.998 187 187 ILE A 188 0.994 0.979 0.997 0.997 188 188 GLN A 189 0.965 0.997 0.997 0.998 0.126 189 189 LEU A 190 0.998 0.996 0.999 0.999 190 190 LEU A 191 0.992 0.999 0.999 1.000 191 191 GLY A 192 0.999 0.996 192 192 GLN A 193 0.989 0.998 0.991 0.996 0.482 193 193 LYS A 194 0.998 0.976 0.608 0.796 0.489 0.100 194 194 LEU A 195 0.990 0.933 0.997 0.998 195 195 GLU A 196 0.387 0.544 0.389 0.328 0.440 HIS A 197 0.759 0.592 0.200 0.438 HIS A 198 0.568 0.614 0.218 0.191 HIS A 199 0.840 0.598 0.323 0.290 HIS A 200 0.758 0.435 0.162 0.450 HIS A 201 0.486 0.589 0.366 0.338 HIS A 202 0.753 0.265 0.155 Ranges: 6 from: A 21 to A 36 from: A 42 to A 82 from: A 84 to A 130 from: A 132 to A 139 from: A 148 to A 175 from: A 184 to A 195 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[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 1 is: 0.848 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 2 is: 0.787 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 3 is: 0.921 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 4 is: 0.893 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 5 is: 0.722 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 6 is: 1.123 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 7 is: 0.861 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 8 is: 0.762 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 9 is: 0.862 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 10 is: 0.753 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 11 is: 0.794 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 12 is: 0.827 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 13 is: 0.675 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 14 is: 0.862 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 15 is: 0.832 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 16 is: 0.624 (*) > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 17 is: 0.915 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 18 is: 1.277 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 19 is: 1.322 > Kabsch RMSD of backbone atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 20 is: 0.939 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[21..36],[42..82],[84..130],[132..139],[148..175],[184..195], is: 0.880 > Range of RMSD values to reference struct. is 0.624 to 1.322 > 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[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 1 is: 1.190 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 2 is: 1.123 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 3 is: 1.256 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 4 is: 1.273 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 5 is: 1.078 (*) > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 6 is: 1.474 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 7 is: 1.202 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 8 is: 1.135 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 9 is: 1.233 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 10 is: 1.185 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 11 is: 1.192 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 12 is: 1.129 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 13 is: 1.115 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 14 is: 1.171 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 15 is: 1.249 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 16 is: 1.188 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 17 is: 1.273 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 18 is: 1.672 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 19 is: 1.748 > Kabsch RMSD of heavy atoms in res. A[21..36],A[42..82],A[84..130],A[132..139],A[148..175],A[184..195],for model 20 is: 1.315 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[21..36],[42..82],[84..130],[132..139],[148..175],[184..195], is: 1.260 > Range of RMSD values to reference struct. is 1.078 to 1.748 PdbStat> PdbStat> *END* of program detected, BYE! ...