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_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP.PDB, 20 MODEL/S TEMP.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 164 MET LYS LYS MET ALA GLU PHE THR PHE GLU ILE GLU GLU 1 > ReadCoordsPdb(): Counting models in file `SPR104_R3_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_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 52640 ATOM records read from file > ReadCoordsPdb(): --> 52640 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 0.308 0.688 0.478 0.253 LYS M 2 0.624 0.567 0.656 0.793 0.930 0.998 LYS M 3 0.766 0.386 0.745 0.927 0.999 0.999 MET M 4 0.559 0.091 0.467 0.479 0.207 ALA M 5 0.249 0.326 GLU M 6 0.594 0.424 0.747 0.862 0.986 PHE M 7 0.761 0.527 0.777 0.789 THR M 8 0.907 0.917 0.635 8 8 PHE M 9 0.893 0.871 0.465 0.744 9 GLU M 10 0.937 0.966 0.700 0.999 0.999 10 10 ILE M 11 0.994 0.996 0.939 1.000 11 11 GLU M 12 0.983 0.992 0.540 0.298 0.836 12 12 GLU M 13 0.979 0.939 0.443 0.998 0.998 13 13 HIS M 14 0.924 0.993 0.603 0.208 14 14 LEU M 15 0.993 0.995 0.604 0.658 15 15 LEU M 16 0.995 0.968 0.431 0.857 16 16 THR M 17 0.975 0.995 1.000 17 17 LEU M 18 0.985 0.996 0.998 0.999 18 18 SER M 19 0.998 0.953 0.550 19 19 GLU M 20 0.916 0.953 0.743 0.998 0.971 20 20 ASN M 21 0.925 0.946 0.640 0.815 21 21 GLU M 22 0.721 0.487 0.833 0.874 0.947 LYS M 23 0.377 0.749 0.796 0.858 0.999 0.999 GLY M 24 0.763 0.913 TRP M 25 0.965 0.875 0.686 0.227 25 THR M 26 0.939 0.988 0.922 26 26 LYS M 27 0.974 0.991 0.765 0.994 0.662 0.995 27 27 GLU M 28 0.978 0.994 0.522 0.996 0.713 28 28 ILE M 29 0.991 0.995 1.000 0.998 29 29 ASN M 30 0.986 0.986 0.780 0.795 30 30 ARG M 31 0.985 0.998 0.836 0.996 0.870 0.921 0.999 31 31 VAL M 32 0.990 0.996 0.846 32 32 SER M 33 0.978 0.980 0.367 33 33 PHE M 34 0.985 0.926 0.934 0.778 34 34 ASN M 35 0.897 0.565 0.654 0.845 GLY M 36 0.499 0.212 ALA M 37 0.660 0.144 PRO M 38 0.979 0.691 0.878 0.813 ALA M 39 0.497 0.928 LYS M 40 0.965 0.992 0.998 0.794 0.998 1.000 40 40 PHE M 41 0.979 0.955 0.997 0.995 41 41 ASP M 42 0.939 0.989 0.996 0.859 42 42 ILE M 43 0.985 0.990 1.000 0.999 43 43 ARG M 44 0.962 0.965 0.363 0.991 0.314 0.682 1.000 44 44 ALA M 45 0.965 0.929 45 45 TRP M 46 0.890 0.924 0.263 0.314 46 SER M 47 0.834 0.792 0.562 PRO M 48 0.985 0.261 0.891 0.823 ASP M 49 0.214 0.268 0.549 0.880 HIS M 50 0.234 0.425 0.578 0.663 THR M 51 0.657 0.395 0.546 LYS M 52 0.813 0.378 0.649 0.661 0.998 0.930 MET M 53 0.697 0.518 0.404 0.178 0.174 GLY M 54 0.491 0.402 LYS M 55 0.557 0.665 0.929 0.745 0.997 0.937 GLY M 56 0.861 0.885 56 ILE M 57 0.974 0.990 0.853 0.999 57 57 THR M 58 0.986 0.996 1.000 58 58 LEU M 59 0.987 0.994 0.997 0.910 59 59 SER M 60 0.983 0.996 0.928 60 60 ASN M 61 0.992 0.964 0.749 0.547 61 61 GLU M 62 0.958 0.997 0.929 0.845 0.969 62 62 GLU M 63 0.999 0.996 0.906 0.912 0.902 63 63 PHE M 64 0.998 0.996 0.947 0.995 64 64 GLN M 65 0.998 0.993 0.636 0.568 0.921 65 65 THR M 66 0.997 0.997 1.000 66 66 MET M 67 0.988 0.972 0.304 0.991 0.565 67 67 VAL M 68 0.996 0.994 0.917 68 68 ASP M 69 0.980 0.992 0.938 0.941 69 69 ALA M 70 0.994 0.989 70 70 PHE M 71 0.966 0.985 0.988 0.693 71 71 LYS M 72 0.977 0.976 0.507 0.899 0.994 0.804 72 72 GLY M 73 0.958 0.853 73 ASN M 74 0.904 0.327 0.497 0.875 LEU M 75 0.186 0.308 0.677 0.750 GLU M 76 0.452 0.268 0.509 0.507 0.831 HIS M 77 0.919 0.418 0.485 0.582 HIS M 78 0.758 0.498 0.396 0.267 HIS M 79 0.610 0.340 0.507 0.644 HIS M 80 0.629 0.367 0.591 0.628 HIS M 81 0.590 0.594 0.661 0.728 HIS M 82 0.954 0.114 0.732 0.758 MET M 93 0.370 0.308 0.688 0.478 0.253 LYS M 94 0.624 0.568 0.656 0.793 0.930 0.998 LYS M 95 0.766 0.387 0.745 0.926 0.999 0.999 MET M 96 0.559 0.091 0.467 0.479 0.207 ALA M 97 0.249 0.326 GLU M 98 0.593 0.424 0.747 0.862 0.985 PHE M 99 0.761 0.527 0.777 0.789 THR M 100 0.907 0.917 0.635 100 100 PHE M 101 0.893 0.871 0.465 0.744 101 GLU M 102 0.937 0.966 0.700 0.999 0.999 102 102 ILE M 103 0.994 0.996 0.939 1.000 103 103 GLU M 104 0.983 0.992 0.540 0.297 0.836 104 104 GLU M 105 0.979 0.939 0.443 0.998 0.998 105 105 HIS M 106 0.924 0.993 0.603 0.208 106 106 LEU M 107 0.993 0.995 0.604 0.658 107 107 LEU M 108 0.995 0.968 0.431 0.857 108 108 THR M 109 0.975 0.995 1.000 109 109 LEU M 110 0.985 0.996 0.998 0.999 110 110 SER M 111 0.998 0.953 0.550 111 111 GLU M 112 0.916 0.953 0.743 0.998 0.971 112 112 ASN M 113 0.925 0.946 0.640 0.815 113 113 GLU M 114 0.721 0.487 0.833 0.874 0.947 LYS M 115 0.377 0.749 0.796 0.857 0.999 0.999 GLY M 116 0.763 0.913 TRP M 117 0.965 0.874 0.686 0.227 117 THR M 118 0.939 0.988 0.922 118 118 LYS M 119 0.974 0.991 0.765 0.994 0.663 0.996 119 119 GLU M 120 0.978 0.994 0.523 0.996 0.713 120 120 ILE M 121 0.991 0.995 1.000 0.998 121 121 ASN M 122 0.986 0.986 0.780 0.795 122 122 ARG M 123 0.985 0.998 0.835 0.996 0.870 0.921 0.999 123 123 VAL M 124 0.990 0.996 0.846 124 124 SER M 125 0.978 0.980 0.367 125 125 PHE M 126 0.985 0.926 0.934 0.778 126 126 ASN M 127 0.897 0.565 0.654 0.845 GLY M 128 0.499 0.212 ALA M 129 0.660 0.144 PRO M 130 0.979 0.691 0.878 0.813 ALA M 131 0.497 0.928 LYS M 132 0.965 0.992 0.998 0.794 0.998 1.000 132 132 PHE M 133 0.979 0.955 0.997 0.995 133 133 ASP M 134 0.939 0.989 0.996 0.859 134 134 ILE M 135 0.985 0.990 1.000 0.999 135 135 ARG M 136 0.962 0.965 0.364 0.991 0.314 0.682 1.000 136 136 ALA M 137 0.965 0.929 137 137 TRP M 138 0.890 0.924 0.263 0.314 138 SER M 139 0.834 0.792 0.562 PRO M 140 0.985 0.261 0.891 0.823 ASP M 141 0.214 0.268 0.549 0.880 HIS M 142 0.234 0.425 0.578 0.663 THR M 143 0.657 0.395 0.546 LYS M 144 0.813 0.379 0.649 0.661 0.998 0.930 MET M 145 0.696 0.518 0.404 0.178 0.174 GLY M 146 0.490 0.402 LYS M 147 0.557 0.665 0.929 0.745 0.998 0.937 GLY M 148 0.861 0.885 148 ILE M 149 0.974 0.990 0.853 0.999 149 149 THR M 150 0.986 0.996 1.000 150 150 LEU M 151 0.987 0.994 0.997 0.910 151 151 SER M 152 0.983 0.996 0.928 152 152 ASN M 153 0.992 0.963 0.749 0.547 153 153 GLU M 154 0.958 0.997 0.929 0.845 0.969 154 154 GLU M 155 0.999 0.996 0.906 0.912 0.902 155 155 PHE M 156 0.998 0.996 0.947 0.995 156 156 GLN M 157 0.998 0.993 0.636 0.568 0.921 157 157 THR M 158 0.997 0.997 1.000 158 158 MET M 159 0.988 0.972 0.304 0.991 0.565 159 159 VAL M 160 0.996 0.994 0.917 160 160 ASP M 161 0.980 0.992 0.937 0.941 161 161 ALA M 162 0.994 0.989 162 162 PHE M 163 0.966 0.985 0.988 0.693 163 163 LYS M 164 0.977 0.976 0.507 0.899 0.994 0.804 164 164 GLY M 165 0.958 0.853 165 ASN M 166 0.904 0.327 0.497 0.875 LEU M 167 0.186 0.308 0.677 0.750 GLU M 168 0.452 0.268 0.509 0.507 0.830 HIS M 169 0.919 0.418 0.485 0.582 HIS M 170 0.758 0.498 0.396 0.268 HIS M 171 0.610 0.340 0.507 0.645 HIS M 172 0.629 0.367 0.591 0.628 HIS M 173 0.590 0.594 0.661 0.728 HIS M 174 0.954 0.732 0.758 Ranges: 8 from: M 10 to M 21 from: M 26 to M 34 from: M 40 to M 45 from: M 57 to M 72 from: M 102 to M 113 from: M 118 to M 126 from: M 132 to M 137 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[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 1 is: 0.599 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 2 is: 0.702 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 3 is: 0.933 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 4 is: 0.739 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 5 is: 0.626 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 6 is: 0.743 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 7 is: 1.021 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 8 is: 0.821 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 9 is: 1.590 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 10 is: 0.776 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 11 is: 0.849 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 12 is: 0.622 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 13 is: 0.944 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 14 is: 0.591 (*) > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 15 is: 0.994 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 16 is: 0.633 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 17 is: 0.975 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 18 is: 0.904 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 19 is: 1.187 > Kabsch RMSD of backbone atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 20 is: 1.035 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[10..21],[26..34],[40..45],[57..72],[102..113],[118..126],[132..137],[149..164], is: 0.864 > Range of RMSD values to reference struct. is 0.591 to 1.590 > 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[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 1 is: 0.909 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 2 is: 0.992 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 3 is: 1.099 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 4 is: 1.121 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 5 is: 0.868 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 6 is: 1.194 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 7 is: 1.345 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 8 is: 1.264 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 9 is: 1.809 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 10 is: 1.100 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 11 is: 1.226 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 12 is: 1.123 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 13 is: 1.341 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 14 is: 0.833 (*) > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 15 is: 1.326 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 16 is: 1.024 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 17 is: 1.273 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 18 is: 1.261 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 19 is: 1.830 > Kabsch RMSD of heavy atoms in res. M[10..21],M[26..34],M[40..45],M[57..72],M[102..113],M[118..126],M[132..137],M[149..164],for model 20 is: 1.224 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[10..21],[26..34],[40..45],[57..72],[102..113],[118..126],[132..137],[149..164], is: 1.208 > Range of RMSD values to reference struct. is 0.833 to 1.830 PdbStat> PdbStat> *END* of program detected, BYE! ...