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_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 175 MET ALA ASP GLU ALA THR ARG ARG VAL VAL SER GLU ILE 1 > ReadCoordsPdb(): Counting models in file `HR41_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 HR41_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 57560 ATOM records read from file > ReadCoordsPdb(): --> 57560 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 0.078 0.599 0.604 0.261 ALA A 2 0.812 0.333 ASP A 3 0.487 0.331 0.605 0.950 GLU A 4 0.993 0.994 0.814 0.999 0.981 4 4 ALA A 5 0.998 0.995 5 5 THR A 6 0.968 0.987 0.502 6 6 ARG A 7 0.995 0.992 0.936 0.991 0.289 0.501 1.000 7 7 ARG A 8 0.995 0.998 0.934 0.999 0.998 0.728 1.000 8 8 VAL A 9 0.995 0.998 0.999 9 9 VAL A 10 0.994 0.988 0.532 10 10 SER A 11 0.996 0.992 0.847 11 11 GLU A 12 0.985 0.968 0.926 0.407 0.928 12 12 ILE A 13 0.976 0.986 0.999 0.999 13 13 PRO A 14 0.996 0.993 0.964 0.937 14 14 VAL A 15 0.987 0.992 0.922 15 15 LEU A 16 0.984 0.953 0.986 0.617 16 16 LYS A 17 0.967 0.967 0.803 0.999 0.999 0.932 17 17 THR A 18 0.921 0.760 0.705 ASN A 19 0.767 0.869 0.346 0.615 ALA A 20 0.887 0.537 GLY A 21 0.531 0.988 PRO A 22 0.994 0.994 0.930 0.866 22 22 ARG A 23 0.985 0.989 0.936 0.999 1.000 0.939 1.000 23 23 ASP A 24 0.995 0.971 0.927 0.929 24 24 ARG A 25 0.985 0.968 0.517 0.999 0.816 0.882 1.000 25 25 GLU A 26 0.973 0.998 0.656 1.000 1.000 26 26 LEU A 27 0.987 0.992 1.000 1.000 27 27 TRP A 28 0.998 0.998 0.999 0.997 28 28 VAL A 29 0.999 0.999 1.000 29 29 GLN A 30 0.998 0.997 0.762 0.572 0.733 30 30 ARG A 31 0.996 0.996 0.867 0.804 0.591 0.219 1.000 31 31 LEU A 32 0.997 0.999 0.999 1.000 32 32 LYS A 33 0.999 0.998 1.000 1.000 1.000 1.000 33 33 GLU A 34 0.993 0.989 0.940 0.552 0.803 34 34 GLU A 35 0.994 0.988 0.390 0.460 0.649 35 35 TYR A 36 0.998 0.994 0.820 0.606 36 36 GLN A 37 0.999 0.997 1.000 0.924 0.916 37 37 SER A 38 0.995 0.995 0.635 38 38 LEU A 39 0.994 0.996 0.644 0.682 39 39 ILE A 40 0.984 0.996 0.999 0.917 40 40 ARG A 41 0.995 0.990 0.702 0.924 0.924 0.651 1.000 41 41 TYR A 42 0.996 0.996 0.996 0.996 42 42 VAL A 43 0.999 0.998 1.000 43 43 GLU A 44 0.997 0.995 0.718 0.471 0.919 44 44 ASN A 45 0.999 0.998 1.000 0.999 45 45 ASN A 46 0.990 0.979 0.897 0.926 46 46 LYS A 47 0.998 0.998 0.819 0.999 0.999 0.999 47 47 ASN A 48 0.998 0.995 1.000 1.000 48 48 ALA A 49 0.998 0.994 49 49 ASP A 50 0.999 0.992 0.844 0.921 50 50 ASN A 51 0.974 0.889 0.556 0.709 51 ASP A 52 0.938 0.975 0.998 0.998 52 52 TRP A 53 0.925 0.908 0.153 0.389 53 53 PHE A 54 0.985 0.949 0.543 0.882 54 54 ARG A 55 0.986 0.978 0.853 0.998 0.991 0.740 1.000 55 55 LEU A 56 0.981 0.996 0.853 0.871 56 56 GLU A 57 0.983 0.983 0.999 0.771 0.998 57 57 SER A 58 0.928 0.998 0.998 58 58 ASN A 59 0.995 0.995 0.743 0.985 59 59 LYS A 60 0.995 0.993 0.934 1.000 1.000 1.000 60 60 GLU A 61 0.977 0.983 0.999 0.999 0.999 61 61 GLY A 62 0.991 0.987 62 62 THR A 63 0.994 0.987 1.000 63 63 ARG A 64 0.975 0.997 0.870 0.933 0.519 0.938 1.000 64 64 TRP A 65 0.999 0.995 0.998 0.993 65 65 PHE A 66 0.995 0.972 0.996 0.699 66 66 GLY A 67 0.940 0.982 67 67 LYS A 68 0.977 0.984 0.636 0.996 0.759 0.887 68 68 CYS A 69 0.976 0.992 0.552 69 69 TRP A 70 0.962 0.957 0.503 0.079 70 70 TYR A 71 0.928 0.975 0.510 0.985 71 71 ILE A 72 0.977 0.993 1.000 0.761 72 72 HIS A 73 0.973 0.969 0.691 0.440 73 73 ASP A 74 0.997 0.633 0.896 0.903 LEU A 75 0.601 0.982 0.998 0.999 LEU A 76 0.982 0.938 0.655 0.674 76 76 LYS A 77 0.949 0.980 0.999 0.995 0.935 0.997 77 77 TYR A 78 0.941 0.946 0.450 0.880 78 78 GLU A 79 0.939 0.986 0.252 0.994 0.716 79 79 PHE A 80 0.983 0.961 0.862 0.794 80 80 ASP A 81 0.988 0.972 0.724 0.999 81 81 ILE A 82 0.986 0.987 0.518 0.854 82 82 GLU A 83 0.973 0.986 0.255 0.998 0.892 83 83 PHE A 84 0.971 0.975 0.849 0.995 84 84 ASP A 85 0.995 0.961 0.697 0.930 85 85 ILE A 86 0.983 0.996 0.999 0.769 86 86 PRO A 87 0.989 0.982 0.898 0.826 87 87 ILE A 88 0.994 0.983 0.175 0.821 88 88 THR A 89 0.991 0.985 1.000 89 89 TYR A 90 0.993 0.999 0.998 0.996 90 90 PRO A 91 0.998 0.978 1.000 0.999 91 91 THR A 92 0.991 0.998 1.000 92 92 THR A 93 0.987 0.973 0.842 93 93 ALA A 94 0.987 0.992 94 94 PRO A 95 0.989 0.982 0.924 0.871 95 95 GLU A 96 0.982 0.874 0.929 0.781 0.833 96 ILE A 97 0.874 0.985 0.999 0.918 97 ALA A 98 0.984 0.589 VAL A 99 0.601 0.994 0.998 PRO A 100 0.994 0.991 0.939 0.886 100 100 GLU A 101 0.988 0.979 0.612 0.184 0.803 101 101 LEU A 102 0.959 0.922 0.998 0.999 102 102 ASP A 103 0.915 0.599 0.684 0.898 GLY A 104 0.554 0.983 LYS A 105 0.991 0.949 0.998 0.553 0.998 0.987 105 105 THR A 106 0.864 0.590 0.216 ALA A 107 0.666 0.145 LYS A 108 0.660 0.643 0.693 0.586 0.996 0.887 MET A 109 0.714 0.805 0.510 0.382 0.053 TYR A 110 0.730 0.342 0.393 0.719 ARG A 111 0.558 0.545 0.490 0.795 0.794 0.781 1.000 GLY A 112 0.620 0.329 GLY A 113 0.226 0.750 LYS A 114 0.809 0.903 0.717 0.924 0.938 0.935 114 ILE A 115 0.939 0.959 0.494 0.779 115 115 CYS A 116 0.960 0.905 0.533 116 116 LEU A 117 0.953 0.796 0.924 0.926 THR A 118 0.860 0.939 0.137 118 ASP A 119 0.992 0.978 0.914 0.999 119 119 HIS A 120 0.970 0.943 0.799 0.507 120 120 PHE A 121 0.975 0.967 0.562 0.765 121 121 LYS A 122 0.988 0.998 0.590 0.999 0.999 0.937 122 122 PRO A 123 0.995 0.992 0.978 0.966 123 123 LEU A 124 0.985 0.982 0.580 0.559 124 124 TRP A 125 0.979 0.995 0.851 0.723 125 125 ALA A 126 0.992 0.992 126 126 ARG A 127 0.986 0.989 0.624 0.555 0.999 0.881 1.000 127 127 ASN A 128 0.976 0.864 0.997 0.946 128 VAL A 129 0.885 0.994 0.856 129 PRO A 130 0.997 0.966 1.000 1.000 130 130 LYS A 131 0.994 0.899 0.999 0.998 1.000 1.000 131 PHE A 132 0.841 0.955 0.710 0.826 132 GLY A 133 0.936 0.977 133 133 LEU A 134 0.989 0.992 0.572 0.469 134 134 ALA A 135 0.997 0.994 135 135 HIS A 136 0.990 0.994 0.997 0.772 136 136 LEU A 137 0.995 0.988 0.810 0.811 137 137 MET A 138 0.993 0.993 0.861 0.361 0.316 138 138 ALA A 139 0.983 0.990 139 139 LEU A 140 0.980 0.971 0.788 0.802 140 140 GLY A 141 0.999 0.997 141 141 LEU A 142 0.996 0.989 0.747 0.748 142 142 GLY A 143 0.999 0.998 143 143 PRO A 144 0.995 0.996 0.931 0.867 144 144 TRP A 145 0.997 0.996 0.997 0.701 145 145 LEU A 146 0.994 0.992 0.999 0.999 146 146 ALA A 147 0.986 0.984 147 147 VAL A 148 0.980 0.994 0.999 148 148 GLU A 149 0.963 0.985 0.725 0.493 0.829 149 149 ILE A 150 0.991 0.997 0.998 0.494 150 150 PRO A 151 0.993 0.989 0.910 0.818 151 151 ASP A 152 0.991 0.997 0.998 0.955 152 152 LEU A 153 0.995 0.993 0.936 0.753 153 153 ILE A 154 0.995 0.999 1.000 1.000 154 154 GLN A 155 0.998 0.998 0.934 0.460 0.909 155 155 LYS A 156 0.995 0.985 0.645 0.999 0.999 0.998 156 156 GLY A 157 0.984 0.990 157 157 VAL A 158 0.968 0.939 0.545 158 158 ILE A 159 0.946 0.965 0.943 0.560 159 159 GLN A 160 0.769 0.818 0.628 0.524 0.912 HIS A 161 0.822 0.531 0.539 0.319 LYS A 162 0.780 0.358 0.516 0.741 0.999 0.929 GLU A 163 0.195 0.678 0.403 0.792 0.904 LYS A 164 0.921 0.933 0.500 0.859 0.946 0.997 164 164 CYS A 165 0.414 0.511 0.677 ASN A 166 0.826 0.255 0.329 0.830 GLN A 167 0.714 0.710 0.460 0.371 0.746 LEU A 168 0.972 0.642 0.716 0.685 GLU A 169 0.936 0.751 0.556 0.929 0.954 HIS A 170 0.832 0.651 0.452 0.561 HIS A 171 0.798 0.515 0.541 0.523 HIS A 172 0.846 0.411 0.562 0.409 HIS A 173 0.845 0.666 0.536 0.620 HIS A 174 0.871 0.239 0.438 0.627 HIS A 175 0.967 0.851 0.802 Ranges: 8 from: A 4 to A 17 from: A 22 to A 50 from: A 52 to A 73 from: A 76 to A 95 from: A 100 to A 102 from: A 115 to A 116 from: A 119 to A 127 from: A 133 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[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 1 is: 1.278 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 2 is: 1.119 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 3 is: 1.177 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 4 is: 1.735 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 5 is: 1.076 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 6 is: 1.204 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 7 is: 1.094 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 8 is: 0.843 (*) > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 9 is: 1.196 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 10 is: 1.133 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 11 is: 1.126 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 12 is: 1.064 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 13 is: 1.129 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 14 is: 1.068 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 15 is: 1.358 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 16 is: 1.153 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 17 is: 1.009 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 18 is: 1.641 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 19 is: 1.559 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 20 is: 1.053 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..17],[22..50],[52..73],[76..95],[100..102],[115..116],[119..127],[133..159], is: 1.201 > Range of RMSD values to reference struct. is 0.843 to 1.735 > 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[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 1 is: 1.675 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 2 is: 1.577 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 3 is: 1.614 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 4 is: 2.228 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 5 is: 1.672 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 6 is: 1.639 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 7 is: 1.558 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 8 is: 1.443 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 9 is: 1.674 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 10 is: 1.531 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 11 is: 1.637 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 12 is: 1.423 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 13 is: 1.511 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 14 is: 1.416 (*) > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 15 is: 1.889 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 16 is: 1.522 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 17 is: 1.639 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 18 is: 2.041 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 19 is: 2.017 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..50],A[52..73],A[76..95],A[100..102],A[115..116],A[119..127],A[133..159],for model 20 is: 1.439 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..17],[22..50],[52..73],[76..95],[100..102],[115..116],[119..127],[133..159], is: 1.657 > Range of RMSD values to reference struct. is 1.416 to 2.228 PdbStat> PdbStat> *END* of program detected, BYE! ...