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 `CCR55_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 116 MET THR LEU ILE TYR LYS ILE LEU SER ARG ALA GLU TRP 1 > ReadCoordsPdb(): Counting models in file `CCR55_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 CCR55_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 35440 ATOM records read from file > ReadCoordsPdb(): --> 35440 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 0.141 0.630 0.593 0.080 THR A 2 0.606 0.600 0.219 LEU A 3 0.959 0.984 0.520 0.486 3 3 ILE A 4 0.988 0.976 0.601 0.872 4 4 TYR A 5 0.991 0.967 0.997 0.997 5 5 LYS A 6 0.975 0.992 0.930 0.103 0.932 0.403 6 6 ILE A 7 0.998 0.998 1.000 0.921 7 7 LEU A 8 0.991 0.997 0.914 0.999 8 8 SER A 9 0.998 0.993 0.607 9 9 ARG A 10 0.996 0.997 0.618 0.935 0.581 0.615 1.000 10 10 ALA A 11 0.998 0.998 11 11 GLU A 12 0.995 0.995 0.998 0.995 0.885 12 12 TRP A 13 1.000 0.998 0.998 0.998 13 13 ASP A 14 0.999 0.998 0.939 0.965 14 14 ALA A 15 1.000 0.997 15 15 ALA A 16 0.999 0.998 16 16 LYS A 17 0.997 0.998 0.733 0.989 0.594 0.990 17 17 ALA A 18 0.999 0.995 18 18 GLN A 19 0.985 0.995 0.907 0.484 0.898 19 19 GLY A 20 0.994 0.965 20 20 ARG A 21 0.965 0.969 0.486 0.996 0.573 0.563 1.000 21 21 PHE A 22 0.938 0.954 0.919 0.987 22 22 GLU A 23 0.775 0.301 0.874 0.849 0.917 GLY A 24 0.435 0.681 SER A 25 0.886 0.975 0.865 25 ALA A 26 0.997 0.991 26 26 VAL A 27 0.990 0.999 1.000 27 27 ASP A 28 0.992 0.992 0.994 0.861 28 28 LEU A 29 0.994 0.993 0.868 0.867 29 29 ALA A 30 1.000 0.998 30 30 ASP A 31 0.982 0.977 0.998 0.975 31 31 GLY A 32 0.888 0.852 32 PHE A 33 0.703 0.956 0.612 0.980 ILE A 34 0.983 0.915 0.919 1.000 34 34 HIS A 35 0.911 0.984 0.617 0.528 35 35 LEU A 36 0.984 0.470 0.995 0.915 SER A 37 0.470 0.952 0.608 ALA A 38 0.892 0.841 38 GLY A 39 0.517 0.818 GLU A 40 0.988 0.994 0.591 0.999 0.976 40 40 GLN A 41 0.966 0.970 0.872 0.409 0.896 41 41 ALA A 42 0.996 0.987 42 42 GLN A 43 0.997 0.992 0.520 0.864 0.904 43 43 GLU A 44 0.985 0.989 0.567 0.922 0.962 44 44 THR A 45 0.998 0.994 0.924 45 45 ALA A 46 0.999 0.994 46 46 ALA A 47 0.990 0.991 47 47 LYS A 48 0.986 0.981 0.868 0.996 0.999 0.999 48 48 TRP A 49 0.977 0.981 0.537 0.791 49 49 PHE A 50 0.970 0.818 0.998 0.994 50 ARG A 51 0.879 0.185 0.605 0.996 0.438 0.732 1.000 GLY A 52 0.383 0.846 GLN A 53 0.858 0.728 0.707 0.696 0.629 ALA A 54 0.702 0.290 ASN A 55 0.234 0.960 0.919 0.838 LEU A 56 0.985 0.974 0.872 0.866 56 56 VAL A 57 0.981 0.993 0.790 57 57 LEU A 58 0.990 0.993 0.999 0.999 58 58 LEU A 59 0.993 0.967 0.999 1.000 59 59 ALA A 60 0.957 0.994 60 60 VAL A 61 0.993 0.989 0.578 61 61 GLU A 62 0.988 0.942 0.678 0.999 1.000 62 62 ALA A 63 0.915 0.717 GLU A 64 0.382 0.190 0.633 0.776 0.944 PRO A 65 0.978 0.482 0.879 0.806 LEU A 66 0.486 0.789 0.922 0.928 GLY A 67 0.169 0.456 GLU A 68 0.745 0.957 0.912 0.862 0.955 ASP A 69 0.952 0.931 0.997 0.940 69 69 LEU A 70 0.963 0.980 0.862 0.845 70 70 LYS A 71 0.981 0.986 0.560 0.997 0.998 0.867 71 71 TRP A 72 0.987 0.985 0.998 0.839 72 72 GLU A 73 0.953 0.963 0.627 0.876 0.904 73 73 ALA A 74 0.951 0.869 74 SER A 75 0.858 0.258 0.291 ARG A 76 0.329 0.185 0.560 0.860 0.708 0.939 1.000 GLY A 77 0.390 0.472 GLY A 78 0.305 0.369 ALA A 79 0.440 0.843 ARG A 80 0.962 0.968 0.889 0.866 0.501 0.794 1.000 80 80 PHE A 81 0.975 0.981 0.828 0.988 81 81 PRO A 82 0.996 0.970 0.985 0.969 82 82 HIS A 83 0.980 0.991 0.995 0.558 83 83 LEU A 84 0.994 0.991 0.934 0.880 84 84 TYR A 85 0.985 0.931 0.996 0.538 85 85 ARG A 86 0.931 0.981 0.206 0.561 0.570 0.315 1.000 86 86 PRO A 87 0.996 0.995 0.965 0.938 87 87 LEU A 88 0.981 0.978 0.792 0.812 88 88 LEU A 89 0.986 0.979 0.856 0.548 89 89 VAL A 90 0.925 0.962 0.914 90 90 SER A 91 0.916 0.989 0.844 91 91 GLU A 92 0.911 0.959 0.932 0.466 0.925 92 92 VAL A 93 0.993 0.998 0.937 93 93 THR A 94 0.991 0.999 0.999 94 94 ARG A 95 0.992 0.976 0.634 0.699 0.879 0.775 1.000 95 95 GLU A 96 0.956 0.905 0.174 0.930 0.628 96 96 ALA A 97 0.881 0.935 97 ASP A 98 0.975 0.945 0.634 0.976 98 98 LEU A 99 0.819 0.900 0.409 0.557 99 ASP A 100 0.908 0.673 0.347 0.948 LEU A 101 0.620 0.931 0.719 0.687 ASP A 102 0.835 0.989 0.404 0.989 102 ALA A 103 0.524 0.783 ASP A 104 0.850 0.942 0.555 0.947 104 GLY A 105 0.792 0.955 VAL A 106 0.772 0.742 0.857 PRO A 107 0.981 0.729 0.890 0.830 GLN A 108 0.887 0.829 0.473 0.495 0.646 108 LEU A 109 0.955 0.952 0.858 0.745 109 109 GLY A 110 0.997 0.994 110 110 ASP A 111 0.960 0.953 0.844 0.940 111 111 HIS A 112 0.951 0.981 0.940 0.121 112 112 LEU A 113 0.973 0.559 0.946 0.999 ALA A 114 0.473 0.421 LEU A 115 0.450 0.358 0.785 0.804 GLU A 116 0.604 0.571 0.928 0.983 Ranges: 8 from: A 3 to A 22 from: A 26 to A 31 from: A 34 to A 35 from: A 40 to A 49 from: A 56 to A 62 from: A 69 to A 73 from: A 80 to A 96 from: A 109 to A 112 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[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 1 is: 1.009 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 2 is: 0.711 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 3 is: 0.947 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 4 is: 1.326 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 5 is: 0.861 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 6 is: 1.241 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 7 is: 0.686 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 8 is: 0.680 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 9 is: 1.408 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 10 is: 0.766 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 11 is: 0.529 (*) > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 12 is: 1.055 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 13 is: 0.597 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 14 is: 1.076 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 15 is: 1.042 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 16 is: 0.747 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 17 is: 1.654 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 18 is: 1.008 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 19 is: 1.054 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 20 is: 0.945 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[3..22],[26..31],[34..35],[40..49],[56..62],[69..73],[80..96],[109..112], is: 0.967 > Range of RMSD values to reference struct. is 0.529 to 1.654 > 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[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 1 is: 1.407 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 2 is: 1.240 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 3 is: 1.440 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 4 is: 1.631 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 5 is: 1.311 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 6 is: 1.623 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 7 is: 1.259 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 8 is: 1.185 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 9 is: 1.945 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 10 is: 1.123 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 11 is: 1.019 (*) > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 12 is: 1.400 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 13 is: 1.081 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 14 is: 1.471 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 15 is: 1.522 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 16 is: 1.088 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 17 is: 1.854 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 18 is: 1.454 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 19 is: 1.335 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[34..35],A[40..49],A[56..62],A[69..73],A[80..96],A[109..112],for model 20 is: 1.352 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[3..22],[26..31],[34..35],[40..49],[56..62],[69..73],[80..96],[109..112], is: 1.387 > Range of RMSD values to reference struct. is 1.019 to 1.945 PdbStat> PdbStat> *END* of program detected, BYE! ...