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 `DHR29B_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 20-OCT-09 2KPU > ReadCoordsPdb(): >> TITLE NMR STRUCTURE OF YBBR FAMILY PROTEIN DHAF_0833 (RESIDUES 32-118) FROM > ReadCoordsPdb(): >> TITLE 2 DESULFITOBACTERIUM HAFNIENSE DCB-2: NORTHEAST STRUCTURAL GENOMICS > ReadCoordsPdb(): >> TITLE 3 CONSORTIUM TARGET DHR29B > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `DHR29B_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 DHR29B_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 30440 ATOM records read from file > ReadCoordsPdb(): --> 30440 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 ----------------------------------------------------------------------------------- SER A 1 0.174 0.457 SER A 2 0.854 0.395 0.448 GLN A 3 0.755 0.273 0.563 0.570 0.787 THR A 4 0.898 0.316 0.744 LEU A 5 0.954 0.247 0.610 0.404 ASP A 6 0.962 0.264 0.360 0.479 ARG A 7 0.758 0.615 0.646 0.905 0.492 0.712 0.999 ASP A 8 0.629 0.976 0.496 0.515 PRO A 9 0.988 0.937 0.947 0.897 9 9 THR A 10 0.989 0.981 0.997 10 10 LEU A 11 0.985 0.984 0.598 0.582 11 11 THR A 12 0.985 0.989 0.920 12 12 LEU A 13 0.988 0.965 0.998 0.912 13 13 SER A 14 0.975 0.996 0.459 14 14 LEU A 15 0.996 0.993 0.999 0.999 15 15 ILE A 16 0.991 0.992 0.999 0.999 16 16 ALA A 17 0.988 0.986 17 17 LYS A 18 0.965 0.529 0.929 0.730 0.996 0.579 ASN A 19 0.527 0.857 0.624 0.845 THR A 20 0.883 0.988 0.793 20 PRO A 21 0.992 0.980 0.955 0.915 21 21 ALA A 22 0.987 0.526 ASN A 23 0.512 0.943 0.778 0.607 SER A 24 0.966 0.961 0.871 24 24 MET A 25 0.979 0.991 0.998 0.990 0.848 25 25 ILE A 26 0.991 0.988 0.999 0.999 26 26 MET A 27 0.989 0.969 0.664 0.728 0.478 27 27 THR A 28 0.987 0.980 0.827 28 28 LYS A 29 0.990 0.990 0.690 0.769 0.927 0.521 29 29 LEU A 30 0.990 0.996 0.996 0.756 30 30 PRO A 31 0.989 0.981 0.952 0.921 31 31 SER A 32 0.976 0.985 0.539 32 32 VAL A 33 0.989 0.992 0.510 33 33 ARG A 34 0.990 0.984 0.625 0.973 0.103 0.630 0.998 34 34 VAL A 35 0.984 0.973 0.997 35 35 LYS A 36 0.983 0.993 0.845 0.789 0.742 0.303 36 36 THR A 37 0.991 0.963 0.999 37 37 GLU A 38 0.958 0.969 0.560 0.856 0.383 38 38 GLY A 39 0.979 0.893 39 TYR A 40 0.943 0.962 0.723 0.185 40 40 ASN A 41 0.930 0.961 0.723 0.450 41 41 PRO A 42 0.990 0.931 0.965 0.926 42 42 SER A 43 0.926 0.644 0.325 ILE A 44 0.741 0.968 0.997 0.788 ASN A 45 0.977 0.854 0.459 0.288 45 VAL A 46 0.993 0.982 0.592 46 46 ASN A 47 0.990 0.987 0.663 0.356 47 47 GLU A 48 0.986 0.989 0.569 0.768 0.315 48 48 LEU A 49 0.993 0.996 0.998 0.998 49 49 PHE A 50 0.990 0.988 0.997 0.994 50 50 ALA A 51 0.992 0.987 51 51 TYR A 52 0.985 0.992 0.852 0.230 52 52 VAL A 53 0.998 0.990 0.998 53 53 ASP A 54 0.990 0.990 0.732 0.332 54 54 LEU A 55 0.989 0.932 0.981 0.777 55 55 SER A 56 0.989 0.523 0.428 GLY A 57 0.416 0.598 SER A 58 0.752 0.705 0.546 GLU A 59 0.956 0.972 0.705 0.610 0.194 59 59 PRO A 60 0.988 0.900 0.946 0.888 60 GLY A 61 0.879 0.976 61 GLU A 62 0.974 0.995 0.582 0.944 0.429 62 62 HIS A 63 0.990 0.989 0.843 0.314 63 63 ASP A 64 0.994 0.986 0.712 0.715 64 64 TYR A 65 0.987 0.983 0.995 0.995 65 65 GLU A 66 0.989 0.993 0.548 0.986 0.298 66 66 VAL A 67 0.993 0.990 1.000 67 67 LYS A 68 0.988 0.970 0.686 0.922 0.932 0.380 68 68 VAL A 69 0.982 0.991 0.999 69 69 GLU A 70 0.994 0.989 0.718 0.479 0.296 70 70 PRO A 71 0.992 0.978 0.938 0.858 71 71 ILE A 72 0.974 0.993 0.999 0.545 72 72 PRO A 73 0.988 0.730 0.935 0.868 ASN A 74 0.626 0.917 0.591 0.557 ILE A 75 0.940 0.990 0.997 0.486 75 75 LYS A 76 0.995 0.976 0.525 0.990 0.788 0.420 76 76 ILE A 77 0.980 0.989 0.998 0.999 77 77 VAL A 78 0.987 0.995 1.000 78 78 GLU A 79 0.980 0.977 0.581 0.625 0.453 79 79 ILE A 80 0.966 0.849 0.793 1.000 80 SER A 81 0.927 0.985 0.611 81 81 PRO A 82 0.990 0.963 0.959 0.918 82 82 ARG A 83 0.966 0.984 0.896 0.994 0.874 0.907 0.998 83 83 VAL A 84 0.992 0.990 0.999 84 84 VAL A 85 0.994 0.994 0.999 85 85 THR A 86 0.992 0.996 0.998 86 86 LEU A 87 0.993 0.990 0.999 1.000 87 87 GLN A 88 0.994 0.987 0.552 0.878 0.809 88 88 LEU A 89 0.984 0.982 0.998 0.997 89 89 GLU A 90 0.974 0.971 0.728 0.340 0.285 90 90 HIS A 91 0.988 0.944 0.856 0.144 91 91 HIS A 92 0.947 0.458 0.883 0.416 HIS A 93 0.915 0.556 0.765 0.261 HIS A 94 0.640 0.200 0.554 0.363 HIS A 95 0.868 0.171 0.445 0.134 HIS A 96 0.585 0.542 0.364 Ranges: 7 from: A 9 to A 17 from: A 24 to A 38 from: A 40 to A 42 from: A 46 to A 55 from: A 62 to A 72 from: A 75 to A 79 from: A 81 to A 91 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[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 1 is: 0.601 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 2 is: 0.499 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 3 is: 0.491 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 4 is: 0.847 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 5 is: 0.488 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 6 is: 0.776 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 7 is: 0.646 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 8 is: 0.830 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 9 is: 0.598 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 10 is: 0.550 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 11 is: 0.533 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 12 is: 0.585 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 13 is: 0.597 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 14 is: 0.423 (*) > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 15 is: 0.504 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 16 is: 0.517 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 17 is: 0.466 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 18 is: 0.501 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 19 is: 0.472 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 20 is: 0.709 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..17],[24..38],[40..42],[46..55],[62..72],[75..79],[81..91], is: 0.582 > Range of RMSD values to reference struct. is 0.423 to 0.847 > 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[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 1 is: 1.132 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 2 is: 0.958 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 3 is: 0.882 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 4 is: 1.245 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 5 is: 0.939 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 6 is: 1.154 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 7 is: 1.212 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 8 is: 1.302 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 9 is: 1.016 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 10 is: 1.007 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 11 is: 1.022 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 12 is: 1.002 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 13 is: 1.123 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 14 is: 0.924 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 15 is: 0.873 (*) > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 16 is: 1.102 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 17 is: 0.899 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 18 is: 1.003 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 19 is: 0.905 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..38],A[40..42],A[46..55],A[62..72],A[75..79],A[81..91],for model 20 is: 1.169 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..17],[24..38],[40..42],[46..55],[62..72],[75..79],[81..91], is: 1.043 > Range of RMSD values to reference struct. is 0.873 to 1.302 PdbStat> PdbStat> *END* of program detected, BYE! ...