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_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 96 SER SER GLN THR LEU ASP ARG ASP PRO THR LEU THR LEU 1 > ReadCoordsPdb(): Counting models in file `DHR29B_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 DHR29B_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 30300 ATOM records read from file > ReadCoordsPdb(): --> 30300 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 0.141 0.410 SER A 2 0.835 0.466 0.599 GLN A 3 0.745 0.336 0.595 0.151 0.734 THR A 4 0.903 0.202 0.333 LEU A 5 0.950 0.175 0.729 0.549 ASP A 6 0.951 0.262 0.666 0.973 ARG A 7 0.757 0.669 0.577 0.927 0.693 0.868 1.000 ASP A 8 0.625 0.951 0.628 0.922 PRO A 9 0.982 0.955 0.900 0.837 9 9 THR A 10 0.983 0.994 1.000 10 10 LEU A 11 0.979 0.974 0.584 0.592 11 11 THR A 12 0.979 0.995 1.000 12 12 LEU A 13 0.989 0.991 0.917 0.713 13 13 SER A 14 0.989 0.982 0.224 14 14 LEU A 15 0.964 0.992 0.928 0.931 15 15 ILE A 16 0.990 0.959 0.420 1.000 16 16 ALA A 17 0.978 0.911 17 17 LYS A 18 0.892 0.508 0.878 0.555 0.870 0.939 ASN A 19 0.516 0.867 0.640 0.862 THR A 20 0.840 0.994 0.926 20 PRO A 21 0.985 0.992 0.902 0.834 21 21 ALA A 22 0.984 0.532 ASN A 23 0.530 0.914 0.912 0.966 SER A 24 0.936 0.924 0.406 24 24 MET A 25 0.944 0.982 0.525 0.723 0.349 25 25 ILE A 26 0.974 0.997 0.999 0.773 26 26 MET A 27 0.986 0.961 0.795 0.695 0.301 27 27 THR A 28 0.980 0.981 0.922 28 28 LYS A 29 0.994 0.991 0.871 1.000 1.000 1.000 29 29 LEU A 30 0.990 0.998 0.980 0.478 30 30 PRO A 31 0.995 0.974 0.937 0.888 31 31 SER A 32 0.979 0.985 0.431 32 32 VAL A 33 0.993 0.984 0.853 33 33 ARG A 34 0.993 0.967 0.823 0.997 0.709 0.996 1.000 34 34 VAL A 35 0.965 0.987 0.924 35 35 LYS A 36 0.987 0.998 0.691 0.996 0.873 0.998 36 36 THR A 37 0.998 0.991 0.998 37 37 GLU A 38 0.982 0.994 0.872 0.999 0.999 38 38 GLY A 39 0.960 0.936 39 39 TYR A 40 0.902 0.977 0.533 0.915 40 40 ASN A 41 0.976 0.961 0.474 0.916 41 41 PRO A 42 0.997 0.960 0.999 0.999 42 42 SER A 43 0.943 0.634 0.660 ILE A 44 0.745 0.973 0.924 0.338 ASN A 45 0.956 0.867 0.530 0.947 45 VAL A 46 0.969 0.982 0.523 46 46 ASN A 47 0.995 0.995 1.000 1.000 47 47 GLU A 48 0.980 0.986 0.999 0.921 0.957 48 48 LEU A 49 0.996 0.965 0.846 0.789 49 49 PHE A 50 0.956 0.989 0.488 0.997 50 50 ALA A 51 0.989 0.985 51 51 TYR A 52 0.966 0.984 0.539 0.995 52 52 VAL A 53 0.978 0.987 0.703 53 53 ASP A 54 0.988 0.996 1.000 0.987 54 54 LEU A 55 0.976 0.887 0.981 0.861 55 SER A 56 0.984 0.471 0.268 GLY A 57 0.324 0.512 SER A 58 0.708 0.539 0.400 GLU A 59 0.892 0.981 0.622 0.926 0.946 59 PRO A 60 0.991 0.976 0.913 0.837 60 60 GLY A 61 0.988 0.998 61 61 GLU A 62 0.997 0.993 0.594 1.000 0.975 62 62 HIS A 63 0.998 0.994 0.929 0.900 63 63 ASP A 64 0.997 0.990 0.817 0.985 64 64 TYR A 65 0.992 0.986 0.998 0.999 65 65 GLU A 66 0.996 0.998 1.000 0.999 0.982 66 66 VAL A 67 0.982 0.998 1.000 67 67 LYS A 68 0.995 0.944 1.000 0.996 0.998 0.995 68 68 VAL A 69 0.963 0.995 0.854 69 69 GLU A 70 0.996 0.992 0.628 0.534 0.904 70 70 PRO A 71 0.995 0.995 0.965 0.940 71 71 ILE A 72 0.985 0.988 0.999 0.964 72 72 PRO A 73 0.989 0.646 0.933 0.888 ASN A 74 0.608 0.831 0.935 0.974 ILE A 75 0.867 0.995 0.877 0.998 75 LYS A 76 0.993 0.991 0.795 1.000 0.999 0.998 76 76 ILE A 77 0.992 0.998 0.999 0.837 77 77 VAL A 78 0.999 0.999 1.000 78 78 GLU A 79 0.982 0.992 0.733 0.929 0.944 79 79 ILE A 80 0.990 0.811 0.703 0.999 80 SER A 81 0.857 0.997 1.000 81 PRO A 82 0.999 0.995 0.986 0.970 82 82 ARG A 83 0.977 0.995 0.924 0.657 0.998 0.734 1.000 83 83 VAL A 84 0.992 0.982 0.783 84 84 VAL A 85 0.989 0.997 0.786 85 85 THR A 86 0.996 0.997 1.000 86 86 LEU A 87 0.993 0.998 0.921 0.933 87 87 GLN A 88 0.995 0.994 1.000 0.999 0.994 88 88 LEU A 89 0.988 0.975 0.786 0.533 89 89 GLU A 90 0.977 0.976 0.712 0.589 0.947 90 90 HIS A 91 0.984 0.974 0.781 0.701 91 91 HIS A 92 0.960 0.263 0.855 0.414 HIS A 93 0.902 0.516 0.513 0.698 HIS A 94 0.667 0.269 0.433 0.435 HIS A 95 0.877 0.111 0.395 0.284 HIS A 96 0.642 0.685 0.553 Ranges: 6 from: A 9 to A 17 from: A 24 to A 42 from: A 46 to A 54 from: A 60 to A 72 from: A 76 to A 79 from: A 82 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..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 1 is: 0.497 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 2 is: 0.514 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 3 is: 0.820 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 4 is: 0.543 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 5 is: 0.783 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 6 is: 0.619 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 7 is: 1.042 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 8 is: 0.590 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 9 is: 0.918 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 10 is: 0.560 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 11 is: 0.916 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 12 is: 0.507 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 13 is: 0.670 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 14 is: 0.545 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 15 is: 0.927 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 16 is: 0.669 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 17 is: 1.049 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 18 is: 0.757 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 19 is: 0.828 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 20 is: 0.445 (*) > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..17],[24..42],[46..54],[60..72],[76..79],[82..91], is: 0.710 > Range of RMSD values to reference struct. is 0.445 to 1.049 > 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..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 1 is: 1.082 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 2 is: 0.896 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 3 is: 1.209 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 4 is: 1.060 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 5 is: 1.251 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 6 is: 1.146 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 7 is: 1.407 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 8 is: 0.938 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 9 is: 1.324 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 10 is: 1.028 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 11 is: 1.359 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 12 is: 0.799 (*) > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 13 is: 1.057 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 14 is: 1.183 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 15 is: 1.227 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 16 is: 0.964 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 17 is: 1.487 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 18 is: 1.157 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 19 is: 1.313 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..54],A[60..72],A[76..79],A[82..91],for model 20 is: 0.963 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..17],[24..42],[46..54],[60..72],[76..79],[82..91], is: 1.142 > Range of RMSD values to reference struct. is 0.799 to 1.487 PdbStat> PdbStat> *END* of program detected, BYE! ...