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 `MRR110B_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 98 MET ASN TYR LYS ILE SER GLU LEU MET PRO ASN LEU SER 1 > ReadCoordsPdb(): Counting models in file `MRR110B_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 MRR110B_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 30560 ATOM records read from file > ReadCoordsPdb(): --> 30560 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 0.964 0.928 0.779 0.910 ASN A 2 0.998 0.980 0.711 0.972 2 2 TYR A 3 0.983 0.997 0.999 0.918 3 3 LYS A 4 0.995 0.994 1.000 0.926 0.933 0.999 4 4 ILE A 5 0.999 0.998 1.000 1.000 5 5 SER A 6 0.999 0.999 0.916 6 6 GLU A 7 0.998 0.995 0.998 0.912 0.947 7 7 LEU A 8 0.995 0.990 0.999 0.999 8 8 MET A 9 0.969 0.998 0.449 0.863 0.459 9 9 PRO A 10 0.999 0.997 0.957 0.910 10 10 ASN A 11 0.998 0.994 0.675 0.824 11 11 LEU A 12 0.988 0.997 1.000 1.000 12 12 SER A 13 0.995 0.995 0.936 13 13 GLY A 14 0.998 0.997 14 14 THR A 15 0.998 0.999 1.000 15 15 ILE A 16 0.997 0.987 0.805 0.999 16 16 ASN A 17 0.982 0.997 0.656 0.893 17 17 ALA A 18 0.998 0.998 18 18 GLU A 19 0.996 0.998 0.931 1.000 0.956 19 19 VAL A 20 0.999 0.999 1.000 20 20 VAL A 21 0.996 0.997 1.000 21 21 ALA A 22 0.996 0.974 22 22 ALA A 23 0.947 0.956 23 23 TYR A 24 0.963 0.989 0.788 0.996 24 24 PRO A 25 0.992 0.994 0.920 0.846 25 25 LYS A 26 0.995 0.991 0.559 0.993 0.738 0.988 26 26 LYS A 27 0.990 0.981 0.928 0.872 0.999 1.000 27 27 GLU A 28 0.974 0.994 0.855 0.936 0.915 28 28 PHE A 29 0.993 0.998 0.917 0.999 29 29 SER A 30 0.988 0.967 0.716 30 30 ARG A 31 0.940 0.977 0.644 0.811 0.521 0.561 1.000 31 31 LYS A 32 0.991 0.985 0.811 1.000 1.000 1.000 32 32 ASP A 33 0.973 0.905 0.386 0.994 33 33 GLY A 34 0.920 0.941 34 34 THR A 35 0.851 0.957 0.767 35 LYS A 36 0.677 0.777 0.638 0.999 0.999 0.999 GLY A 37 0.891 0.919 37 GLN A 38 0.980 0.996 0.996 0.620 0.602 38 38 LEU A 39 0.997 0.985 0.850 0.740 39 39 LYS A 40 0.986 0.996 0.999 0.997 0.896 0.874 40 40 SER A 41 0.997 0.989 0.503 41 41 LEU A 42 0.987 0.934 0.397 0.795 42 42 PHE A 43 0.960 0.997 0.868 0.980 43 43 LEU A 44 0.999 0.999 0.993 0.949 44 44 LYS A 45 0.999 0.997 1.000 0.999 1.000 1.000 45 45 ASP A 46 0.978 0.985 0.486 0.844 46 46 ASP A 47 0.993 0.986 0.914 0.999 47 47 THR A 48 0.978 0.989 0.999 48 48 GLY A 49 0.964 0.989 49 49 SER A 50 0.980 0.996 0.930 50 50 ILE A 51 0.997 0.990 0.918 0.999 51 51 ARG A 52 0.989 0.989 0.871 0.997 0.615 0.880 1.000 52 52 GLY A 53 0.989 0.989 53 53 THR A 54 0.998 0.996 0.606 54 54 LEU A 55 0.999 0.986 0.999 1.000 55 55 TRP A 56 0.990 0.994 1.000 0.998 56 56 ASN A 57 0.997 0.989 1.000 1.000 57 57 GLU A 58 0.997 0.995 0.820 0.923 0.976 58 58 LEU A 59 0.997 0.996 0.999 0.999 59 59 ALA A 60 0.998 0.994 60 60 ASP A 61 0.991 0.993 0.913 0.952 61 61 PHE A 62 0.997 0.997 0.997 0.999 62 62 GLU A 63 0.975 0.985 0.700 0.738 0.925 63 63 VAL A 64 0.947 0.973 0.314 64 64 LYS A 65 0.987 0.993 0.996 0.615 0.998 0.997 65 65 LYS A 66 0.986 0.992 0.743 1.000 0.999 1.000 66 66 GLY A 67 0.988 0.972 67 67 ASP A 68 0.951 0.991 0.910 0.957 68 68 ILE A 69 0.994 0.994 0.999 0.691 69 69 ALA A 70 0.994 0.992 70 70 GLU A 71 0.996 0.998 1.000 1.000 1.000 71 71 VAL A 72 0.999 0.998 1.000 72 72 SER A 73 0.995 0.999 0.694 73 73 GLY A 74 0.997 0.999 74 74 TYR A 75 0.997 0.994 0.670 0.993 75 75 VAL A 76 0.995 0.995 0.929 76 76 LYS A 77 0.964 0.985 0.139 0.998 0.991 0.892 77 77 GLN A 78 0.959 0.974 0.688 0.934 0.979 78 78 GLY A 79 0.819 0.839 79 TYR A 80 0.945 0.379 0.478 0.974 SER A 81 0.340 0.783 0.558 GLY A 82 0.815 0.817 82 LEU A 83 0.905 0.951 0.567 0.498 83 83 GLU A 84 0.978 0.964 0.105 0.801 0.761 84 84 ILE A 85 0.973 0.993 0.660 0.958 85 85 SER A 86 0.995 0.997 1.000 86 86 VAL A 87 0.999 0.999 1.000 87 87 ASP A 88 0.999 0.999 1.000 1.000 88 88 ASN A 89 0.996 0.975 0.565 0.848 89 89 ILE A 90 0.981 1.000 0.999 1.000 90 90 GLY A 91 0.998 0.991 91 91 ILE A 92 0.994 0.998 0.999 0.564 92 92 ILE A 93 0.994 0.995 1.000 1.000 93 93 GLU A 94 0.915 0.841 0.585 0.780 0.952 94 LYS A 95 0.956 0.750 0.520 0.999 0.997 0.999 SER A 96 0.774 0.784 0.379 LEU A 97 0.888 0.248 0.393 0.669 GLU A 98 0.842 0.594 0.931 0.983 Ranges: 3 from: A 2 to A 34 from: A 38 to A 78 from: A 83 to A 93 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[2..34],A[38..78],A[83..93],for model 1 is: 0.632 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 2 is: 0.506 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 3 is: 0.371 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 4 is: 0.397 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 5 is: 0.770 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 6 is: 0.547 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 7 is: 0.479 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 8 is: 0.395 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 9 is: 0.338 (*) > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 10 is: 0.342 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 11 is: 0.567 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 12 is: 0.865 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 13 is: 1.012 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 14 is: 0.437 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 15 is: 0.358 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 16 is: 0.602 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 17 is: 0.808 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 18 is: 1.376 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 19 is: 0.709 > Kabsch RMSD of backbone atoms in res. A[2..34],A[38..78],A[83..93],for model 20 is: 0.596 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..34],[38..78],[83..93], is: 0.605 > Range of RMSD values to reference struct. is 0.338 to 1.376 > 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[2..34],A[38..78],A[83..93],for model 1 is: 0.920 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 2 is: 0.852 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 3 is: 0.984 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 4 is: 0.771 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 5 is: 1.342 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 6 is: 0.814 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 7 is: 0.861 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 8 is: 0.764 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 9 is: 0.642 (*) > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 10 is: 0.748 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 11 is: 0.828 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 12 is: 1.338 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 13 is: 1.460 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 14 is: 0.820 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 15 is: 0.833 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 16 is: 0.996 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 17 is: 1.388 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 18 is: 1.707 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 19 is: 1.049 > Kabsch RMSD of heavy atoms in res. A[2..34],A[38..78],A[83..93],for model 20 is: 0.892 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..34],[38..78],[83..93], is: 1.000 > Range of RMSD values to reference struct. is 0.642 to 1.707 PdbStat> PdbStat> *END* of program detected, BYE! ...