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 `LKR112_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 114 MET LYS ASN THR GLY ASP GLU VAL VAL ALA ILE ILE SER 1 > ReadCoordsPdb(): Counting models in file `LKR112_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 LKR112_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 35900 ATOM records read from file > ReadCoordsPdb(): --> 35900 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 0.360 0.800 0.507 0.304 LYS A 2 0.610 0.583 0.519 0.999 1.000 0.997 ASN A 3 0.894 0.840 0.727 0.936 3 THR A 4 0.927 0.895 0.925 4 GLY A 5 0.842 0.835 5 ASP A 6 0.910 0.839 0.723 0.949 6 GLU A 7 0.966 0.996 0.572 0.929 0.806 7 7 VAL A 8 0.992 0.988 0.524 8 8 VAL A 9 0.999 0.998 0.842 9 9 ALA A 10 0.998 0.998 10 10 ILE A 11 0.998 0.998 0.999 0.759 11 11 ILE A 12 0.997 0.999 1.000 0.963 12 12 SER A 13 0.997 0.986 0.699 13 13 GLN A 14 0.976 0.997 0.999 0.931 0.975 14 14 ASN A 15 0.999 0.994 0.847 0.893 15 15 GLY A 16 0.995 0.983 16 16 LYS A 17 0.975 0.993 0.658 0.929 0.999 0.999 17 17 VAL A 18 0.997 0.999 1.000 18 18 ILE A 19 1.000 0.999 1.000 1.000 19 19 ARG A 20 0.996 0.981 0.859 0.753 0.613 0.767 1.000 20 20 GLU A 21 0.988 0.997 0.701 0.999 1.000 21 21 ILE A 22 0.999 0.998 1.000 1.000 22 22 PRO A 23 1.000 0.998 1.000 1.000 23 23 LEU A 24 0.999 0.999 1.000 1.000 24 24 THR A 25 0.997 0.998 1.000 25 25 GLY A 26 0.996 0.990 26 26 HIS A 27 0.998 0.944 0.999 0.991 27 27 LYS A 28 0.950 0.928 0.642 0.858 0.999 0.926 28 28 GLY A 29 0.915 0.981 29 29 ASN A 30 0.984 0.958 0.588 0.911 30 30 GLU A 31 0.935 0.995 0.933 0.934 0.846 31 31 GLN A 32 0.994 0.997 0.999 0.999 0.832 32 32 PHE A 33 0.995 0.996 0.771 0.991 33 33 THR A 34 0.998 0.997 1.000 34 34 ILE A 35 0.987 0.993 1.000 0.921 35 35 LYS A 36 0.969 0.949 0.698 0.999 1.000 0.997 36 36 GLY A 37 0.955 0.884 37 LYS A 38 0.911 0.884 0.656 0.923 0.999 0.941 38 GLY A 39 0.836 0.731 ALA A 40 0.707 0.935 GLN A 41 0.947 0.836 0.933 0.738 0.717 41 TYR A 42 0.912 0.982 0.683 0.772 42 42 ASN A 43 0.991 0.971 0.604 0.723 43 43 LEU A 44 0.984 0.997 1.000 1.000 44 44 MET A 45 0.994 0.997 0.998 0.934 0.759 45 45 GLU A 46 0.993 0.998 0.999 0.996 0.977 46 46 VAL A 47 0.999 0.980 1.000 47 47 ASP A 48 0.958 0.900 0.991 0.929 48 48 GLY A 49 0.876 0.316 GLU A 50 0.352 0.994 0.847 0.996 0.570 ARG A 51 0.993 0.999 0.931 0.998 0.928 0.952 0.999 51 51 ILE A 52 0.997 0.999 1.000 1.000 52 52 ARG A 53 0.992 0.997 0.993 0.884 0.866 0.659 0.999 53 53 ILE A 54 0.996 0.998 1.000 0.999 54 54 LYS A 55 0.998 0.995 0.998 0.998 0.997 0.844 55 55 GLU A 56 0.971 0.995 0.684 0.999 0.933 56 56 ASP A 57 0.976 0.908 0.507 0.704 57 57 ASN A 58 0.956 0.900 0.744 0.866 58 58 SER A 59 0.823 0.980 0.555 59 PRO A 60 0.991 0.993 0.920 0.864 60 60 ASP A 61 0.983 0.967 0.997 0.944 61 61 GLN A 62 0.998 0.994 0.999 0.613 0.779 62 62 VAL A 63 0.996 0.993 1.000 63 63 GLY A 64 0.994 0.991 64 64 VAL A 65 0.997 0.995 0.941 65 65 LYS A 66 0.996 0.984 0.999 0.998 0.999 0.995 66 66 MET A 67 0.996 0.999 0.936 0.559 0.189 67 67 GLY A 68 0.995 0.974 68 68 TRP A 69 0.996 0.999 1.000 0.998 69 69 LYS A 70 0.999 0.997 0.998 1.000 1.000 0.999 70 70 SER A 71 0.988 0.935 0.681 71 71 LYS A 72 0.974 0.988 0.848 1.000 1.000 1.000 72 72 ALA A 73 0.992 0.921 73 73 GLY A 74 0.948 0.978 74 74 ASP A 75 0.995 0.990 1.000 0.999 75 75 THR A 76 0.995 0.977 0.448 76 76 ILE A 77 0.981 0.996 1.000 0.848 77 77 VAL A 78 0.997 0.997 0.927 78 78 CYS A 79 0.994 0.994 0.932 79 79 LEU A 80 0.999 0.998 0.586 0.543 80 80 PRO A 81 0.999 0.997 0.984 0.966 81 81 HIS A 82 0.994 0.998 0.998 0.629 82 82 LYS A 83 0.999 0.996 0.999 0.927 0.997 0.998 83 83 VAL A 84 0.997 0.993 1.000 84 84 PHE A 85 0.989 0.992 0.418 0.986 85 85 VAL A 86 0.997 0.990 1.000 86 86 GLU A 87 0.989 0.995 0.804 0.996 0.918 87 87 ILE A 88 0.998 0.989 1.000 0.779 88 88 LYS A 89 0.982 0.997 0.689 0.938 0.933 0.949 89 89 SER A 90 0.989 0.992 0.692 90 90 THR A 91 0.991 0.995 0.999 91 91 GLN A 92 0.978 0.829 0.997 0.861 0.967 92 LYS A 93 0.818 0.855 0.552 0.926 0.999 0.999 93 ASP A 94 0.723 0.820 0.529 0.910 SER A 95 0.827 0.514 0.397 LYS A 96 0.890 0.821 0.619 0.612 0.998 0.937 96 ASP A 97 0.982 0.960 0.621 0.977 97 97 PRO A 98 0.989 0.845 0.898 0.814 98 ASP A 99 0.809 0.668 0.597 0.968 THR A 100 0.910 0.399 0.270 ASP A 101 0.699 0.775 0.718 0.992 LEU A 102 0.867 0.907 0.337 0.573 102 ILE A 103 0.937 0.716 0.921 0.765 VAL A 104 0.849 0.963 0.926 104 PRO A 105 0.987 0.905 0.897 0.815 105 105 ASN A 106 0.792 0.667 0.375 0.837 LEU A 107 0.969 0.769 0.582 0.610 GLU A 108 0.961 0.757 0.612 0.805 0.934 HIS A 109 0.862 0.672 0.429 0.460 HIS A 110 0.888 0.472 0.337 0.415 HIS A 111 0.534 0.505 0.564 0.398 HIS A 112 0.860 0.683 0.479 0.632 HIS A 113 0.839 0.434 0.432 0.536 HIS A 114 0.744 0.601 0.624 Ranges: 4 from: A 7 to A 36 from: A 42 to A 48 from: A 51 to A 58 from: A 60 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[7..36],A[42..48],A[51..58],A[60..91],for model 1 is: 0.865 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 2 is: 0.632 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 3 is: 0.401 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 4 is: 0.559 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 5 is: 0.819 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 6 is: 0.638 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 7 is: 0.856 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 8 is: 0.689 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 9 is: 0.680 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 10 is: 0.503 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 11 is: 0.926 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 12 is: 0.629 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 13 is: 0.312 (*) > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 14 is: 0.461 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 15 is: 0.479 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 16 is: 0.506 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 17 is: 0.515 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 18 is: 0.458 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 19 is: 0.637 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 20 is: 0.503 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[7..36],[42..48],[51..58],[60..91], is: 0.603 > Range of RMSD values to reference struct. is 0.312 to 0.926 > 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[7..36],A[42..48],A[51..58],A[60..91],for model 1 is: 1.345 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 2 is: 0.900 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 3 is: 0.807 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 4 is: 1.113 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 5 is: 1.234 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 6 is: 0.902 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 7 is: 1.386 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 8 is: 1.047 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 9 is: 1.153 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 10 is: 0.795 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 11 is: 1.149 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 12 is: 1.023 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 13 is: 0.626 (*) > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 14 is: 0.871 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 15 is: 0.751 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 16 is: 0.770 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 17 is: 0.780 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 18 is: 0.803 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 19 is: 1.139 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..58],A[60..91],for model 20 is: 0.811 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[7..36],[42..48],[51..58],[60..91], is: 0.970 > Range of RMSD values to reference struct. is 0.626 to 1.386 PdbStat> PdbStat> *END* of program detected, BYE! ...