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 `STR65_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 19 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 18 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 109 VAL ASN PHE LYS ASP LYS SER MET PRO THR ALA ILE GLU 1 > ReadCoordsPdb(): Counting models in file `STR65_R3Cons_em_bcr3.pdb'; Model: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 > ReadCoordsPdb(): After scanning there is(are) 18 model(s) > ReadCoordsPdb(): what model do you want [(1 to 18) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file STR65_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (18) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 30600 ATOM records read from file > ReadCoordsPdb(): --> 30600 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 ----------------------------------------------------------------------------------- VAL A 1 0.181 0.533 ASN A 2 0.795 0.328 0.474 0.676 PHE A 3 0.390 0.217 0.582 0.770 LYS A 4 0.336 0.542 0.415 0.791 0.778 0.920 ASP A 5 0.558 0.619 0.476 0.911 LYS A 6 0.701 0.105 0.483 0.918 0.998 0.998 SER A 7 0.303 0.640 0.376 MET A 8 0.651 0.769 0.491 0.063 0.287 PRO A 9 0.984 0.502 0.912 0.855 THR A 10 0.674 0.279 0.831 ALA A 11 0.975 0.981 11 11 ILE A 12 0.993 0.992 0.998 0.556 12 12 GLU A 13 0.989 0.991 0.595 0.704 0.900 13 13 LYS A 14 0.996 0.999 0.639 0.337 0.998 0.997 14 14 ALA A 15 0.998 0.999 15 15 LEU A 16 0.997 0.996 0.781 0.619 16 16 ASP A 17 0.998 1.000 0.794 0.864 17 17 PHE A 18 0.990 0.995 0.982 0.290 18 18 ILE A 19 0.986 0.991 0.999 0.912 19 19 GLY A 20 0.960 0.801 20 GLY A 21 0.255 0.338 MET A 22 0.483 0.503 0.427 0.370 0.060 ASN A 23 0.150 0.427 0.676 0.876 THR A 24 0.714 0.149 0.397 SER A 25 0.288 0.513 0.214 ALA A 26 0.696 0.755 SER A 27 0.854 0.839 0.287 27 VAL A 28 0.822 0.320 0.679 PRO A 29 0.948 0.601 0.857 0.819 HIS A 30 0.476 0.546 0.760 0.273 SER A 31 0.959 0.967 0.760 31 31 MET A 32 0.938 0.960 0.465 0.329 0.180 32 32 ASP A 33 0.982 0.957 0.507 0.899 33 33 GLU A 34 0.985 0.993 0.788 0.995 0.942 34 34 SER A 35 0.995 0.990 0.752 35 35 THR A 36 0.999 0.995 0.999 36 36 ALA A 37 0.999 0.997 37 37 LYS A 38 0.999 0.999 0.763 0.998 0.719 0.998 38 38 GLY A 39 1.000 0.998 39 39 ILE A 40 0.999 0.998 1.000 1.000 40 40 LEU A 41 0.999 0.998 0.754 0.503 41 41 LYS A 42 0.995 0.997 0.702 0.996 0.429 0.654 42 42 TYR A 43 0.999 0.997 0.998 0.998 43 43 LEU A 44 0.999 0.999 0.999 0.999 44 44 HIS A 45 0.998 0.997 0.802 0.530 45 45 ASP A 46 0.999 0.998 1.000 1.000 46 46 LEU A 47 0.998 0.993 0.999 0.999 47 47 GLY A 48 0.992 0.986 48 48 VAL A 49 0.995 0.995 0.999 49 49 PRO A 50 0.998 0.926 1.000 0.999 50 50 VAL A 51 0.982 0.995 1.000 51 51 SER A 52 0.986 0.993 0.999 52 52 PRO A 53 0.993 0.995 0.907 0.820 53 53 GLU A 54 0.998 0.999 0.640 0.926 0.980 54 54 VAL A 55 0.998 0.992 0.746 55 55 VAL A 56 0.999 0.999 1.000 56 56 VAL A 57 0.999 0.997 1.000 57 57 ALA A 58 0.999 0.998 58 58 ARG A 59 0.999 0.998 0.778 0.636 0.621 0.668 1.000 59 59 GLY A 60 0.998 0.997 60 60 GLU A 61 0.999 0.998 1.000 0.675 0.940 61 61 GLN A 62 0.998 0.991 0.717 0.998 0.851 62 62 GLU A 63 0.988 0.987 0.647 0.410 0.834 63 63 GLY A 64 0.983 0.782 TRP A 65 0.720 0.602 0.997 0.986 ASN A 66 0.609 0.988 0.687 0.911 PRO A 67 0.992 0.995 0.975 0.965 67 67 GLU A 68 0.994 0.992 0.998 0.913 0.970 68 68 PHE A 69 0.998 0.997 0.944 0.939 69 69 THR A 70 0.999 0.998 1.000 70 70 LYS A 71 0.999 0.999 1.000 0.999 0.932 1.000 71 71 LYS A 72 0.999 0.999 1.000 0.997 0.864 0.625 72 72 VAL A 73 1.000 1.000 1.000 73 73 ALA A 74 0.999 0.999 74 74 GLY A 75 1.000 0.999 75 75 TRP A 76 1.000 0.999 0.999 0.999 76 76 ALA A 77 1.000 0.999 77 77 GLU A 78 0.998 0.999 1.000 1.000 1.000 78 78 LYS A 79 0.999 0.998 1.000 0.928 1.000 1.000 79 79 VAL A 80 0.999 0.998 1.000 80 80 ALA A 81 0.997 0.998 81 81 SER A 82 0.998 0.999 1.000 82 82 GLY A 83 0.989 0.988 83 83 ASN A 84 0.992 0.741 0.999 0.948 ARG A 85 0.645 0.929 0.500 0.998 0.874 0.813 1.000 ILE A 86 0.877 0.785 0.920 0.999 LEU A 87 0.891 0.853 0.636 0.670 87 ILE A 88 0.799 0.325 0.623 0.843 LYS A 89 0.366 0.830 0.918 0.696 0.823 0.847 ASN A 90 0.860 0.707 0.505 0.347 PRO A 91 0.978 0.751 0.905 0.844 GLU A 92 0.484 0.422 0.482 0.700 0.929 TYR A 93 0.362 0.677 0.997 0.589 PHE A 94 0.672 0.771 0.514 0.865 SER A 95 0.981 0.984 0.637 95 95 THR A 96 0.995 0.996 0.843 96 96 TYR A 97 0.998 0.998 0.998 0.999 97 97 MET A 98 0.998 0.995 0.999 0.993 0.530 98 98 GLN A 99 0.998 0.990 0.555 0.998 0.954 99 99 GLU A 100 0.999 0.998 1.000 0.750 0.952 100 100 GLN A 101 0.999 0.993 0.801 0.747 0.848 101 101 LEU A 102 0.998 0.999 0.999 0.999 102 102 LYS A 103 0.999 0.998 1.000 1.000 1.000 1.000 103 103 GLU A 104 1.000 0.999 1.000 1.000 1.000 104 104 LEU A 105 0.998 0.995 0.733 0.526 105 105 VAL A 106 0.996 0.998 0.999 106 106 LEU A 107 0.996 0.988 0.857 0.780 107 107 GLU A 108 0.996 0.980 0.902 0.836 0.961 108 108 HIS A 109 0.434 0.565 0.433 Ranges: 4 from: A 11 to A 19 from: A 31 to A 63 from: A 67 to A 83 from: A 95 to A 108 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[11..19],A[31..63],A[67..83],A[95..108],for model 1 is: 0.940 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 2 is: 0.964 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 3 is: 0.705 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 4 is: 0.822 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 5 is: 0.793 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 6 is: 0.827 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 7 is: 0.848 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 8 is: 0.647 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 9 is: 0.941 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 10 is: 0.925 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 11 is: 0.771 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 12 is: 0.807 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 13 is: 0.597 (*) > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 14 is: 0.661 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 15 is: 0.888 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 16 is: 0.683 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 17 is: 0.830 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 18 is: 0.740 > > Kabsch RMSD statistics for 18 structures: > Mean RMSD using as refer. str. `average' for res.[11..19],[31..63],[67..83],[95..108], is: 0.799 > Range of RMSD values to reference struct. is 0.597 to 0.964 > 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[11..19],A[31..63],A[67..83],A[95..108],for model 1 is: 1.198 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 2 is: 1.263 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 3 is: 0.914 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 4 is: 1.077 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 5 is: 1.071 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 6 is: 1.044 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 7 is: 1.108 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 8 is: 0.917 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 9 is: 1.211 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 10 is: 1.171 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 11 is: 0.967 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 12 is: 1.093 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 13 is: 0.910 (*) > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 14 is: 0.921 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 15 is: 1.160 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 16 is: 0.963 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 17 is: 0.985 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..63],A[67..83],A[95..108],for model 18 is: 1.056 > > Kabsch RMSD statistics for 18 structures: > Mean RMSD using as refer. str. `average' for res.[11..19],[31..63],[67..83],[95..108], is: 1.057 > Range of RMSD values to reference struct. is 0.910 to 1.263 PdbStat> PdbStat> *END* of program detected, BYE! ...