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 `HR4527E_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 91 MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET LEU THR 1 > ReadCoordsPdb(): Counting models in file `HR4527E_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 HR4527E_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 28540 ATOM records read from file > ReadCoordsPdb(): --> 28540 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 0.563 0.998 0.611 0.648 GLY A 2 0.302 0.248 HIS A 3 0.550 0.424 0.502 0.443 HIS A 4 0.650 0.591 0.605 0.462 HIS A 5 0.870 0.606 0.338 0.340 HIS A 6 0.708 0.705 0.785 0.719 HIS A 7 0.726 0.419 0.521 0.640 HIS A 8 0.637 0.423 0.671 0.732 SER A 9 0.529 0.383 0.199 HIS A 10 0.735 0.722 0.357 0.395 MET A 11 0.874 0.816 0.496 0.316 0.514 11 LEU A 12 0.990 0.882 0.999 0.999 12 THR A 13 0.858 0.445 0.549 LYS A 14 0.708 0.260 0.529 0.862 0.999 1.000 HIS A 15 0.618 0.307 0.698 0.725 GLY A 16 0.264 0.966 LYS A 17 0.981 0.666 0.757 0.734 0.859 0.994 ASN A 18 0.750 0.992 0.932 0.887 PRO A 19 0.997 0.997 0.982 0.970 19 19 VAL A 20 0.994 0.999 1.000 20 20 MET A 21 0.997 0.992 0.864 0.515 0.459 21 21 GLU A 22 0.991 0.995 0.879 0.703 0.790 22 22 LEU A 23 0.998 0.999 1.000 1.000 23 23 ASN A 24 0.997 0.993 0.795 0.845 24 24 GLU A 25 0.994 0.991 0.869 0.999 0.981 25 25 LYS A 26 0.991 0.995 0.994 0.999 0.998 0.937 26 26 ARG A 27 0.991 0.944 0.602 0.460 0.605 0.718 1.000 27 27 ARG A 28 0.934 0.985 0.482 0.998 0.268 0.994 1.000 28 28 GLY A 29 0.993 0.990 29 29 LEU A 30 0.980 0.993 0.997 0.999 30 30 LYS A 31 0.986 0.989 0.627 0.933 0.817 0.928 31 31 TYR A 32 0.986 0.975 0.999 0.995 32 32 GLU A 33 0.985 0.997 0.844 1.000 1.000 33 33 LEU A 34 0.998 0.997 0.999 1.000 34 34 ILE A 35 0.995 0.998 0.998 0.561 35 35 SER A 36 0.991 0.989 0.640 36 36 GLU A 37 0.975 0.910 0.455 0.943 0.959 37 37 THR A 38 0.965 0.922 0.034 38 38 GLY A 39 0.706 0.369 GLY A 40 0.249 0.418 SER A 41 0.528 0.746 0.205 HIS A 42 0.587 0.369 0.348 0.541 ASP A 43 0.465 0.763 0.568 0.969 LYS A 44 0.911 0.895 0.997 0.633 0.997 0.929 44 ARG A 45 0.968 0.950 0.867 0.544 0.939 0.701 1.000 45 45 PHE A 46 0.990 0.995 0.998 0.997 46 46 VAL A 47 0.996 0.998 1.000 47 47 MET A 48 0.997 0.999 1.000 0.939 0.843 48 48 GLU A 49 0.997 0.998 1.000 0.999 0.926 49 49 VAL A 50 0.997 0.997 0.493 50 50 GLU A 51 0.995 0.999 0.999 0.999 0.937 51 51 VAL A 52 0.996 0.990 1.000 52 52 ASP A 53 0.999 0.997 0.771 0.843 53 53 GLY A 54 0.999 0.992 54 54 GLN A 55 0.993 0.979 0.845 0.837 0.829 55 55 LYS A 56 0.991 0.998 1.000 0.999 1.000 1.000 56 56 PHE A 57 0.999 0.999 0.999 0.700 57 57 GLN A 58 1.000 0.999 1.000 1.000 0.999 58 58 GLY A 59 0.997 0.997 59 59 ALA A 60 0.990 0.995 60 60 GLY A 61 0.990 0.932 61 61 SER A 62 0.909 0.936 0.689 62 62 ASN A 63 0.967 0.993 0.675 0.924 63 63 LYS A 64 0.998 0.991 0.718 0.999 1.000 0.999 64 64 LYS A 65 0.993 0.996 0.934 1.000 0.999 1.000 65 65 VAL A 66 0.998 0.995 0.915 66 66 ALA A 67 1.000 0.999 67 67 LYS A 68 0.999 0.998 0.648 0.991 0.341 0.999 68 68 ALA A 69 1.000 0.999 69 69 TYR A 70 0.998 0.996 0.914 0.895 70 70 ALA A 71 0.999 0.999 71 71 ALA A 72 0.999 0.999 72 72 LEU A 73 1.000 0.999 0.999 1.000 73 73 ALA A 74 0.999 1.000 74 74 ALA A 75 1.000 0.999 75 75 LEU A 76 0.998 0.986 0.999 1.000 76 76 GLU A 77 0.983 0.984 0.578 1.000 0.977 77 77 LYS A 78 0.993 0.981 0.993 0.622 0.999 0.998 78 78 LEU A 79 0.973 0.996 0.692 0.658 79 79 PHE A 80 0.997 0.990 0.998 0.898 80 80 PRO A 81 0.990 0.976 0.944 0.908 81 81 ASP A 82 0.991 0.714 0.883 0.905 THR A 83 0.917 0.971 0.655 83 83 PRO A 84 0.988 0.859 0.895 0.812 84 LEU A 85 0.833 0.962 0.226 0.623 85 ALA A 86 0.776 0.747 LEU A 87 0.887 0.950 0.925 0.848 87 ASP A 88 0.689 0.426 0.444 0.904 ALA A 89 0.626 0.514 ASN A 90 0.734 0.416 0.327 0.915 LYS A 91 0.808 0.569 0.932 1.000 1.000 Ranges: 2 from: A 19 to A 38 from: A 45 to A 81 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[19..38],A[45..81],for model 1 is: 0.482 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 2 is: 0.432 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 3 is: 0.400 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 4 is: 0.345 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 5 is: 0.395 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 6 is: 0.454 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 7 is: 0.480 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 8 is: 0.444 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 9 is: 0.564 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 10 is: 0.453 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 11 is: 0.430 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 12 is: 0.623 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 13 is: 0.438 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 14 is: 0.565 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 15 is: 0.310 (*) > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 16 is: 0.461 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 17 is: 0.557 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 18 is: 0.546 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 19 is: 0.390 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 20 is: 0.364 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[19..38],[45..81], is: 0.457 > Range of RMSD values to reference struct. is 0.310 to 0.623 > 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[19..38],A[45..81],for model 1 is: 0.890 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 2 is: 0.819 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 3 is: 0.783 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 4 is: 0.735 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 5 is: 0.909 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 6 is: 0.873 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 7 is: 0.773 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 8 is: 0.784 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 9 is: 0.859 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 10 is: 0.880 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 11 is: 0.995 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 12 is: 1.061 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 13 is: 0.811 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 14 is: 1.029 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 15 is: 0.713 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 16 is: 0.887 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 17 is: 0.933 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 18 is: 1.016 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 19 is: 0.660 (*) > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 20 is: 0.768 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[19..38],[45..81], is: 0.859 > Range of RMSD values to reference struct. is 0.660 to 1.061 PdbStat> PdbStat> *END* of program detected, BYE! ...