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 `HR4694F_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 86 HIS MET PRO LYS SER PRO GLN LYS PRO ILE VAL ARG VAL 1 > ReadCoordsPdb(): Counting models in file `HR4694F_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 HR4694F_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 27960 ATOM records read from file > ReadCoordsPdb(): --> 27960 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 ----------------------------------------------------------------------------------- HIS A 1 0.328 0.561 0.338 MET A 2 0.274 0.907 0.521 0.244 0.376 PRO A 3 0.989 0.907 0.913 0.849 3 3 LYS A 4 0.927 0.631 0.696 0.931 0.999 0.999 SER A 5 0.506 0.920 0.863 PRO A 6 0.990 0.726 0.930 0.885 GLN A 7 0.898 0.675 0.729 0.433 0.854 LYS A 8 0.964 0.997 0.998 0.594 0.998 1.000 8 8 PRO A 9 0.994 0.980 0.907 0.818 9 9 ILE A 10 0.999 0.999 1.000 0.789 10 10 VAL A 11 0.999 0.998 1.000 11 11 ARG A 12 0.994 0.993 0.813 0.989 0.465 0.835 1.000 12 12 VAL A 13 0.995 0.996 1.000 13 13 PHE A 14 0.984 0.991 0.677 0.997 14 14 LEU A 15 0.992 1.000 0.999 1.000 15 15 PRO A 16 0.999 0.997 0.983 0.969 16 16 ASN A 17 1.000 0.994 0.710 0.903 17 17 LYS A 18 1.000 0.999 1.000 1.000 1.000 1.000 18 18 GLN A 19 0.999 0.996 1.000 1.000 0.999 19 19 ARG A 20 0.994 0.991 0.503 0.990 0.512 0.602 1.000 20 20 THR A 21 0.996 0.973 0.933 21 21 VAL A 22 0.982 0.998 1.000 22 22 VAL A 23 0.998 0.982 0.719 23 23 PRO A 24 0.991 0.997 0.920 0.850 24 24 ALA A 25 0.981 0.881 25 ARG A 26 0.879 0.990 0.611 0.552 0.996 0.662 1.000 26 CYS A 27 0.996 0.997 0.748 27 27 GLY A 28 0.995 0.991 28 28 VAL A 29 0.987 0.996 1.000 29 29 THR A 30 1.000 1.000 1.000 30 30 VAL A 31 1.000 0.999 1.000 31 31 ARG A 32 0.998 0.989 0.855 0.760 0.111 0.482 1.000 32 32 ASP A 33 0.990 0.986 0.999 0.970 33 33 SER A 34 0.995 0.992 0.410 34 34 LEU A 35 0.992 0.990 0.994 0.857 35 35 LYS A 36 0.997 0.959 0.694 0.999 1.000 0.998 36 36 LYS A 37 0.971 0.993 0.631 0.998 1.000 0.999 37 37 ALA A 38 0.998 0.999 38 38 LEU A 39 0.997 0.997 0.999 0.999 39 39 MET A 40 0.998 0.997 0.774 0.858 0.537 40 40 MET A 41 0.996 0.979 1.000 0.720 0.503 41 41 ARG A 42 0.963 0.991 0.926 0.442 0.928 0.474 1.000 42 42 GLY A 43 0.994 0.992 43 43 LEU A 44 0.992 0.990 1.000 1.000 44 44 ILE A 45 0.968 0.988 0.435 0.697 45 45 PRO A 46 0.994 0.988 0.935 0.884 46 46 GLU A 47 0.994 0.994 0.999 0.644 0.904 47 47 CYS A 48 0.993 0.993 0.654 48 48 CYS A 49 0.991 0.996 0.999 49 49 ALA A 50 0.996 0.998 50 50 VAL A 51 0.991 1.000 0.447 51 51 TYR A 52 0.998 0.995 0.999 0.899 52 52 ARG A 53 0.979 0.979 0.540 0.997 0.346 0.566 1.000 53 53 ILE A 54 0.980 0.995 1.000 0.920 54 54 GLN A 55 0.973 0.973 0.857 0.529 0.855 55 55 ASP A 56 1.000 0.998 1.000 1.000 56 56 GLY A 57 0.993 0.984 57 57 GLU A 58 0.969 0.981 0.865 0.998 1.000 58 58 LYS A 59 0.988 0.970 0.751 0.998 0.999 0.991 59 59 LYS A 60 0.964 0.989 0.569 0.927 0.999 0.999 60 60 PRO A 61 0.994 0.998 0.919 0.846 61 61 ILE A 62 0.998 0.990 0.923 0.706 62 62 GLY A 63 0.996 0.995 63 63 TRP A 64 0.997 0.999 0.999 0.998 64 64 ASP A 65 0.998 0.991 0.539 0.972 65 65 THR A 66 0.994 0.996 0.925 66 66 ASP A 67 0.999 0.999 0.999 0.970 67 67 ILE A 68 1.000 0.999 0.999 0.941 68 68 SER A 69 0.998 0.999 0.913 69 69 TRP A 70 1.000 0.999 1.000 0.996 70 70 LEU A 71 0.999 0.997 1.000 1.000 71 71 THR A 72 1.000 0.999 1.000 72 72 GLY A 73 0.997 0.983 73 73 GLU A 74 0.982 0.997 0.999 0.692 0.882 74 74 GLU A 75 0.998 0.997 0.701 0.996 0.868 75 75 LEU A 76 0.996 0.974 0.920 0.929 76 76 HIS A 77 0.988 0.994 0.803 0.796 77 77 VAL A 78 0.997 0.999 0.999 78 78 GLU A 79 0.995 0.991 0.834 0.999 0.976 79 79 VAL A 80 0.988 0.996 0.687 80 80 LEU A 81 0.991 0.996 0.925 0.930 81 81 GLU A 82 0.940 0.937 0.593 0.605 0.908 82 82 ASN A 83 0.987 0.831 0.617 0.933 83 VAL A 84 0.773 0.955 0.857 PRO A 85 0.993 0.979 0.963 0.938 85 85 LEU A 86 0.876 0.567 0.662 Ranges: 2 from: A 8 to A 24 from: A 27 to A 82 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[8..24],A[27..82],for model 1 is: 0.379 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 2 is: 0.249 (*) > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 3 is: 0.521 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 4 is: 0.503 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 5 is: 0.347 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 6 is: 0.430 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 7 is: 0.435 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 8 is: 0.324 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 9 is: 0.311 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 10 is: 0.585 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 11 is: 0.343 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 12 is: 0.489 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 13 is: 0.484 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 14 is: 0.552 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 15 is: 0.504 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 16 is: 0.671 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 17 is: 0.530 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 18 is: 0.532 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 19 is: 0.399 > Kabsch RMSD of backbone atoms in res. A[8..24],A[27..82],for model 20 is: 0.734 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[8..24],[27..82], is: 0.466 > Range of RMSD values to reference struct. is 0.249 to 0.734 > 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[8..24],A[27..82],for model 1 is: 0.713 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 2 is: 0.589 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 3 is: 0.926 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 4 is: 0.862 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 5 is: 0.876 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 6 is: 0.812 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 7 is: 0.801 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 8 is: 0.868 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 9 is: 0.609 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 10 is: 1.029 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 11 is: 0.565 (*) > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 12 is: 0.909 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 13 is: 1.033 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 14 is: 0.997 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 15 is: 0.966 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 16 is: 1.110 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 17 is: 0.963 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 18 is: 0.910 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 19 is: 0.810 > Kabsch RMSD of heavy atoms in res. A[8..24],A[27..82],for model 20 is: 1.073 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[8..24],[27..82], is: 0.871 > Range of RMSD values to reference struct. is 0.565 to 1.110 PdbStat> PdbStat> *END* of program detected, BYE! ...