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 `GMR137_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 78 MET ASN LEU THR VAL ASN GLY LYS PRO SER THR VAL ASP 1 > ReadCoordsPdb(): Counting models in file `GMR137_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 GMR137_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 23480 ATOM records read from file > ReadCoordsPdb(): --> 23480 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 0.512 0.802 0.640 ASN A 2 0.973 0.978 0.568 0.836 2 2 LEU A 3 0.970 0.959 0.553 0.660 3 3 THR A 4 0.980 0.980 0.999 4 4 VAL A 5 0.972 0.990 0.926 5 5 ASN A 6 0.999 0.999 0.726 0.595 6 6 GLY A 7 0.989 0.977 7 7 LYS A 8 0.977 0.973 0.550 0.928 1.000 0.999 8 8 PRO A 9 0.988 0.954 0.904 0.824 9 9 SER A 10 0.936 0.910 0.646 10 10 THR A 11 0.968 0.996 1.000 11 11 VAL A 12 0.984 0.991 1.000 12 12 ASP A 13 0.899 0.944 0.534 0.990 13 GLY A 14 0.869 0.783 ALA A 15 0.694 0.919 GLU A 16 0.928 0.581 0.796 0.999 1.000 SER A 17 0.487 0.844 0.501 LEU A 18 0.938 0.993 0.649 0.803 18 18 ASN A 19 0.974 0.978 0.480 0.907 19 19 VAL A 20 0.996 0.998 1.000 20 20 THR A 21 0.999 0.998 1.000 21 21 GLU A 22 0.999 0.998 0.999 0.623 0.922 22 22 LEU A 23 0.997 0.996 0.598 0.565 23 23 LEU A 24 0.997 0.996 0.996 0.919 24 24 SER A 25 0.995 0.994 0.545 25 25 ALA A 26 0.999 0.998 26 26 LEU A 27 0.990 0.987 0.871 0.706 27 27 LYS A 28 0.998 0.994 0.998 0.999 1.000 0.929 28 28 VAL A 29 0.977 0.959 0.567 29 29 ALA A 30 0.968 0.363 GLN A 31 0.405 0.825 0.999 0.531 0.900 ALA A 32 0.943 0.976 32 32 GLU A 33 0.958 0.980 0.653 0.999 0.971 33 33 TYR A 34 0.988 0.920 0.998 0.799 34 34 VAL A 35 0.952 0.961 0.657 35 35 THR A 36 0.934 0.972 0.927 36 36 VAL A 37 0.964 0.942 0.537 37 37 GLU A 38 0.973 0.962 0.267 0.997 0.929 38 38 LEU A 39 0.980 0.995 0.942 0.945 39 39 ASN A 40 0.999 0.998 0.777 0.891 40 40 GLY A 41 0.994 0.960 41 41 GLU A 42 0.951 0.995 0.866 0.999 0.999 42 42 VAL A 43 0.997 0.999 0.935 43 43 LEU A 44 0.992 0.995 0.993 0.932 44 44 GLU A 45 0.983 0.988 0.930 1.000 0.950 45 45 ARG A 46 0.995 0.980 0.406 0.996 0.437 0.672 1.000 46 46 GLU A 47 0.991 0.992 0.999 0.893 0.998 47 47 ALA A 48 0.992 0.993 48 48 PHE A 49 0.998 0.994 0.997 0.934 49 49 ASP A 50 0.989 0.999 0.934 0.909 50 50 ALA A 51 0.994 0.976 51 51 THR A 52 0.966 0.996 1.000 52 52 THR A 53 0.991 0.999 1.000 53 53 VAL A 54 0.988 0.992 0.927 54 54 LYS A 55 0.976 0.917 0.772 0.999 0.999 0.934 55 55 ASP A 56 0.902 0.953 0.999 0.814 56 56 GLY A 57 0.938 0.906 57 57 ASP A 58 0.914 0.976 0.841 0.971 58 58 ALA A 59 0.956 0.907 59 59 VAL A 60 0.974 0.974 0.788 60 60 GLU A 61 0.986 0.959 0.537 0.863 0.915 61 61 PHE A 62 0.929 0.964 0.693 0.959 62 62 LEU A 63 0.947 0.889 0.633 0.750 63 TYR A 64 0.132 0.880 0.849 0.777 PHE A 65 0.590 0.497 0.730 0.813 MET A 66 0.437 0.623 0.318 0.286 0.129 GLY A 67 0.469 0.707 GLY A 68 0.162 0.106 GLY A 69 0.384 0.517 LYS A 70 0.430 0.843 0.508 0.937 0.999 0.856 LEU A 71 0.649 0.598 0.514 0.619 GLU A 72 0.710 0.355 0.542 0.924 0.957 HIS A 73 0.556 0.353 0.296 0.320 HIS A 74 0.538 0.505 0.465 0.385 HIS A 75 0.590 0.780 0.549 0.343 HIS A 76 0.676 0.811 0.608 0.334 HIS A 77 0.881 0.931 0.364 0.431 77 HIS A 78 0.962 0.798 0.805 Ranges: 3 from: A 2 to A 12 from: A 18 to A 29 from: A 32 to A 62 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..12],A[18..29],A[32..62],for model 1 is: 0.602 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 2 is: 0.775 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 3 is: 1.212 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 4 is: 0.627 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 5 is: 0.812 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 6 is: 0.996 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 7 is: 0.990 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 8 is: 0.680 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 9 is: 0.694 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 10 is: 0.723 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 11 is: 0.482 (*) > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 12 is: 0.766 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 13 is: 0.859 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 14 is: 0.573 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 15 is: 0.957 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 16 is: 0.928 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 17 is: 1.172 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 18 is: 0.891 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 19 is: 0.940 > Kabsch RMSD of backbone atoms in res. A[2..12],A[18..29],A[32..62],for model 20 is: 1.068 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..12],[18..29],[32..62], is: 0.837 > Range of RMSD values to reference struct. is 0.482 to 1.212 > 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..12],A[18..29],A[32..62],for model 1 is: 0.929 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 2 is: 1.287 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 3 is: 1.532 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 4 is: 0.921 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 5 is: 1.123 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 6 is: 1.228 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 7 is: 1.421 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 8 is: 1.107 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 9 is: 1.145 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 10 is: 1.122 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 11 is: 0.854 (*) > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 12 is: 1.165 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 13 is: 1.052 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 14 is: 0.882 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 15 is: 1.248 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 16 is: 1.372 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 17 is: 1.502 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 18 is: 1.334 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 19 is: 1.236 > Kabsch RMSD of heavy atoms in res. A[2..12],A[18..29],A[32..62],for model 20 is: 1.576 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..12],[18..29],[32..62], is: 1.202 > Range of RMSD values to reference struct. is 0.854 to 1.576 PdbStat> PdbStat> *END* of program detected, BYE! ...