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 `ER382A_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 50 ASP TYR VAL MET ALA THR LYS ASP GLY ARG MET ILE LEU 1 > ReadCoordsPdb(): Counting models in file `ER382A_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 ER382A_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 15400 ATOM records read from file > ReadCoordsPdb(): --> 15400 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 ----------------------------------------------------------------------------------- ASP A 1 0.222 0.459 0.891 TYR A 2 0.934 0.470 0.714 0.861 VAL A 3 0.384 0.933 0.559 MET A 4 0.945 0.981 0.857 0.998 0.354 4 4 ALA A 5 0.991 0.997 5 5 THR A 6 0.989 0.998 0.999 6 6 LYS A 7 0.991 0.985 0.421 0.999 1.000 0.997 7 7 ASP A 8 0.992 0.982 0.829 0.988 8 8 GLY A 9 0.985 0.973 9 9 ARG A 10 0.963 0.984 0.813 0.930 0.805 0.741 1.000 10 10 MET A 11 0.990 0.991 0.857 0.428 0.101 11 11 ILE A 12 0.985 0.994 1.000 0.919 12 12 LEU A 13 0.994 0.927 0.540 0.573 13 13 THR A 14 0.912 0.935 0.608 14 14 ASP A 15 0.977 0.298 0.535 0.947 GLY A 16 0.407 0.626 LYS A 17 0.743 0.969 0.789 0.929 0.999 0.675 PRO A 18 0.995 0.968 0.963 0.938 18 18 GLU A 19 0.969 0.981 0.595 0.998 0.999 19 19 ILE A 20 0.991 0.997 1.000 1.000 20 20 ASP A 21 0.992 0.956 0.930 0.979 21 21 ASP A 22 0.969 0.960 0.532 0.957 22 22 ASP A 23 0.979 0.996 0.998 0.950 23 23 THR A 24 0.994 0.995 0.928 24 24 GLY A 25 0.996 0.996 25 25 LEU A 26 0.997 0.996 1.000 1.000 26 26 VAL A 27 0.989 0.996 1.000 27 27 SER A 28 0.996 0.981 0.788 28 28 TYR A 29 0.982 0.993 0.997 0.497 29 29 HIS A 30 0.984 0.974 0.865 0.661 30 30 ASP A 31 0.988 0.968 0.155 0.921 31 31 GLN A 32 0.985 0.974 0.206 0.653 0.829 32 32 GLN A 33 0.978 0.986 0.998 0.518 0.907 33 33 GLY A 34 0.982 0.990 34 34 ASN A 35 0.976 0.947 0.714 0.963 35 35 ALA A 36 0.956 0.989 36 36 MET A 37 0.984 0.991 0.766 0.932 0.348 37 37 GLN A 38 0.973 0.986 0.640 0.941 0.814 38 38 ILE A 39 0.992 0.965 0.630 0.999 39 39 ASN A 40 0.990 0.978 0.631 0.935 40 40 ARG A 41 0.997 0.997 0.865 0.999 0.649 0.542 1.000 41 41 ASP A 42 0.990 0.977 0.831 0.975 42 42 ASP A 43 0.983 0.969 0.999 0.994 43 43 VAL A 44 0.985 0.987 0.614 44 44 SER A 45 0.982 0.992 0.782 45 45 GLN A 46 0.970 0.975 0.645 0.593 0.787 46 46 ILE A 47 0.974 0.200 0.635 0.793 ILE A 48 0.549 0.362 0.526 0.758 GLU A 49 0.711 0.304 0.584 0.946 0.942 ARG A 50 0.255 0.666 1.000 0.933 0.933 1.000 Ranges: 2 from: A 4 to A 14 from: A 18 to A 46 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[4..14],A[18..46],for model 1 is: 0.653 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 2 is: 0.584 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 3 is: 0.575 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 4 is: 0.762 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 5 is: 0.481 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 6 is: 0.578 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 7 is: 0.645 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 8 is: 1.343 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 9 is: 0.539 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 10 is: 0.589 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 11 is: 0.674 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 12 is: 0.418 (*) > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 13 is: 0.454 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 14 is: 0.682 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 15 is: 0.869 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 16 is: 0.674 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 17 is: 0.755 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 18 is: 0.654 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 19 is: 0.689 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 20 is: 0.481 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..14],[18..46], is: 0.655 > Range of RMSD values to reference struct. is 0.418 to 1.343 > 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[4..14],A[18..46],for model 1 is: 1.200 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 2 is: 1.013 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 3 is: 1.016 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 4 is: 1.149 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 5 is: 0.929 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 6 is: 1.036 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 7 is: 1.193 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 8 is: 1.692 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 9 is: 1.013 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 10 is: 0.954 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 11 is: 1.137 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 12 is: 0.900 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 13 is: 0.860 (*) > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 14 is: 1.118 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 15 is: 1.311 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 16 is: 1.133 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 17 is: 1.208 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 18 is: 1.246 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 19 is: 1.181 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 20 is: 0.962 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..14],[18..46], is: 1.113 > Range of RMSD values to reference struct. is 0.860 to 1.692 PdbStat> PdbStat> *END* of program detected, BYE! ...