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_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.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_R3Cons_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_R3Cons_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 0.396 0.223 0.924 TYR A 2 0.920 0.481 0.568 0.868 VAL A 3 0.416 0.928 0.562 MET A 4 0.958 0.989 0.999 0.999 0.564 4 4 ALA A 5 0.996 0.999 5 5 THR A 6 0.997 0.997 0.999 6 6 LYS A 7 0.973 0.972 1.000 1.000 1.000 0.833 7 7 ASP A 8 0.977 0.985 0.844 0.891 8 8 GLY A 9 0.986 0.937 9 9 ARG A 10 0.918 0.995 0.843 0.873 0.541 0.814 1.000 10 10 MET A 11 0.995 0.987 0.564 0.406 0.374 11 11 ILE A 12 0.985 0.997 1.000 0.879 12 12 LEU A 13 0.995 0.949 0.995 0.926 13 13 THR A 14 0.966 0.944 0.997 14 14 ASP A 15 0.985 0.320 0.599 0.913 GLY A 16 0.406 0.632 LYS A 17 0.753 0.965 0.682 0.918 0.996 0.530 PRO A 18 0.994 0.902 0.977 0.966 18 18 GLU A 19 0.987 0.992 0.871 1.000 1.000 19 19 ILE A 20 0.993 0.999 1.000 1.000 20 20 ASP A 21 0.997 0.987 0.937 0.938 21 21 ASP A 22 0.984 0.963 0.476 0.982 22 22 ASP A 23 0.979 0.995 0.998 0.941 23 23 THR A 24 0.993 0.999 1.000 24 24 GLY A 25 0.999 0.996 25 25 LEU A 26 0.995 0.998 0.995 0.943 26 26 VAL A 27 0.997 0.998 1.000 27 27 SER A 28 0.997 0.988 0.862 28 28 TYR A 29 0.983 0.997 0.997 0.101 29 29 HIS A 30 0.988 0.977 0.999 0.998 30 30 ASP A 31 0.992 0.991 0.879 0.935 31 31 GLN A 32 0.987 0.948 0.341 0.558 0.779 32 32 GLN A 33 0.960 0.973 0.998 0.719 0.935 33 33 GLY A 34 0.981 0.992 34 34 ASN A 35 0.986 0.972 0.998 0.963 35 35 ALA A 36 0.972 0.994 36 36 MET A 37 0.991 0.986 0.613 0.995 0.430 37 37 GLN A 38 0.993 0.975 0.855 0.999 0.730 38 38 ILE A 39 0.991 0.984 0.870 0.904 39 39 ASN A 40 0.990 0.988 0.627 0.929 40 40 ARG A 41 0.994 0.996 0.932 0.998 0.674 0.324 1.000 41 41 ASP A 42 0.996 0.991 1.000 1.000 42 42 ASP A 43 0.983 0.958 0.998 0.979 43 43 VAL A 44 0.993 0.969 0.507 44 44 SER A 45 0.970 0.996 1.000 45 45 GLN A 46 0.956 0.966 0.575 0.377 0.764 46 46 ILE A 47 0.953 0.185 0.560 0.697 ILE A 48 0.536 0.263 0.575 0.685 GLU A 49 0.695 0.309 0.575 0.924 0.964 ARG A 50 0.257 0.670 1.000 0.871 0.944 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: 0.449 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 2 is: 0.578 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 3 is: 0.420 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 4 is: 0.536 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 5 is: 0.478 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 6 is: 0.724 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 7 is: 0.370 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 8 is: 0.338 (*) > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 9 is: 0.512 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 10 is: 0.409 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 11 is: 0.602 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 12 is: 0.398 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 13 is: 0.385 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 14 is: 0.723 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 15 is: 0.453 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 16 is: 0.476 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 17 is: 0.505 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 18 is: 0.565 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 19 is: 0.478 > Kabsch RMSD of backbone atoms in res. A[4..14],A[18..46],for model 20 is: 0.369 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..14],[18..46], is: 0.488 > Range of RMSD values to reference struct. is 0.338 to 0.724 > 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: 0.974 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 2 is: 0.994 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 3 is: 0.844 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 4 is: 0.767 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 5 is: 0.799 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 6 is: 1.049 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 7 is: 0.873 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 8 is: 0.902 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 9 is: 0.779 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 10 is: 0.753 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 11 is: 0.941 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 12 is: 0.672 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 13 is: 0.626 (*) > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 14 is: 1.078 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 15 is: 0.769 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 16 is: 0.796 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 17 is: 0.815 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 18 is: 0.975 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 19 is: 0.852 > Kabsch RMSD of heavy atoms in res. A[4..14],A[18..46],for model 20 is: 0.797 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..14],[18..46], is: 0.853 > Range of RMSD values to reference struct. is 0.626 to 1.078 PdbStat> PdbStat> *END* of program detected, BYE! ...