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_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 91 MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET LEU THR 1 > ReadCoordsPdb(): Counting models in file `HR4527E_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 HR4527E_R3Cons_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 0.379 0.998 0.534 0.412 GLY A 2 0.343 0.306 HIS A 3 0.638 0.477 0.613 0.713 HIS A 4 0.594 0.435 0.521 0.537 HIS A 5 0.824 0.512 0.382 0.202 HIS A 6 0.622 0.543 0.434 0.641 HIS A 7 0.673 0.460 0.335 0.480 HIS A 8 0.599 0.366 0.724 0.498 SER A 9 0.503 0.277 0.154 HIS A 10 0.747 0.748 0.446 0.195 MET A 11 0.815 0.886 0.435 0.337 0.215 11 LEU A 12 0.977 0.883 0.949 0.940 12 THR A 13 0.818 0.425 0.541 LYS A 14 0.697 0.285 0.612 0.450 0.929 0.864 HIS A 15 0.645 0.285 0.998 0.989 GLY A 16 0.261 0.953 LYS A 17 0.979 0.718 0.998 0.572 0.927 0.999 ASN A 18 0.786 0.996 0.999 0.968 PRO A 19 0.998 0.999 0.998 0.999 19 19 VAL A 20 0.999 1.000 1.000 20 20 MET A 21 1.000 0.999 1.000 1.000 0.999 21 21 GLU A 22 1.000 1.000 0.999 0.945 0.704 22 22 LEU A 23 1.000 1.000 1.000 1.000 23 23 ASN A 24 1.000 1.000 1.000 0.999 24 24 GLU A 25 1.000 1.000 1.000 1.000 1.000 25 25 LYS A 26 1.000 0.999 0.999 1.000 1.000 0.936 26 26 ARG A 27 0.999 0.955 1.000 0.999 1.000 0.899 1.000 27 27 ARG A 28 0.960 0.992 0.998 0.804 0.546 0.758 1.000 28 28 GLY A 29 0.997 0.993 29 29 LEU A 30 0.997 0.999 0.999 0.999 30 30 LYS A 31 0.989 0.998 1.000 0.999 1.000 0.999 31 31 TYR A 32 0.995 0.999 0.998 0.999 32 32 GLU A 33 0.999 1.000 1.000 1.000 1.000 33 33 LEU A 34 1.000 0.999 0.999 1.000 34 34 ILE A 35 0.998 1.000 1.000 1.000 35 35 SER A 36 0.999 0.999 1.000 36 36 GLU A 37 0.993 0.973 0.552 0.999 0.955 37 37 THR A 38 0.987 0.971 0.052 38 38 GLY A 39 0.764 0.452 GLY A 40 0.283 0.344 SER A 41 0.545 0.765 0.328 HIS A 42 0.557 0.327 0.495 0.374 ASP A 43 0.437 0.772 0.599 0.966 LYS A 44 0.907 0.913 0.867 0.822 0.834 0.600 44 44 ARG A 45 0.956 0.972 0.999 0.999 0.768 0.951 1.000 45 45 PHE A 46 0.994 0.998 0.999 0.995 46 46 VAL A 47 0.998 0.999 1.000 47 47 MET A 48 0.999 1.000 1.000 1.000 0.999 48 48 GLU A 49 1.000 1.000 0.999 0.999 0.451 49 49 VAL A 50 1.000 1.000 1.000 50 50 GLU A 51 0.999 0.999 1.000 1.000 0.982 51 51 VAL A 52 1.000 0.997 1.000 52 52 ASP A 53 0.999 0.996 0.792 0.919 53 53 GLY A 54 0.996 0.989 54 54 GLN A 55 0.989 0.998 1.000 0.999 0.999 55 55 LYS A 56 0.995 1.000 0.987 0.998 0.991 0.662 56 56 PHE A 57 1.000 0.999 1.000 0.100 57 57 GLN A 58 1.000 1.000 1.000 1.000 0.997 58 58 GLY A 59 0.999 0.999 59 59 ALA A 60 0.998 0.998 60 60 GLY A 61 0.997 0.940 61 61 SER A 62 0.920 0.966 0.452 62 62 ASN A 63 0.975 0.999 0.999 0.979 63 63 LYS A 64 0.999 0.999 0.730 1.000 1.000 0.999 64 64 LYS A 65 1.000 0.999 1.000 0.996 0.799 0.933 65 65 VAL A 66 1.000 0.999 1.000 66 66 ALA A 67 1.000 1.000 67 67 LYS A 68 1.000 1.000 1.000 0.999 1.000 1.000 68 68 ALA A 69 1.000 1.000 69 69 TYR A 70 1.000 1.000 0.999 0.898 70 70 ALA A 71 1.000 1.000 71 71 ALA A 72 1.000 1.000 72 72 LEU A 73 1.000 0.999 0.999 0.999 73 73 ALA A 74 1.000 1.000 74 74 ALA A 75 1.000 1.000 75 75 LEU A 76 1.000 1.000 1.000 1.000 76 76 GLU A 77 0.999 1.000 1.000 0.701 0.945 77 77 LYS A 78 0.999 0.997 1.000 0.998 0.997 0.400 78 78 LEU A 79 0.997 0.993 1.000 1.000 79 79 PHE A 80 0.998 0.994 0.998 0.100 80 80 PRO A 81 0.991 0.981 0.943 0.907 81 81 ASP A 82 0.993 0.731 0.895 0.930 THR A 83 0.940 0.996 1.000 83 83 PRO A 84 0.992 0.820 0.915 0.837 84 LEU A 85 0.844 0.945 0.566 0.677 85 ALA A 86 0.789 0.802 LEU A 87 0.899 0.955 0.998 1.000 87 ASP A 88 0.700 0.446 0.519 0.926 ALA A 89 0.645 0.549 ASN A 90 0.745 0.482 0.319 0.895 LYS A 91 0.808 0.588 0.999 0.808 0.999 Ranges: 2 from: A 19 to A 38 from: A 44 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[44..81],for model 1 is: 0.360 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 2 is: 0.239 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 3 is: 0.260 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 4 is: 0.364 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 5 is: 0.138 (*) > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 6 is: 0.369 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 7 is: 0.210 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 8 is: 0.253 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 9 is: 0.300 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 10 is: 0.322 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 11 is: 0.266 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 12 is: 0.312 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 13 is: 0.314 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 14 is: 0.194 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 15 is: 0.274 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 16 is: 0.299 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 17 is: 0.265 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 18 is: 0.316 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 19 is: 0.302 > Kabsch RMSD of backbone atoms in res. A[19..38],A[44..81],for model 20 is: 0.282 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[19..38],[44..81], is: 0.282 > Range of RMSD values to reference struct. is 0.138 to 0.369 > 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[44..81],for model 1 is: 0.609 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 2 is: 0.493 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 3 is: 0.438 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 4 is: 0.616 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 5 is: 0.402 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 6 is: 0.568 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 7 is: 0.386 (*) > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 8 is: 0.560 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 9 is: 0.535 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 10 is: 0.544 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 11 is: 0.619 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 12 is: 0.599 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 13 is: 0.556 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 14 is: 0.441 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 15 is: 0.429 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 16 is: 0.624 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 17 is: 0.521 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 18 is: 0.655 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 19 is: 0.616 > Kabsch RMSD of heavy atoms in res. A[19..38],A[44..81],for model 20 is: 0.565 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[19..38],[44..81], is: 0.539 > Range of RMSD values to reference struct. is 0.386 to 0.655 PdbStat> PdbStat> *END* of program detected, BYE! ...