Running PDBSTAT from Linux Ayuda is on: /farm/software/PdbStat/PdbStat-5.9 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2013 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.9-exp mar may 14 00:20:00 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 ...) 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 `ZR18_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 11 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP.PDB, 10 MODEL/S TEMP.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 91 MET LYS ILE ILE SER ILE SER GLU THR PRO ASN HIS ASN > ReadCoordsPdb(): Counting models in file `ZR18_R3_em_bcr3.pdb'; Model: > ReadCoordsPdb(): After scanning there is(are) 10 model(s) > ReadCoordsPdb(): what model do you want [(1 to 10) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file ZR18_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (10) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 14440 ATOM records read from file > ReadCoordsPdb(): --> 14440 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 0.758 0.867 0.998 0.138 LYS A 2 0.873 0.720 0.390 0.999 0.999 0.998 ILE A 3 0.628 0.976 0.877 0.703 ILE A 4 0.986 0.970 0.703 0.569 4 4 SER A 5 0.988 0.992 0.871 5 5 ILE A 6 0.941 0.725 0.572 0.482 SER A 7 0.257 0.662 0.721 GLU A 8 0.860 0.291 0.409 0.892 0.953 THR A 9 0.910 0.465 0.431 PRO A 10 0.988 0.891 0.916 0.843 10 ASN A 11 0.873 0.429 0.271 0.911 HIS A 12 0.351 0.188 0.617 0.792 ASN A 13 0.122 0.947 0.551 0.732 THR A 14 0.930 0.948 0.549 14 14 MET A 15 0.956 0.926 0.526 0.435 0.234 15 15 LYS A 16 0.963 0.956 0.578 0.999 0.999 0.999 16 16 ILE A 17 0.972 0.991 0.999 0.683 17 17 THR A 18 0.986 0.998 1.000 18 18 LEU A 19 0.992 0.746 0.991 0.834 SER A 20 0.807 0.994 0.992 20 GLU A 21 0.433 0.803 0.541 0.449 0.831 SER A 22 0.864 0.618 0.181 ARG A 23 0.294 0.220 0.570 0.998 0.748 0.996 1.000 GLU A 24 0.793 0.383 0.760 0.717 0.906 GLY A 25 0.719 0.048 MET A 26 0.551 0.193 0.729 0.490 0.503 THR A 27 0.121 0.895 0.545 SER A 28 0.993 0.919 0.478 28 28 ASP A 29 0.998 0.997 1.000 1.000 29 29 THR A 30 0.975 0.999 0.850 30 30 TYR A 31 0.997 0.967 0.999 0.599 31 31 THR A 32 0.990 0.895 0.999 32 LYS A 33 0.813 0.675 0.330 0.999 0.999 0.864 VAL A 34 0.753 0.630 0.543 ASP A 35 0.375 0.310 0.429 0.815 ASP A 36 0.524 0.418 0.775 0.868 SER A 37 0.189 0.783 0.259 GLN A 38 0.976 0.984 0.474 0.876 0.502 38 38 PRO A 39 0.998 0.996 1.000 1.000 39 39 ALA A 40 0.996 0.986 40 40 PHE A 41 0.987 0.991 0.993 0.868 41 41 ILE A 42 0.991 0.992 0.733 0.276 42 42 ASN A 43 0.988 0.997 0.784 0.751 43 43 ASP A 44 0.995 0.986 1.000 1.000 44 44 ILE A 45 0.998 0.999 1.000 1.000 45 45 LEU A 46 0.996 0.996 0.880 0.682 46 46 LYS A 47 0.996 0.992 0.868 1.000 1.000 0.997 47 47 VAL A 48 0.995 0.999 1.000 48 48 GLU A 49 0.998 0.999 1.000 1.000 1.000 49 49 GLY A 50 0.995 0.982 50 50 VAL A 51 0.988 0.451 0.775 LYS A 52 0.431 0.974 0.735 0.996 0.999 0.994 SER A 53 0.997 0.996 1.000 53 53 ILE A 54 0.993 0.984 0.365 0.924 54 54 PHE A 55 0.982 0.987 0.609 0.894 55 55 HIS A 56 0.977 0.981 0.642 0.710 56 56 VAL A 57 0.965 0.950 0.529 57 57 MET A 58 0.995 0.966 0.998 0.589 0.665 58 58 ASP A 59 0.960 0.997 1.000 0.998 59 59 PHE A 60 0.999 0.996 1.000 1.000 60 60 ILE A 61 0.976 0.999 0.734 0.689 61 61 SER A 62 0.995 0.988 0.727 62 62 VAL A 63 0.992 0.994 1.000 63 63 ASP A 64 0.971 0.964 0.882 0.923 64 64 LYS A 65 0.909 0.993 0.540 0.994 0.637 0.879 65 65 GLU A 66 0.987 0.937 0.880 0.571 0.890 66 66 ASN A 67 0.998 0.993 1.000 1.000 67 67 ASP A 68 0.906 0.957 0.767 0.869 68 68 ALA A 69 0.438 0.843 ASN A 70 0.948 0.827 0.448 0.712 70 TRP A 71 0.965 0.968 0.559 0.236 71 71 GLU A 72 0.957 0.979 0.999 1.000 0.999 72 72 THR A 73 0.994 0.985 0.470 73 73 VAL A 74 0.971 0.999 0.999 74 74 LEU A 75 0.999 0.998 0.681 0.563 75 75 PRO A 76 0.999 1.000 1.000 1.000 76 76 LYS A 77 0.992 0.997 0.999 0.604 1.000 0.999 77 77 VAL A 78 0.993 0.993 1.000 78 78 GLU A 79 0.997 0.997 0.761 1.000 1.000 79 79 ALA A 80 0.981 0.986 80 80 VAL A 81 0.994 0.991 0.999 81 81 PHE A 82 0.972 0.829 0.980 0.825 82 GLU A 83 0.839 0.437 0.674 0.856 0.885 LEU A 84 0.342 0.554 0.545 0.582 GLU A 85 0.397 0.531 0.660 1.000 0.962 HIS A 86 0.945 0.319 0.487 0.450 HIS A 87 0.667 0.136 0.180 0.321 HIS A 88 0.673 0.607 0.599 0.688 HIS A 89 0.944 0.279 0.219 0.349 HIS A 90 0.652 0.288 0.110 0.292 HIS A 91 0.294 0.667 0.288 Ranges: 6 from: A 4 to A 5 from: A 14 to A 18 from: A 28 to A 31 from: A 38 to A 50 from: A 53 to A 68 from: A 71 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[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 1 is: 1.391 > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 2 is: 1.569 > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 3 is: 0.733 (*) > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 4 is: 1.268 > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 5 is: 1.212 > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 6 is: 1.173 > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 7 is: 2.038 > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 8 is: 0.808 > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 9 is: 1.170 > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 10 is: 0.947 > > Kabsch RMSD statistics for 10 structures: > Mean RMSD using as refer. str. `average' for res.[4..5],[14..18],[28..31],[38..50],[53..68],[71..81], is: 1.231 > Range of RMSD values to reference struct. is 0.733 to 2.038 > 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..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 1 is: 1.765 > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 2 is: 2.053 > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 3 is: 1.303 > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 4 is: 1.635 > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 5 is: 1.687 > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 6 is: 1.609 > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 7 is: 2.329 > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 8 is: 1.150 (*) > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 9 is: 1.713 > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..31],A[38..50],A[53..68],A[71..81],for model 10 is: 1.377 > > Kabsch RMSD statistics for 10 structures: > Mean RMSD using as refer. str. `average' for res.[4..5],[14..18],[28..31],[38..50],[53..68],[71..81], is: 1.662 > Range of RMSD values to reference struct. is 1.150 to 2.329 PdbStat> PdbStat> *END* of program detected, BYE! ...