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 `STR65_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 29-DEC-06 2JN8 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF Q8ZRJ2 FROM SALMONELLA > ReadCoordsPdb(): >> TITLE 2 TYPHIMURIUM. NORTHEAST STRUCTURAL GENOMICS TARGET STR65. > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): >> COMPND 2 MOLECULE: PUTATIVE CYTOPLASMIC PROTEIN; 1 > ReadCoordsPdb(): Counting models in file `STR65_NMR_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 STR65_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 34000 ATOM records read from file > ReadCoordsPdb(): --> 34000 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 ----------------------------------------------------------------------------------- VAL A 1 0.510 0.135 ASN A 2 0.768 0.263 0.257 0.407 PHE A 3 0.443 0.203 0.569 0.362 LYS A 4 0.349 0.808 0.340 0.563 0.490 0.224 ASP A 5 0.475 0.716 0.291 0.351 LYS A 6 0.671 0.333 0.341 0.686 0.433 0.159 SER A 7 0.388 0.742 0.321 MET A 8 0.661 0.824 0.263 0.674 0.134 PRO A 9 0.977 0.609 0.943 0.888 THR A 10 0.768 0.472 0.591 ALA A 11 0.991 0.991 11 11 ILE A 12 0.996 0.993 0.947 0.492 12 12 GLU A 13 0.994 0.992 0.633 0.456 0.322 13 13 LYS A 14 0.996 0.990 0.656 0.270 0.727 0.419 14 14 ALA A 15 0.999 0.999 15 15 LEU A 16 0.998 0.992 0.668 0.112 16 16 ASP A 17 0.993 0.991 0.950 0.701 17 17 PHE A 18 0.994 0.989 0.972 0.634 18 18 ILE A 19 0.992 0.979 0.999 0.999 19 19 GLY A 20 0.961 0.808 20 GLY A 21 0.257 0.391 MET A 22 0.430 0.449 0.210 0.429 0.577 ASN A 23 0.255 0.361 0.537 0.324 THR A 24 0.752 0.077 0.118 SER A 25 0.348 0.402 0.297 ALA A 26 0.537 0.701 SER A 27 0.862 0.850 0.389 27 VAL A 28 0.731 0.372 0.677 PRO A 29 0.922 0.655 0.903 0.897 HIS A 30 0.540 0.529 0.780 0.573 SER A 31 0.961 0.961 0.711 31 31 MET A 32 0.947 0.953 0.507 0.301 0.381 32 32 ASP A 33 0.973 0.906 0.436 0.477 33 33 GLU A 34 0.934 0.984 0.900 0.613 0.610 34 34 SER A 35 0.993 0.992 0.280 35 35 THR A 36 0.996 0.991 0.997 36 36 ALA A 37 0.998 0.996 37 37 LYS A 38 0.998 0.995 0.775 0.930 0.721 0.668 38 38 GLY A 39 0.998 0.998 39 39 ILE A 40 0.998 0.999 0.998 0.999 40 40 LEU A 41 0.999 0.998 0.656 0.543 41 41 LYS A 42 0.998 0.993 0.632 0.929 0.130 0.198 42 42 TYR A 43 0.998 0.997 0.997 0.993 43 43 LEU A 44 0.999 0.997 0.990 0.815 44 44 HIS A 45 0.995 0.990 0.782 0.601 45 45 ASP A 46 0.994 0.977 0.717 0.787 46 46 LEU A 47 0.993 0.986 0.998 0.999 47 47 GLY A 48 0.967 0.931 48 48 VAL A 49 0.976 0.987 0.742 49 49 PRO A 50 0.997 0.895 0.986 0.967 50 VAL A 51 0.958 0.961 0.252 51 51 SER A 52 0.979 0.980 0.959 52 52 PRO A 53 0.997 0.996 0.949 0.878 53 53 GLU A 54 0.996 0.997 0.873 0.481 0.274 54 54 VAL A 55 0.998 0.992 0.679 55 55 VAL A 56 0.998 0.999 1.000 56 56 VAL A 57 0.999 0.996 1.000 57 57 ALA A 58 0.998 0.997 58 58 ARG A 59 0.999 0.997 0.839 0.805 0.570 0.741 0.998 59 59 GLY A 60 0.999 0.995 60 60 GLU A 61 0.995 0.990 0.363 0.509 0.376 61 61 GLN A 62 0.993 0.998 0.931 0.815 0.622 62 62 GLU A 63 0.992 0.981 0.719 0.321 0.679 63 63 GLY A 64 0.972 0.710 TRP A 65 0.646 0.592 0.994 0.978 ASN A 66 0.599 0.982 0.547 0.544 PRO A 67 0.986 0.967 0.938 0.873 67 67 GLU A 68 0.982 0.987 0.937 0.305 0.316 68 68 PHE A 69 0.998 0.992 0.953 0.980 69 69 THR A 70 0.999 0.998 0.999 70 70 LYS A 71 0.996 0.993 0.996 0.589 0.618 0.410 71 71 LYS A 72 0.995 0.992 0.897 0.599 0.867 0.225 72 72 VAL A 73 1.000 0.999 0.998 73 73 ALA A 74 0.999 0.999 74 74 GLY A 75 0.998 0.999 75 75 TRP A 76 0.999 0.998 0.998 0.997 76 76 ALA A 77 0.999 0.999 77 77 GLU A 78 0.998 0.997 0.818 0.263 0.219 78 78 LYS A 79 0.995 0.989 0.995 0.812 0.761 0.203 79 79 VAL A 80 0.998 0.996 0.996 80 80 ALA A 81 0.997 0.996 81 81 SER A 82 0.992 0.982 0.280 82 82 GLY A 83 0.967 0.971 83 83 ASN A 84 0.993 0.720 0.989 0.427 ARG A 85 0.649 0.953 0.694 0.924 0.563 0.676 0.999 ILE A 86 0.884 0.838 0.996 0.998 86 LEU A 87 0.903 0.876 0.342 0.646 87 ILE A 88 0.807 0.321 0.762 0.854 LYS A 89 0.369 0.849 0.688 0.279 0.601 0.268 ASN A 90 0.863 0.783 0.564 0.594 PRO A 91 0.979 0.689 0.917 0.859 GLU A 92 0.405 0.392 0.370 0.350 0.493 TYR A 93 0.392 0.717 0.979 0.279 PHE A 94 0.651 0.714 0.459 0.797 SER A 95 0.964 0.972 0.282 95 95 THR A 96 0.994 0.991 0.489 96 96 TYR A 97 0.995 0.992 0.700 0.740 97 97 MET A 98 0.997 0.993 0.988 0.614 0.455 98 98 GLN A 99 0.998 0.995 0.556 0.732 0.154 99 99 GLU A 100 0.996 0.991 0.682 0.279 0.406 100 100 GLN A 101 0.997 0.998 0.789 0.374 0.221 101 101 LEU A 102 0.998 0.995 0.993 0.870 102 102 LYS A 103 0.997 0.990 0.988 0.991 0.874 0.225 103 103 GLU A 104 0.997 0.989 0.706 0.394 0.445 104 104 LEU A 105 0.994 0.981 0.645 0.491 105 105 VAL A 106 0.986 0.984 0.998 106 106 LEU A 107 0.993 0.977 0.884 0.716 107 107 GLU A 108 0.987 0.894 0.444 0.338 0.283 108 HIS A 109 0.483 0.472 0.099 Ranges: 5 from: A 11 to A 19 from: A 31 to A 49 from: A 51 to A 63 from: A 67 to A 83 from: A 95 to A 107 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[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 1 is: 0.707 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 2 is: 0.794 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 3 is: 0.817 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 4 is: 0.842 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 5 is: 0.539 (*) > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 6 is: 0.937 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 7 is: 0.830 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 8 is: 0.962 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 9 is: 0.582 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 10 is: 0.893 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 11 is: 0.660 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 12 is: 0.732 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 13 is: 0.699 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 14 is: 0.656 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 15 is: 1.003 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 16 is: 0.717 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 17 is: 0.683 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 18 is: 0.621 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 19 is: 0.697 > Kabsch RMSD of backbone atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 20 is: 0.803 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[11..19],[31..49],[51..63],[67..83],[95..107], is: 0.759 > Range of RMSD values to reference struct. is 0.539 to 1.003 > 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[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 1 is: 1.117 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 2 is: 1.146 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 3 is: 1.212 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 4 is: 1.264 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 5 is: 0.954 (*) > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 6 is: 1.396 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 7 is: 1.132 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 8 is: 1.317 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 9 is: 1.038 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 10 is: 1.290 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 11 is: 1.196 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 12 is: 1.089 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 13 is: 1.143 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 14 is: 1.066 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 15 is: 1.315 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 16 is: 1.084 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 17 is: 1.115 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 18 is: 0.994 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 19 is: 1.168 > Kabsch RMSD of heavy atoms in res. A[11..19],A[31..49],A[51..63],A[67..83],A[95..107],for model 20 is: 1.302 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[11..19],[31..49],[51..63],[67..83],[95..107], is: 1.167 > Range of RMSD values to reference struct. is 0.954 to 1.396 PdbStat> PdbStat> *END* of program detected, BYE! ...