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 `SR213_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 23-JUN-06 2HFI > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF PROTEIN YPPE FROM BACILLUS > ReadCoordsPdb(): >> TITLE 2 SUBTILIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET > ReadCoordsPdb(): >> TITLE 3 SR213 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `SR213_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 SR213_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 40620 ATOM records read from file > ReadCoordsPdb(): --> 40620 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 0.601 0.439 0.375 0.346 LEU A 2 0.672 0.680 0.430 0.390 SER A 3 0.519 0.639 0.475 GLN A 4 0.571 0.461 0.552 0.246 0.518 THR A 5 0.401 0.312 0.568 LEU A 6 0.637 0.966 0.999 0.999 LEU A 7 0.995 0.994 0.937 0.647 7 7 GLU A 8 0.996 0.996 0.123 0.336 0.324 8 8 MET A 9 0.998 0.997 0.650 0.869 0.782 9 9 THR A 10 0.999 0.998 0.999 10 10 GLU A 11 0.999 0.998 0.991 0.863 0.281 11 11 GLN A 12 0.999 0.999 0.954 0.303 0.851 12 12 MET A 13 0.999 0.999 0.638 0.937 0.467 13 13 ILE A 14 0.999 0.999 0.999 0.867 14 14 GLU A 15 0.998 0.998 0.996 0.675 0.631 15 15 VAL A 16 1.000 0.999 0.998 16 16 ALA A 17 0.998 0.999 17 17 GLU A 18 0.998 0.995 0.933 0.678 0.501 18 18 LYS A 19 0.996 0.985 0.917 0.382 0.636 0.210 19 19 GLY A 20 0.999 0.998 20 20 ALA A 21 0.998 0.998 21 21 ASP A 22 0.995 0.997 0.930 0.648 22 22 ARG A 23 0.998 0.997 0.975 0.444 0.381 0.798 0.997 23 23 TYR A 24 0.997 0.999 0.983 0.895 24 24 GLN A 25 0.998 0.988 0.733 0.619 0.329 25 25 GLU A 26 0.992 0.979 0.619 0.387 0.348 26 26 GLY A 27 0.361 0.224 LYS A 28 0.571 0.399 0.165 0.518 0.564 0.379 ASN A 29 0.709 0.219 0.445 0.435 SER A 30 0.641 0.392 0.286 ASN A 31 0.673 0.296 0.389 0.229 HIS A 32 0.754 0.537 0.339 0.393 SER A 33 0.466 0.431 0.529 TYR A 34 0.567 0.328 0.219 0.279 ASP A 35 0.603 0.515 0.653 0.417 PHE A 36 0.128 0.352 0.741 0.609 PHE A 37 0.451 0.551 0.456 0.227 GLU A 38 0.646 0.948 0.693 0.486 0.299 THR A 39 0.964 0.968 0.201 39 39 ILE A 40 0.986 0.714 0.996 0.512 LYS A 41 0.701 0.998 0.803 0.440 0.664 0.375 PRO A 42 0.994 0.986 0.943 0.858 42 42 ALA A 43 0.995 0.996 43 43 VAL A 44 0.999 0.996 0.999 44 44 GLU A 45 0.996 0.998 0.994 0.464 0.322 45 45 GLU A 46 0.998 0.997 0.799 0.533 0.237 46 46 ASN A 47 0.997 0.993 0.997 0.318 47 47 ASP A 48 0.998 0.998 0.995 0.708 48 48 GLU A 49 0.995 0.993 0.981 0.671 0.349 49 49 LEU A 50 0.999 1.000 0.975 0.997 50 50 ALA A 51 0.998 0.997 51 51 ALA A 52 0.999 0.995 52 52 ARG A 53 0.997 0.997 0.893 0.780 0.748 0.851 0.996 53 53 TRP A 54 0.999 0.999 0.999 0.999 54 54 ALA A 55 1.000 0.999 55 55 GLU A 56 1.000 0.997 0.712 0.666 0.266 56 56 GLY A 57 0.998 0.999 57 57 ALA A 58 0.999 0.999 58 58 LEU A 59 0.999 0.999 0.999 1.000 59 59 GLU A 60 0.997 0.997 0.991 0.999 0.552 60 60 LEU A 61 0.999 0.997 0.731 0.319 61 61 ILE A 62 0.998 0.988 0.998 1.000 62 62 LYS A 63 1.000 0.987 0.576 0.359 0.621 0.271 63 63 VAL A 64 0.989 0.996 0.998 64 64 ARG A 65 0.952 0.524 0.407 0.644 0.292 0.607 0.998 ARG A 66 0.552 0.967 0.738 0.519 0.455 0.828 0.998 PRO A 67 0.986 0.741 0.945 0.892 LYS A 68 0.752 0.587 0.477 0.443 0.531 0.138 TYR A 69 0.575 0.986 0.986 0.801 VAL A 70 0.980 0.992 0.998 70 70 HIS A 71 0.976 0.986 0.758 0.587 71 71 LYS A 72 0.998 0.993 0.419 0.748 0.244 0.370 72 72 GLU A 73 0.997 0.994 0.576 0.581 0.243 73 73 GLN A 74 0.997 0.997 0.942 0.611 0.475 74 74 ILE A 75 0.999 0.999 0.997 0.653 75 75 GLU A 76 0.997 0.997 0.995 0.709 0.384 76 76 ALA A 77 0.997 0.995 77 77 VAL A 78 0.998 0.999 0.999 78 78 LYS A 79 0.999 0.998 0.993 0.814 0.864 0.861 79 79 ASP A 80 0.996 0.997 0.899 0.735 80 80 ASN A 81 0.997 0.997 0.996 0.757 81 81 PHE A 82 0.999 0.996 0.998 0.994 82 82 LEU A 83 0.999 0.998 0.996 0.923 83 83 GLU A 84 0.997 0.995 0.602 0.125 0.255 84 84 LEU A 85 0.999 0.999 0.994 0.997 85 85 VAL A 86 0.999 0.999 1.000 86 86 LEU A 87 0.998 0.996 0.999 1.000 87 87 GLN A 88 0.988 0.977 0.446 0.515 0.285 88 88 SER A 89 0.997 0.986 0.615 89 89 TYR A 90 0.979 0.991 0.995 0.984 90 90 VAL A 91 0.996 0.990 0.998 91 91 HIS A 92 0.995 0.944 0.926 0.805 92 92 HIS A 93 0.973 0.832 0.490 0.624 93 ILE A 94 0.904 0.845 0.442 0.559 94 HIS A 95 0.864 0.253 0.634 0.230 LYS A 96 0.496 0.900 0.506 0.540 0.503 0.415 LYS A 97 0.995 0.987 0.477 0.588 0.606 0.577 97 97 ARG A 98 0.990 0.991 0.661 0.491 0.259 0.865 0.998 98 98 PHE A 99 0.998 0.997 0.995 0.602 99 99 LYS A 100 0.998 0.993 0.692 0.378 0.707 0.335 100 100 ASP A 101 0.997 0.997 0.938 0.253 101 101 ILE A 102 1.000 0.999 0.999 0.999 102 102 THR A 103 0.999 0.999 1.000 103 103 GLU A 104 0.999 0.997 0.688 0.524 0.392 104 104 SER A 105 0.998 0.999 0.526 105 105 VAL A 106 0.999 0.999 0.999 106 106 LEU A 107 0.999 0.998 0.987 0.659 107 107 TYR A 108 0.999 0.998 0.987 0.890 108 108 THR A 109 0.998 0.999 0.999 109 109 LEU A 110 1.000 0.999 0.999 0.999 110 110 HIS A 111 0.998 0.998 0.987 0.772 111 111 ALA A 112 0.999 0.997 112 112 VAL A 113 0.997 0.997 1.000 113 113 LYS A 114 0.999 0.998 0.992 0.624 0.560 0.327 114 114 ASP A 115 0.998 0.995 0.987 0.579 115 115 GLU A 116 0.996 0.992 0.649 0.452 0.485 116 116 ILE A 117 0.999 0.998 0.999 0.999 117 117 ALA A 118 0.994 0.991 118 118 ARG A 119 0.984 0.950 0.972 0.661 0.453 0.547 0.998 119 119 GLU A 120 0.985 0.968 0.590 0.266 0.354 120 120 ASP A 121 0.229 0.583 0.848 0.630 SER A 122 0.854 0.339 0.461 ARG A 123 0.578 0.299 0.461 0.406 0.735 0.998 Ranges: 4 from: A 7 to A 26 from: A 42 to A 64 from: A 70 to A 92 from: A 97 to A 120 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[7..26],A[42..64],A[70..92],A[97..120],for model 1 is: 0.564 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 2 is: 0.502 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 3 is: 0.632 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 4 is: 0.615 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 5 is: 0.599 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 6 is: 0.507 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 7 is: 0.543 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 8 is: 0.649 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 9 is: 0.658 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 10 is: 0.566 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 11 is: 0.693 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 12 is: 0.629 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 13 is: 0.513 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 14 is: 0.579 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 15 is: 0.579 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 16 is: 0.582 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 17 is: 0.661 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 18 is: 0.625 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 19 is: 0.544 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 20 is: 0.469 (*) > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[7..26],[42..64],[70..92],[97..120], is: 0.585 > Range of RMSD values to reference struct. is 0.469 to 0.693 > 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[7..26],A[42..64],A[70..92],A[97..120],for model 1 is: 1.041 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 2 is: 0.963 (*) > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 3 is: 1.000 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 4 is: 1.043 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 5 is: 1.028 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 6 is: 1.063 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 7 is: 1.060 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 8 is: 1.203 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 9 is: 1.149 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 10 is: 1.134 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 11 is: 1.241 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 12 is: 1.115 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 13 is: 1.138 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 14 is: 1.182 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 15 is: 1.079 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 16 is: 1.088 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 17 is: 1.095 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 18 is: 1.119 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 19 is: 1.067 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 20 is: 1.071 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[7..26],[42..64],[70..92],[97..120], is: 1.094 > Range of RMSD values to reference struct. is 0.963 to 1.241 PdbStat> PdbStat> *END* of program detected, BYE! ...