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 `HR3646E_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP.PDB, 20 MODEL/S TEMP.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 121 MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET ALA GLN 1 > ReadCoordsPdb(): Counting models in file `HR3646E_R3_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 HR3646E_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 37880 ATOM records read from file > ReadCoordsPdb(): --> 37880 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 0.666 0.917 0.520 0.111 GLY A 2 0.419 0.069 HIS A 3 0.543 0.598 0.658 0.829 HIS A 4 0.632 0.635 0.400 0.513 HIS A 5 0.854 0.744 0.784 0.522 HIS A 6 0.595 0.645 0.457 0.270 HIS A 7 0.742 0.633 0.398 0.670 HIS A 8 0.501 0.674 0.687 0.749 SER A 9 0.768 0.775 0.515 HIS A 10 0.855 0.576 0.381 0.463 MET A 11 0.657 0.741 0.551 0.412 0.180 ALA A 12 0.666 0.566 GLN A 13 0.693 0.630 0.503 0.373 0.750 PHE A 14 0.779 0.835 0.526 0.938 PRO A 15 0.991 0.930 0.933 0.888 15 15 THR A 16 0.870 0.753 0.703 PRO A 17 0.981 0.832 0.902 0.849 17 PHE A 18 0.535 0.698 0.649 0.867 GLY A 19 0.334 0.277 GLY A 20 0.402 0.301 SER A 21 0.766 0.467 0.435 LEU A 22 0.536 0.305 0.706 0.695 ASP A 23 0.257 0.559 0.487 0.917 THR A 24 0.917 0.934 0.486 24 24 TRP A 25 0.974 0.892 0.849 0.305 25 ALA A 26 0.926 0.992 26 26 ILE A 27 0.964 0.992 0.999 0.643 27 27 THR A 28 0.990 0.995 0.999 28 28 VAL A 29 0.999 0.993 0.780 29 29 GLU A 30 0.990 0.998 0.811 0.998 0.951 30 30 GLU A 31 0.998 0.997 0.998 0.435 0.920 31 31 ARG A 32 0.997 0.992 0.603 0.898 0.674 0.724 1.000 32 32 ALA A 33 0.990 0.990 33 33 LYS A 34 0.995 0.984 0.871 0.928 0.920 0.998 34 34 HIS A 35 0.988 0.980 0.302 0.443 35 35 ASP A 36 0.997 0.995 0.941 0.966 36 36 GLN A 37 0.974 0.994 0.816 0.786 0.912 37 37 GLN A 38 0.982 0.992 0.932 0.925 0.850 38 38 PHE A 39 0.998 0.996 0.889 0.977 39 39 HIS A 40 0.996 0.996 0.934 0.645 40 40 SER A 41 0.998 0.989 0.589 41 41 LEU A 42 0.988 0.971 0.853 0.791 42 42 LYS A 43 0.999 0.999 1.000 1.000 1.000 1.000 43 43 PRO A 44 0.992 0.985 0.909 0.825 44 44 ILE A 45 0.971 0.429 0.998 0.840 SER A 46 0.413 0.599 0.318 GLY A 47 0.527 0.983 PHE A 48 0.971 0.967 0.558 0.996 48 48 ILE A 49 0.994 0.989 1.000 0.960 49 49 THR A 50 0.928 0.987 0.594 50 50 GLY A 51 0.998 0.990 51 51 ASP A 52 0.996 0.998 0.944 0.926 52 52 GLN A 53 0.991 0.996 0.819 0.200 0.732 53 53 ALA A 54 0.999 0.997 54 54 ARG A 55 0.997 0.989 0.840 0.933 0.360 0.582 1.000 55 55 ASN A 56 0.998 0.995 1.000 1.000 56 56 PHE A 57 0.995 0.996 0.993 0.994 57 57 PHE A 58 0.966 0.977 0.833 0.537 58 58 PHE A 59 0.990 0.979 0.559 0.670 59 59 GLN A 60 0.988 0.975 0.878 0.560 0.913 60 60 SER A 61 0.995 0.992 0.420 61 61 GLY A 62 0.983 0.971 62 62 LEU A 63 0.976 0.993 0.992 0.928 63 63 PRO A 64 0.988 0.991 0.904 0.835 64 64 GLN A 65 0.997 0.999 0.601 1.000 0.998 65 65 PRO A 66 0.994 0.995 0.911 0.813 66 66 VAL A 67 0.998 0.997 0.918 67 67 LEU A 68 0.991 0.989 0.865 0.632 68 68 ALA A 69 0.996 0.998 69 69 GLN A 70 0.996 0.996 0.602 0.637 0.884 70 70 ILE A 71 0.999 0.998 1.000 0.919 71 71 TRP A 72 0.998 0.998 0.929 0.425 72 72 ALA A 73 0.999 0.998 73 73 LEU A 74 0.995 0.989 0.927 0.780 74 74 ALA A 75 0.998 0.985 75 75 ASP A 76 0.995 0.984 0.998 0.949 76 76 MET A 77 0.975 0.965 0.716 0.551 0.652 77 77 ASN A 78 0.967 0.986 0.999 0.901 78 78 ASN A 79 0.996 0.987 0.710 0.831 79 79 ASP A 80 0.982 0.978 0.552 0.900 80 80 GLY A 81 0.979 0.975 81 81 ARG A 82 0.953 0.885 0.854 0.575 0.668 0.598 1.000 82 MET A 83 0.867 0.826 0.647 0.711 0.387 83 ASP A 84 0.906 0.992 0.409 0.899 84 84 GLN A 85 0.996 0.991 0.506 0.996 0.992 85 85 VAL A 86 0.991 0.994 0.940 86 86 GLU A 87 0.997 0.997 0.994 0.793 0.794 87 87 PHE A 88 0.998 0.994 0.833 0.910 88 88 SER A 89 0.996 0.981 0.266 89 89 ILE A 90 0.973 0.973 0.368 0.933 90 90 ALA A 91 0.998 0.989 91 91 MET A 92 0.995 0.993 0.605 0.323 0.175 92 92 LYS A 93 0.986 0.994 0.693 0.372 0.712 0.715 93 93 LEU A 94 0.999 0.996 0.935 0.855 94 94 ILE A 95 0.996 0.999 0.999 0.776 95 95 LYS A 96 0.997 0.989 0.591 0.998 0.998 0.927 96 96 LEU A 97 0.993 0.993 0.780 0.707 97 97 LYS A 98 0.990 0.992 0.660 0.335 0.724 0.804 98 98 LEU A 99 0.997 0.991 0.816 0.809 99 99 GLN A 100 0.990 0.975 0.935 0.625 0.898 100 100 GLY A 101 0.976 0.989 101 101 TYR A 102 0.976 0.970 0.862 0.916 102 102 GLN A 103 0.921 0.557 0.525 0.436 0.755 LEU A 104 0.540 0.970 0.616 0.700 PRO A 105 0.991 0.991 0.952 0.916 105 105 SER A 106 0.987 0.995 0.916 106 106 ALA A 107 0.904 0.936 107 107 LEU A 108 0.973 0.976 0.762 0.658 108 108 PRO A 109 0.992 0.991 0.906 0.826 109 109 PRO A 110 0.993 0.992 0.909 0.825 110 110 VAL A 111 0.987 0.966 0.475 111 111 MET A 112 0.970 0.986 0.858 0.730 0.290 112 112 LYS A 113 0.970 0.963 0.209 0.932 0.865 0.999 113 113 GLN A 114 0.900 0.647 0.808 0.601 0.777 GLN A 115 0.534 0.813 0.509 0.649 0.860 PRO A 116 0.987 0.908 0.896 0.821 116 116 VAL A 117 0.929 0.961 0.786 117 117 ALA A 118 0.531 0.487 ILE A 119 0.746 0.486 0.926 0.561 SER A 120 0.806 0.469 0.584 SER A 121 0.761 0.928 Ranges: 5 from: A 26 to A 44 from: A 48 to A 81 from: A 84 to A 102 from: A 105 to A 113 from: A 116 to A 117 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[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 1 is: 1.363 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 2 is: 1.046 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 3 is: 2.284 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 4 is: 1.177 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 5 is: 1.498 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 6 is: 1.489 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 7 is: 1.582 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 8 is: 1.540 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 9 is: 0.873 (*) > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 10 is: 1.698 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 11 is: 1.667 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 12 is: 1.671 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 13 is: 1.462 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 14 is: 1.375 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 15 is: 1.385 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 16 is: 1.600 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 17 is: 1.014 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 18 is: 1.593 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 19 is: 1.723 > Kabsch RMSD of backbone atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 20 is: 1.733 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[26..44],[48..81],[84..102],[105..113],[116..117], is: 1.489 > Range of RMSD values to reference struct. is 0.873 to 2.284 > 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[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 1 is: 1.734 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 2 is: 1.324 (*) > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 3 is: 2.551 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 4 is: 1.457 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 5 is: 1.980 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 6 is: 1.733 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 7 is: 1.982 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 8 is: 1.720 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 9 is: 1.380 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 10 is: 2.015 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 11 is: 1.897 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 12 is: 1.863 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 13 is: 1.877 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 14 is: 1.784 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 15 is: 1.752 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 16 is: 1.932 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 17 is: 1.437 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 18 is: 1.981 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 19 is: 1.929 > Kabsch RMSD of heavy atoms in res. A[26..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 20 is: 2.022 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[26..44],[48..81],[84..102],[105..113],[116..117], is: 1.817 > Range of RMSD values to reference struct. is 1.324 to 2.551 PdbStat> PdbStat> *END* of program detected, BYE! ...