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_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 19 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 18 MODEL/S TEMP_BCM_111.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_R3Cons_em_bcr3.pdb'; Model: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 > ReadCoordsPdb(): After scanning there is(are) 18 model(s) > ReadCoordsPdb(): what model do you want [(1 to 18) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file HR3646E_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (18) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 34092 ATOM records read from file > ReadCoordsPdb(): --> 34092 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 0.504 0.923 0.542 0.350 GLY A 2 0.287 0.329 HIS A 3 0.456 0.611 0.621 0.721 HIS A 4 0.640 0.568 0.504 0.485 HIS A 5 0.804 0.683 0.710 0.420 HIS A 6 0.553 0.514 0.356 0.099 HIS A 7 0.717 0.757 0.382 0.646 HIS A 8 0.460 0.606 0.525 0.505 SER A 9 0.813 0.709 0.619 HIS A 10 0.881 0.689 0.594 0.700 MET A 11 0.595 0.679 0.479 0.260 0.263 ALA A 12 0.637 0.489 GLN A 13 0.784 0.581 0.549 0.442 0.763 PHE A 14 0.846 0.833 0.513 0.976 14 PRO A 15 0.991 0.911 0.944 0.905 15 15 THR A 16 0.863 0.802 0.534 16 PRO A 17 0.991 0.763 0.928 0.887 PHE A 18 0.469 0.628 0.566 0.228 GLY A 19 0.302 0.149 GLY A 20 0.391 0.316 SER A 21 0.784 0.487 0.282 LEU A 22 0.531 0.368 0.922 0.928 ASP A 23 0.218 0.731 0.514 0.867 THR A 24 0.948 0.997 0.999 24 24 TRP A 25 0.980 0.965 0.989 0.937 25 25 ALA A 26 0.940 0.991 26 26 ILE A 27 0.991 0.995 1.000 0.999 27 27 THR A 28 0.994 0.989 0.680 28 28 VAL A 29 0.999 0.998 0.876 29 29 GLU A 30 1.000 1.000 0.932 1.000 0.954 30 30 GLU A 31 1.000 1.000 0.996 0.843 0.859 31 31 ARG A 32 0.999 0.998 0.998 0.897 0.443 0.786 1.000 32 32 ALA A 33 1.000 0.998 33 33 LYS A 34 1.000 0.999 0.999 0.843 0.998 1.000 34 34 HIS A 35 0.999 0.997 0.542 0.576 35 35 ASP A 36 1.000 0.999 0.824 0.898 36 36 GLN A 37 0.999 0.997 0.798 0.924 0.980 37 37 GLN A 38 1.000 1.000 0.999 0.626 0.890 38 38 PHE A 39 1.000 1.000 0.990 0.457 39 39 HIS A 40 1.000 1.000 0.865 0.893 40 40 SER A 41 1.000 0.999 0.482 41 41 LEU A 42 0.997 0.997 0.711 0.836 42 42 LYS A 43 1.000 1.000 1.000 1.000 1.000 1.000 43 43 PRO A 44 0.990 0.997 0.915 0.845 44 44 ILE A 45 0.991 0.477 0.999 1.000 SER A 46 0.469 0.618 0.341 GLY A 47 0.562 0.985 PHE A 48 0.989 0.996 0.677 0.888 48 48 ILE A 49 0.997 0.997 1.000 0.769 49 49 THR A 50 0.973 0.993 0.999 50 50 GLY A 51 1.000 0.999 51 51 ASP A 52 1.000 1.000 0.877 0.928 52 52 GLN A 53 1.000 1.000 0.998 0.479 0.671 53 53 ALA A 54 1.000 1.000 54 54 ARG A 55 0.999 0.999 0.603 0.993 0.928 0.855 1.000 55 55 ASN A 56 1.000 0.999 1.000 1.000 56 56 PHE A 57 1.000 1.000 1.000 0.999 57 57 PHE A 58 0.980 0.984 0.722 0.727 58 58 PHE A 59 1.000 1.000 0.999 1.000 59 59 GLN A 60 1.000 0.998 0.999 0.838 0.943 60 60 SER A 61 0.999 0.999 0.634 61 61 GLY A 62 0.990 0.986 62 62 LEU A 63 0.982 0.996 1.000 0.999 63 63 PRO A 64 0.988 0.997 0.899 0.820 64 64 GLN A 65 0.999 0.999 1.000 1.000 1.000 65 65 PRO A 66 0.994 0.995 0.907 0.812 66 66 VAL A 67 0.997 0.997 1.000 67 67 LEU A 68 1.000 0.999 0.999 0.999 68 68 ALA A 69 1.000 1.000 69 69 GLN A 70 1.000 1.000 0.903 0.824 0.897 70 70 ILE A 71 1.000 1.000 1.000 1.000 71 71 TRP A 72 1.000 1.000 0.997 0.998 72 72 ALA A 73 1.000 0.999 73 73 LEU A 74 0.995 0.996 0.996 0.714 74 74 ALA A 75 0.999 0.992 75 75 ASP A 76 0.998 0.994 0.959 0.962 76 76 MET A 77 1.000 1.000 1.000 0.996 0.728 77 77 ASN A 78 0.997 0.997 0.905 0.961 78 78 ASN A 79 0.997 0.996 0.813 0.833 79 79 ASP A 80 0.991 0.982 0.558 0.962 80 80 GLY A 81 0.988 0.969 81 81 ARG A 82 0.986 0.887 0.907 0.709 0.604 0.557 1.000 82 MET A 83 0.878 0.870 0.634 0.993 0.530 83 ASP A 84 0.934 0.997 0.329 0.885 84 84 GLN A 85 0.999 1.000 0.999 0.998 0.984 85 85 VAL A 86 0.999 1.000 1.000 86 86 GLU A 87 1.000 0.998 0.999 0.880 0.931 87 87 PHE A 88 1.000 0.998 0.945 0.872 88 88 SER A 89 1.000 0.995 0.450 89 89 ILE A 90 0.995 0.984 0.701 0.999 90 90 ALA A 91 0.994 0.995 91 91 MET A 92 0.995 0.992 0.761 0.456 0.159 92 92 LYS A 93 0.994 0.993 0.939 0.646 0.919 0.708 93 93 LEU A 94 1.000 0.998 0.938 0.849 94 94 ILE A 95 1.000 1.000 0.999 0.917 95 95 LYS A 96 1.000 1.000 0.999 0.999 0.998 0.993 96 96 LEU A 97 0.994 0.996 0.999 0.999 97 97 LYS A 98 1.000 0.999 0.685 0.227 0.205 0.620 98 98 LEU A 99 1.000 0.999 0.999 0.999 99 99 GLN A 100 1.000 0.999 0.996 0.847 0.552 100 100 GLY A 101 0.994 0.996 101 101 TYR A 102 0.995 0.993 0.999 0.993 102 102 GLN A 103 0.928 0.658 0.556 0.921 0.940 LEU A 104 0.637 0.939 0.409 0.633 PRO A 105 0.991 0.989 0.923 0.863 105 105 SER A 106 0.953 0.990 0.576 106 106 ALA A 107 0.908 0.958 107 107 LEU A 108 0.982 0.990 0.788 0.810 108 108 PRO A 109 0.993 1.000 0.907 0.832 109 109 PRO A 110 0.994 0.996 0.963 0.932 110 110 VAL A 111 0.996 0.995 0.443 111 111 MET A 112 0.996 0.999 0.854 0.397 0.316 112 112 LYS A 113 0.998 0.998 0.906 0.990 0.849 0.998 113 113 GLN A 114 0.897 0.691 0.998 0.921 0.787 GLN A 115 0.543 0.801 0.776 0.921 0.878 PRO A 116 0.986 0.915 0.899 0.822 116 116 VAL A 117 0.934 0.973 0.540 117 117 ALA A 118 0.517 0.557 ILE A 119 0.819 0.545 0.922 0.821 SER A 120 0.810 0.399 0.594 SER A 121 0.724 1.000 Ranges: 5 from: A 24 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[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 1 is: 0.791 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 2 is: 1.304 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 3 is: 0.890 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 4 is: 1.905 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 5 is: 1.331 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 6 is: 0.924 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 7 is: 0.814 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 8 is: 1.184 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 9 is: 0.929 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 10 is: 1.224 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 11 is: 0.774 (*) > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 12 is: 1.154 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 13 is: 0.938 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 14 is: 1.008 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 15 is: 0.824 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 16 is: 0.778 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 17 is: 0.969 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 18 is: 1.261 > > Kabsch RMSD statistics for 18 structures: > Mean RMSD using as refer. str. `average' for res.[24..44],[48..81],[84..102],[105..113],[116..117], is: 1.056 > Range of RMSD values to reference struct. is 0.774 to 1.905 > 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[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 1 is: 1.025 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 2 is: 1.493 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 3 is: 1.156 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 4 is: 1.958 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 5 is: 1.563 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 6 is: 1.159 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 7 is: 1.017 (*) > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 8 is: 1.418 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 9 is: 1.041 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 10 is: 1.522 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 11 is: 1.092 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 12 is: 1.251 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 13 is: 1.360 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 14 is: 1.192 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 15 is: 1.136 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 16 is: 1.063 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 17 is: 1.203 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],A[116..117],for model 18 is: 1.409 > > Kabsch RMSD statistics for 18 structures: > Mean RMSD using as refer. str. `average' for res.[24..44],[48..81],[84..102],[105..113],[116..117], is: 1.281 > Range of RMSD values to reference struct. is 1.017 to 1.958 PdbStat> PdbStat> *END* of program detected, BYE! ...