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 `SSR10_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS 23-MAY-07 2JPU > ReadCoordsPdb(): >> TITLE SOLUTION STRUCTURE OF NESG TARGET SSR10, ORF C02003 PROTEIN > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): >> COMPND 2 MOLECULE: ORF C02003 PROTEIN; > ReadCoordsPdb(): >> COMPND 3 CHAIN: A; 1 > ReadCoordsPdb(): Counting models in file `SSR10_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 SSR10_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 42780 ATOM records read from file > ReadCoordsPdb(): --> 42780 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 0.326 0.421 0.148 0.785 SER A 2 0.882 0.310 0.663 ILE A 3 0.853 0.987 0.863 0.888 3 SER A 4 0.166 0.951 0.535 THR A 5 0.799 0.990 0.815 SER A 6 0.998 0.995 0.620 6 6 ALA A 7 0.999 0.998 7 7 GLU A 8 0.995 0.993 0.700 0.613 0.368 8 8 VAL A 9 0.998 0.999 0.999 9 9 TYR A 10 0.997 0.997 0.992 0.880 10 10 TYR A 11 0.999 0.999 0.991 0.995 11 11 GLU A 12 0.997 0.996 0.949 0.795 0.258 12 12 GLU A 13 0.999 0.997 0.997 0.782 0.490 13 13 ALA A 14 0.999 0.999 14 14 GLU A 15 0.999 0.997 0.993 0.786 0.419 15 15 GLU A 16 0.999 0.996 0.888 0.926 0.379 16 16 PHE A 17 0.998 0.998 0.996 0.910 17 17 LEU A 18 0.998 0.998 0.989 0.921 18 18 SER A 19 0.993 0.987 0.608 19 19 LYS A 20 0.987 0.975 0.991 0.481 0.590 0.451 20 20 GLY A 21 0.965 0.984 21 21 ASP A 22 0.983 0.959 0.838 0.537 22 22 LEU A 23 0.974 0.993 0.998 0.999 23 23 VAL A 24 0.995 0.997 0.999 24 24 GLN A 25 0.997 0.997 0.997 0.865 0.480 25 25 ALA A 26 0.994 0.996 26 26 CYS A 27 0.998 0.992 0.437 27 27 GLU A 28 0.997 0.996 0.597 0.338 0.467 28 28 LYS A 29 0.993 0.977 0.860 0.433 0.756 0.227 29 29 TYR A 30 0.993 0.978 0.287 0.455 30 30 TYR A 31 0.999 0.997 0.990 0.898 31 31 LYS A 32 0.997 0.992 0.952 0.502 0.574 0.454 32 32 ALA A 33 0.997 0.998 33 33 ALA A 34 0.996 0.998 34 34 GLU A 35 0.998 0.995 0.388 0.980 0.306 35 35 GLU A 36 0.998 0.994 0.929 0.872 0.691 36 36 ALA A 37 0.997 0.997 37 37 ILE A 38 0.999 0.999 0.998 1.000 38 38 LYS A 39 0.993 0.990 0.316 0.781 0.394 0.078 39 39 LEU A 40 0.997 0.998 0.987 0.669 40 40 LEU A 41 0.997 0.995 0.982 0.641 41 41 VAL A 42 0.994 0.995 0.998 42 42 ILE A 43 0.997 0.995 0.999 0.515 43 43 GLU A 44 0.995 0.986 0.068 0.317 0.305 44 44 ASN A 45 0.991 0.927 0.928 0.857 45 45 ASN A 46 0.865 0.931 0.994 0.422 46 LEU A 47 0.988 0.976 0.999 0.999 47 47 LYS A 48 0.996 0.985 0.788 0.753 0.679 0.642 48 48 GLU A 49 0.995 0.984 0.628 0.542 0.624 49 49 ILE A 50 0.988 0.995 0.996 0.679 50 50 THR A 51 0.995 0.990 0.644 51 51 ASN A 52 0.994 0.990 0.294 0.543 52 52 ASN A 53 0.992 0.984 0.725 0.554 53 53 VAL A 54 0.982 0.973 0.807 54 54 LYS A 55 0.994 0.990 0.836 0.391 0.778 0.425 55 55 ASN A 56 0.929 0.971 0.947 0.402 56 56 LYS A 57 0.984 0.444 0.918 0.746 0.472 0.568 GLY A 58 0.409 0.907 ARG A 59 0.948 0.979 0.970 0.518 0.485 0.811 0.999 59 59 TRP A 60 0.984 0.836 0.970 0.979 60 LYS A 61 0.798 0.429 0.363 0.666 0.506 0.626 SER A 62 0.658 0.966 0.616 GLU A 63 0.996 0.992 0.325 0.640 0.328 63 63 ASN A 64 0.993 0.994 0.629 0.494 64 64 LEU A 65 0.997 0.996 0.998 0.997 65 65 PHE A 66 0.998 0.995 0.623 0.713 66 66 LYS A 67 0.995 0.997 0.980 0.451 0.602 0.572 67 67 ALA A 68 0.996 0.996 68 68 SER A 69 0.997 0.999 0.520 69 69 LYS A 70 0.999 0.998 0.906 0.711 0.857 0.644 70 70 LEU A 71 0.991 0.660 0.999 0.999 LEU A 72 0.599 0.989 0.998 1.000 ARG A 73 0.998 0.997 0.989 0.756 0.533 0.734 0.998 73 73 SER A 74 0.994 0.989 0.397 74 74 ASN A 75 0.987 0.995 0.789 0.455 75 75 ASN A 76 0.987 0.988 0.940 0.544 76 76 THR A 77 0.993 0.993 0.438 77 77 GLU A 78 0.992 0.987 0.996 0.986 0.289 78 78 ILE A 79 0.999 0.999 0.996 0.509 79 79 PRO A 80 0.999 0.999 0.970 0.928 80 80 ILE A 81 0.998 0.997 0.999 0.924 81 81 LEU A 82 0.995 0.997 0.997 0.998 82 82 TRP A 83 0.999 0.997 0.998 0.999 83 83 LYS A 84 0.996 0.996 0.992 0.634 0.807 0.569 84 84 SER A 85 0.998 0.999 0.931 85 85 ALA A 86 0.999 0.999 86 86 TRP A 87 0.997 0.995 0.990 0.995 87 87 THR A 88 0.999 0.995 0.999 88 88 LEU A 89 0.998 0.993 0.861 0.866 89 89 HIS A 90 0.988 0.987 0.889 0.300 90 90 VAL A 91 0.997 0.986 0.999 91 91 GLU A 92 0.776 0.772 0.610 0.316 0.312 GLY A 93 0.741 0.427 PHE A 94 0.419 0.779 0.607 0.510 HIS A 95 0.417 0.609 0.741 0.185 GLU A 96 0.525 0.318 0.399 0.415 0.233 LEU A 97 0.974 0.977 0.995 0.998 97 97 SER A 98 0.587 0.757 0.648 LEU A 99 0.420 0.874 0.998 0.756 ASN A 100 0.919 0.985 0.785 0.231 100 100 GLU A 101 0.995 0.994 0.942 0.790 0.411 101 101 LYS A 102 0.999 0.997 0.972 0.475 0.772 0.631 102 102 GLU A 103 0.995 0.989 0.666 0.097 0.278 103 103 VAL A 104 0.997 0.995 0.998 104 104 LYS A 105 0.997 0.997 0.738 0.532 0.716 0.287 105 105 LYS A 106 0.995 0.995 0.642 0.800 0.226 0.374 106 106 LEU A 107 0.998 0.999 0.978 0.997 107 107 LYS A 108 0.998 0.994 0.465 0.655 0.305 0.464 108 108 GLU A 109 0.996 0.994 0.527 0.436 0.247 109 109 ASP A 110 0.995 0.993 0.920 0.595 110 110 VAL A 111 0.998 0.999 0.999 111 111 ARG A 112 0.998 0.998 0.954 0.924 0.445 0.726 0.999 112 112 LYS A 113 0.998 0.993 0.952 0.635 0.365 0.093 113 113 LEU A 114 0.995 0.998 0.765 0.861 114 114 VAL A 115 0.999 0.999 0.998 115 115 ILE A 116 0.999 0.999 0.999 0.769 116 116 PHE A 117 0.997 0.997 0.906 0.410 117 117 ALA A 118 0.998 0.998 118 118 VAL A 119 0.998 0.997 0.997 119 119 ASN A 120 0.996 0.991 0.993 0.891 120 120 SER A 121 0.995 0.991 0.647 121 121 LEU A 122 0.985 0.937 0.920 0.719 122 122 GLU A 123 0.640 0.850 0.978 0.776 0.349 HIS A 124 0.611 0.687 0.541 0.289 HIS A 125 0.518 0.673 0.632 0.393 HIS A 126 0.116 0.061 0.756 0.320 HIS A 127 0.519 0.688 0.381 0.429 HIS A 128 0.421 0.337 0.422 0.355 HIS A 129 0.868 0.266 0.113 Ranges: 5 from: A 6 to A 45 from: A 47 to A 56 from: A 63 to A 70 from: A 73 to A 91 from: A 100 to A 122 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[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 1 is: 0.636 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 2 is: 0.760 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 3 is: 0.809 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 4 is: 0.764 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 5 is: 0.586 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 6 is: 0.786 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 7 is: 0.926 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 8 is: 0.737 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 9 is: 1.123 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 10 is: 0.779 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 11 is: 0.660 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 12 is: 0.663 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 13 is: 0.656 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 14 is: 0.689 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 15 is: 0.584 (*) > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 16 is: 0.686 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 17 is: 0.774 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 18 is: 0.738 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 19 is: 0.819 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 20 is: 0.618 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[6..45],[47..56],[63..70],[73..91],[100..122], is: 0.740 > Range of RMSD values to reference struct. is 0.584 to 1.123 > 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[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 1 is: 1.046 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 2 is: 1.241 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 3 is: 1.213 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 4 is: 1.207 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 5 is: 0.997 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 6 is: 1.165 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 7 is: 1.369 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 8 is: 1.172 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 9 is: 1.457 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 10 is: 1.211 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 11 is: 1.109 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 12 is: 1.014 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 13 is: 0.997 (*) > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 14 is: 1.138 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 15 is: 1.072 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 16 is: 1.092 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 17 is: 1.245 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 18 is: 1.174 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 19 is: 1.265 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 20 is: 1.077 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[6..45],[47..56],[63..70],[73..91],[100..122], is: 1.163 > Range of RMSD values to reference struct. is 0.997 to 1.457 PdbStat> PdbStat> *END* of program detected, BYE! ...