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 `OR8C_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 134 MET PRO ALA SER ARG TYR ILE THR ASP MET THR ILE GLU 1 > ReadCoordsPdb(): Counting models in file `OR8C_R3Cons_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 OR8C_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 42760 ATOM records read from file > ReadCoordsPdb(): --> 42760 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 0.610 0.536 0.271 0.095 PRO A 2 0.982 0.357 0.886 0.818 ALA A 3 0.523 0.528 SER A 4 0.725 0.882 0.569 ARG A 5 0.945 0.998 0.998 1.000 0.812 0.952 1.000 5 5 TYR A 6 0.995 0.999 0.997 0.899 6 6 ILE A 7 0.998 0.999 1.000 1.000 7 7 THR A 8 0.994 0.997 1.000 8 8 ASP A 9 0.996 0.997 0.662 0.783 9 9 MET A 10 0.993 0.989 0.261 0.998 0.282 10 10 THR A 11 0.999 0.999 0.999 11 11 ILE A 12 0.998 1.000 1.000 1.000 12 12 GLU A 13 0.999 0.995 0.999 0.999 1.000 13 13 GLU A 14 0.998 0.996 0.501 0.577 0.899 14 14 LEU A 15 0.998 0.998 0.819 0.940 15 15 SER A 16 0.997 0.999 0.695 16 16 ARG A 17 0.999 0.999 1.000 0.998 0.997 0.932 1.000 17 17 ASP A 18 0.998 0.986 0.610 0.996 18 18 TRP A 19 0.997 0.999 0.998 0.999 19 19 PHE A 20 0.990 0.995 0.930 0.998 20 20 MET A 21 0.995 0.989 0.845 0.918 0.528 21 21 LEU A 22 0.973 0.979 0.715 0.762 22 22 MET A 23 0.995 0.998 1.000 0.997 0.849 23 23 PRO A 24 0.993 0.998 0.911 0.823 24 24 LYS A 25 0.990 0.997 0.997 0.751 0.876 0.930 25 25 GLN A 26 0.996 0.995 1.000 0.751 0.942 26 26 LYS A 27 0.994 0.999 0.996 0.781 0.999 0.877 27 27 VAL A 28 0.997 0.999 1.000 28 28 GLU A 29 0.999 1.000 0.999 1.000 1.000 29 29 GLY A 30 0.999 0.999 30 30 PRO A 31 0.998 0.996 0.999 1.000 31 31 LEU A 32 0.997 0.999 0.992 0.764 32 32 CYS A 33 0.998 0.999 1.000 33 33 ILE A 34 1.000 0.999 1.000 1.000 34 34 ARG A 35 0.997 0.999 0.923 0.996 0.774 0.821 1.000 35 35 ILE A 36 0.997 0.998 0.874 0.738 36 36 ASP A 37 0.999 0.998 0.999 0.971 37 37 GLN A 38 0.999 0.998 1.000 0.999 0.888 38 38 ALA A 39 0.995 0.985 39 39 ILE A 40 0.990 0.995 0.991 0.486 40 40 MET A 41 0.997 0.999 0.999 1.000 0.833 41 41 ASP A 42 0.998 0.998 1.000 1.000 42 42 LYS A 43 0.999 0.999 0.999 0.999 0.999 0.942 43 43 ASN A 44 0.999 0.999 0.999 0.942 44 44 ILE A 45 0.999 0.999 1.000 1.000 45 45 MET A 46 0.999 0.999 0.993 0.997 0.725 46 46 LEU A 47 0.997 0.993 0.999 1.000 47 47 LYS A 48 0.998 0.998 0.998 0.841 0.454 0.859 48 48 ALA A 49 0.995 0.995 49 49 ASN A 50 0.998 0.996 0.996 0.947 50 50 PHE A 51 0.998 0.999 1.000 0.999 51 51 SER A 52 0.999 0.998 0.929 52 52 VAL A 53 0.999 0.998 0.999 53 53 ILE A 54 0.996 0.995 0.997 0.729 54 54 PHE A 55 0.999 0.933 0.999 0.808 55 55 ASP A 56 0.911 0.996 0.769 0.879 56 56 ARG A 57 0.995 0.997 0.998 0.642 0.935 0.894 1.000 57 57 LEU A 58 0.998 0.998 0.995 0.999 58 58 GLU A 59 0.999 0.999 0.999 0.998 0.939 59 59 THR A 60 0.998 0.999 1.000 60 60 LEU A 61 1.000 1.000 0.999 1.000 61 61 ILE A 62 1.000 0.999 1.000 1.000 62 62 LEU A 63 1.000 0.999 0.999 1.000 63 63 LEU A 64 0.999 0.999 0.998 1.000 64 64 ARG A 65 0.997 0.996 0.513 0.990 0.223 0.660 0.995 65 65 ALA A 66 0.995 0.999 66 66 PHE A 67 0.965 0.996 0.492 0.599 67 67 THR A 68 0.997 0.997 1.000 68 68 GLU A 69 0.999 0.998 0.383 0.995 0.868 69 69 GLU A 70 0.998 0.999 1.000 1.000 0.928 70 70 GLY A 71 0.999 0.997 71 71 ALA A 72 0.998 0.995 72 72 ILE A 73 0.997 0.999 1.000 0.954 73 73 VAL A 74 0.999 0.994 1.000 74 74 GLY A 75 0.996 0.999 75 75 GLU A 76 0.999 0.999 0.997 0.999 0.784 76 76 ILE A 77 0.999 0.999 1.000 0.999 77 77 SER A 78 0.998 0.994 0.724 78 78 PRO A 79 0.995 0.999 0.915 0.818 79 79 LEU A 80 0.990 0.997 1.000 1.000 80 80 PRO A 81 0.995 0.758 0.940 0.885 SER A 82 0.747 0.966 0.705 PHE A 83 0.992 0.944 0.998 0.993 83 83 PRO A 84 0.978 0.852 0.921 0.886 84 GLY A 85 0.633 0.722 HIS A 86 0.944 0.982 0.929 0.899 86 86 THR A 87 0.995 0.999 1.000 87 87 ILE A 88 0.999 1.000 0.999 1.000 88 88 GLU A 89 0.999 0.999 1.000 0.648 0.937 89 89 ASP A 90 0.996 0.999 0.999 0.991 90 90 VAL A 91 0.999 0.998 1.000 91 91 LYS A 92 0.999 0.994 0.492 0.998 0.861 0.785 92 92 ASN A 93 0.997 1.000 1.000 0.999 93 93 ALA A 94 1.000 0.999 94 94 ILE A 95 1.000 0.999 1.000 1.000 95 95 GLY A 96 1.000 0.999 96 96 VAL A 97 1.000 1.000 1.000 97 97 LEU A 98 0.999 0.998 0.999 0.999 98 98 ILE A 99 1.000 0.998 0.946 1.000 99 99 GLY A 100 0.999 1.000 100 100 GLY A 101 1.000 1.000 101 101 LEU A 102 1.000 0.999 1.000 1.000 102 102 GLU A 103 1.000 0.999 1.000 0.856 0.984 103 103 ARG A 104 1.000 0.999 1.000 0.999 0.930 0.665 1.000 104 104 ASN A 105 0.987 0.972 0.995 0.679 105 105 ASP A 106 0.996 0.990 0.840 0.924 106 106 ASN A 107 0.990 0.981 0.485 0.617 107 107 THR A 108 0.996 0.994 1.000 108 108 VAL A 109 0.997 0.998 0.544 109 109 ARG A 110 0.994 0.999 0.999 1.000 0.933 0.999 1.000 110 110 VAL A 111 0.998 0.999 1.000 111 111 SER A 112 0.997 0.996 0.754 112 112 LYS A 113 0.998 0.998 0.640 0.999 1.000 1.000 113 113 THR A 114 0.996 0.992 0.999 114 114 LEU A 115 0.997 0.998 0.999 1.000 115 115 GLN A 116 0.998 0.991 0.999 0.997 0.967 116 116 ARG A 117 0.997 0.984 0.607 0.650 0.865 0.822 0.999 117 117 PHE A 118 0.993 0.996 0.998 0.400 118 118 ALA A 119 0.993 0.996 119 119 TRP A 120 0.987 0.756 0.994 0.993 GLY A 121 0.671 0.240 SER A 122 0.569 0.663 0.490 SER A 123 0.849 0.383 0.294 ASN A 124 0.503 0.566 0.408 0.858 GLU A 125 0.851 0.746 0.544 0.556 0.878 ASN A 126 0.867 0.566 0.327 0.855 GLY A 127 0.354 0.018 ARG A 128 0.418 0.916 0.839 0.738 0.933 0.840 1.000 PRO A 129 0.991 0.985 0.914 0.833 129 129 PRO A 130 0.995 0.942 0.910 0.820 130 130 LEU A 131 0.985 0.837 0.998 1.000 131 THR A 132 0.974 0.883 0.856 132 LEU A 133 0.966 0.952 0.999 0.999 133 133 GLU A 134 0.939 0.696 1.000 1.000 Ranges: 3 from: A 5 to A 80 from: A 86 to A 119 from: A 129 to A 130 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[5..80],A[86..119],A[129..130],for model 1 is: 2.148 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 2 is: 2.257 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 3 is: 2.873 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 4 is: 3.086 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 5 is: 1.979 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 6 is: 2.939 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 7 is: 3.119 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 8 is: 3.851 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 9 is: 3.967 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 10 is: 1.858 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 11 is: 2.631 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 12 is: 3.920 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 13 is: 2.541 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 14 is: 2.302 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 15 is: 1.728 (*) > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 16 is: 1.819 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 17 is: 2.420 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 18 is: 2.785 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 19 is: 2.526 > Kabsch RMSD of backbone atoms in res. A[5..80],A[86..119],A[129..130],for model 20 is: 2.316 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[5..80],[86..119],[129..130], is: 2.653 > Range of RMSD values to reference struct. is 1.728 to 3.967 > 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[5..80],A[86..119],A[129..130],for model 1 is: 2.128 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 2 is: 2.217 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 3 is: 2.735 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 4 is: 2.986 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 5 is: 1.972 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 6 is: 2.794 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 7 is: 2.965 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 8 is: 3.675 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 9 is: 3.795 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 10 is: 1.849 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 11 is: 2.515 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 12 is: 3.765 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 13 is: 2.500 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 14 is: 2.258 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 15 is: 1.754 (*) > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 16 is: 1.843 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 17 is: 2.366 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 18 is: 2.704 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 19 is: 2.474 > Kabsch RMSD of heavy atoms in res. A[5..80],A[86..119],A[129..130],for model 20 is: 2.287 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[5..80],[86..119],[129..130], is: 2.579 > Range of RMSD values to reference struct. is 1.754 to 3.795 PdbStat> PdbStat> *END* of program detected, BYE! ...