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_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 134 MET PRO ALA SER ARG TYR ILE THR ASP MET THR ILE GLU 1 > ReadCoordsPdb(): Counting models in file `OR8C_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 OR8C_R3_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 0.842 0.814 0.462 0.429 PRO A 2 0.995 0.680 0.911 0.821 ALA A 3 0.703 0.811 SER A 4 0.912 0.952 0.853 4 4 ARG A 5 0.935 0.972 0.691 0.575 0.660 0.625 1.000 5 5 TYR A 6 0.971 0.987 0.869 0.871 6 6 ILE A 7 0.976 0.987 0.999 0.707 7 7 THR A 8 0.999 0.966 0.609 8 8 ASP A 9 0.985 0.984 0.693 0.769 9 9 MET A 10 0.978 0.960 0.701 0.995 0.477 10 10 THR A 11 0.993 0.998 0.999 11 11 ILE A 12 0.998 0.997 0.890 0.877 12 12 GLU A 13 0.995 0.991 0.758 0.999 0.979 13 13 GLU A 14 0.978 0.988 0.756 0.475 0.916 14 14 LEU A 15 0.989 0.992 0.769 0.764 15 15 SER A 16 0.981 0.945 0.632 16 16 ARG A 17 0.984 0.979 0.995 0.999 0.496 0.676 1.000 17 17 ASP A 18 0.979 0.875 0.680 0.996 18 TRP A 19 0.994 0.954 0.688 0.978 19 19 PHE A 20 0.956 0.974 0.543 0.997 20 20 MET A 21 0.974 0.959 0.999 0.999 0.681 21 21 LEU A 22 0.988 0.995 0.999 1.000 22 22 MET A 23 0.997 0.989 0.939 0.926 0.845 23 23 PRO A 24 0.996 0.993 0.907 0.816 24 24 LYS A 25 0.972 0.994 0.999 0.645 0.998 0.998 25 25 GLN A 26 0.983 0.986 0.594 0.998 0.748 26 26 LYS A 27 0.987 0.947 0.652 0.664 0.995 0.926 27 27 VAL A 28 0.963 0.994 1.000 28 28 GLU A 29 0.983 0.993 0.877 0.835 0.946 29 29 GLY A 30 0.996 0.997 30 30 PRO A 31 0.997 0.992 0.999 1.000 31 31 LEU A 32 0.997 0.994 0.983 0.838 32 32 CYS A 33 0.991 0.998 1.000 33 33 ILE A 34 0.999 0.998 0.999 0.907 34 34 ARG A 35 0.994 0.996 0.987 0.943 0.532 0.812 1.000 35 35 ILE A 36 0.995 0.997 1.000 0.922 36 36 ASP A 37 0.995 0.998 1.000 0.964 37 37 GLN A 38 0.995 0.997 0.998 0.725 0.746 38 38 ALA A 39 0.994 0.971 39 39 ILE A 40 0.987 0.996 0.999 0.622 40 40 MET A 41 0.993 0.992 0.183 0.996 0.553 41 41 ASP A 42 0.997 0.994 0.664 0.844 42 42 LYS A 43 0.993 0.997 0.999 0.999 0.999 0.950 43 43 ASN A 44 0.997 0.994 0.999 0.953 44 44 ILE A 45 0.991 0.998 1.000 0.915 45 45 MET A 46 0.995 0.995 0.928 0.780 0.672 46 46 LEU A 47 0.990 0.991 0.923 0.668 47 47 LYS A 48 0.989 0.985 0.998 0.997 0.744 0.936 48 48 ALA A 49 0.982 0.992 49 49 ASN A 50 0.997 0.979 0.620 0.953 50 50 PHE A 51 0.990 0.997 0.998 0.998 51 51 SER A 52 0.996 0.994 0.798 52 52 VAL A 53 0.989 0.995 0.848 53 53 ILE A 54 0.991 0.995 0.762 0.999 54 54 PHE A 55 0.996 0.929 0.887 0.893 55 55 ASP A 56 0.912 0.994 0.643 0.818 56 56 ARG A 57 0.989 0.981 0.649 0.612 0.785 0.677 1.000 57 57 LEU A 58 0.994 0.998 0.998 0.909 58 58 GLU A 59 0.998 0.994 1.000 0.997 0.909 59 59 THR A 60 0.984 0.992 0.797 60 60 LEU A 61 0.991 0.998 0.999 1.000 61 61 ILE A 62 0.997 0.997 1.000 1.000 62 62 LEU A 63 0.992 0.994 0.502 0.644 63 63 LEU A 64 0.996 0.995 0.996 0.945 64 64 ARG A 65 0.996 0.994 0.769 0.663 0.693 0.184 0.999 65 65 ALA A 66 0.986 0.995 66 66 PHE A 67 0.952 0.989 0.472 0.999 67 67 THR A 68 0.989 0.995 1.000 68 68 GLU A 69 0.994 0.987 0.637 0.810 0.864 69 69 GLU A 70 0.986 0.995 0.998 0.878 0.842 70 70 GLY A 71 0.993 0.988 71 71 ALA A 72 0.982 0.983 72 72 ILE A 73 0.992 0.994 0.934 0.835 73 73 VAL A 74 0.992 0.983 0.917 74 74 GLY A 75 0.986 0.995 75 75 GLU A 76 0.997 0.994 0.998 0.995 0.762 76 76 ILE A 77 0.995 0.994 1.000 1.000 77 77 SER A 78 0.990 0.993 0.455 78 78 PRO A 79 0.996 0.997 0.917 0.825 79 79 LEU A 80 0.977 0.994 0.934 0.938 80 80 PRO A 81 0.992 0.761 0.926 0.861 SER A 82 0.739 0.961 0.774 PHE A 83 0.985 0.846 0.998 0.992 83 PRO A 84 0.984 0.851 0.927 0.884 84 GLY A 85 0.535 0.549 HIS A 86 0.822 0.949 0.925 0.898 86 THR A 87 0.988 0.997 0.923 87 87 ILE A 88 0.999 0.994 0.718 0.919 88 88 GLU A 89 0.991 0.987 0.934 0.694 0.957 89 89 ASP A 90 0.981 0.998 0.998 0.991 90 90 VAL A 91 0.997 0.999 1.000 91 91 LYS A 92 0.997 0.989 0.549 0.953 0.650 0.918 92 92 ASN A 93 0.998 0.999 1.000 1.000 93 93 ALA A 94 0.999 0.999 94 94 ILE A 95 1.000 0.999 1.000 1.000 95 95 GLY A 96 0.999 0.998 96 96 VAL A 97 0.999 1.000 1.000 97 97 LEU A 98 0.999 0.998 1.000 1.000 98 98 ILE A 99 0.999 0.998 1.000 1.000 99 99 GLY A 100 0.999 0.999 100 100 GLY A 101 0.999 0.991 101 101 LEU A 102 0.991 0.996 0.999 0.999 102 102 GLU A 103 0.999 0.993 0.999 0.538 0.940 103 103 ARG A 104 0.998 0.995 0.999 0.998 0.925 0.564 1.000 104 104 ASN A 105 0.994 0.989 1.000 0.975 105 105 ASP A 106 0.995 0.976 0.676 0.878 106 106 ASN A 107 0.923 0.980 0.511 0.606 107 107 THR A 108 0.992 0.979 1.000 108 108 VAL A 109 0.983 0.996 1.000 109 109 ARG A 110 0.998 0.980 0.931 0.926 1.000 0.936 1.000 110 110 VAL A 111 0.973 0.989 0.704 111 111 SER A 112 0.993 0.985 0.568 112 112 LYS A 113 0.996 0.990 0.708 1.000 1.000 1.000 113 113 THR A 114 0.974 0.968 0.714 114 114 LEU A 115 0.971 0.995 0.934 0.862 115 115 GLN A 116 0.992 0.979 0.725 0.921 0.931 116 116 ARG A 117 0.968 0.961 0.605 0.862 0.790 0.889 1.000 117 117 PHE A 118 0.969 0.942 0.992 0.792 118 118 ALA A 119 0.936 0.988 119 119 TRP A 120 0.984 0.734 0.870 0.635 GLY A 121 0.727 0.273 SER A 122 0.570 0.613 0.424 SER A 123 0.803 0.442 0.282 ASN A 124 0.475 0.545 0.292 0.674 GLU A 125 0.887 0.735 0.484 0.601 0.939 ASN A 126 0.859 0.581 0.378 0.858 GLY A 127 0.364 0.068 ARG A 128 0.395 0.910 0.694 0.875 0.789 0.936 1.000 PRO A 129 0.993 0.982 0.904 0.814 129 129 PRO A 130 0.994 0.933 0.908 0.818 130 130 LEU A 131 0.978 0.899 0.529 0.574 131 THR A 132 0.957 0.853 0.519 132 LEU A 133 0.958 0.947 0.855 0.805 133 133 GLU A 134 0.871 0.575 0.999 0.978 Ranges: 4 from: A 4 to A 17 from: A 19 to A 80 from: A 87 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[4..17],A[19..80],A[87..119],A[129..130],for model 1 is: 3.697 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 2 is: 2.235 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 3 is: 2.274 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 4 is: 3.104 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 5 is: 3.245 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 6 is: 1.904 (*) > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 7 is: 3.395 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 8 is: 3.022 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 9 is: 2.411 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 10 is: 2.854 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 11 is: 2.133 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 12 is: 2.493 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 13 is: 2.657 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 14 is: 2.284 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 15 is: 2.364 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 16 is: 2.031 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 17 is: 3.090 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 18 is: 3.305 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 19 is: 2.279 > Kabsch RMSD of backbone atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 20 is: 2.844 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..17],[19..80],[87..119],[129..130], is: 2.681 > Range of RMSD values to reference struct. is 1.904 to 3.697 > 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[4..17],A[19..80],A[87..119],A[129..130],for model 1 is: 3.606 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 2 is: 2.241 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 3 is: 2.348 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 4 is: 3.036 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 5 is: 3.198 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 6 is: 2.026 (*) > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 7 is: 3.332 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 8 is: 2.998 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 9 is: 2.538 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 10 is: 2.866 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 11 is: 2.149 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 12 is: 2.543 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 13 is: 2.680 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 14 is: 2.285 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 15 is: 2.412 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 16 is: 2.039 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 17 is: 3.059 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 18 is: 3.225 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 19 is: 2.444 > Kabsch RMSD of heavy atoms in res. A[4..17],A[19..80],A[87..119],A[129..130],for model 20 is: 2.940 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..17],[19..80],[87..119],[129..130], is: 2.698 > Range of RMSD values to reference struct. is 2.026 to 3.606 PdbStat> PdbStat> *END* of program detected, BYE! ...