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_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 129 MET SER ILE SER THR SER ALA GLU VAL TYR TYR GLU GLU 1 > ReadCoordsPdb(): Counting models in file `SSR10_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 SSR10_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 42620 ATOM records read from file > ReadCoordsPdb(): --> 42620 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 0.343 0.564 0.638 0.190 SER A 2 0.903 0.288 0.298 ILE A 3 0.893 0.966 0.717 0.950 3 SER A 4 0.105 0.852 0.420 THR A 5 0.768 0.986 0.917 SER A 6 0.985 0.985 0.777 6 6 ALA A 7 0.996 0.998 7 7 GLU A 8 0.991 0.994 0.428 0.935 0.794 8 8 VAL A 9 0.997 0.999 1.000 9 9 TYR A 10 0.998 0.998 0.998 0.801 10 10 TYR A 11 0.999 0.999 0.997 0.999 11 11 GLU A 12 0.997 0.997 0.594 1.000 1.000 12 12 GLU A 13 0.999 0.997 1.000 0.919 0.951 13 13 ALA A 14 0.998 0.999 14 14 GLU A 15 0.998 0.997 0.596 0.691 0.815 15 15 GLU A 16 0.997 0.995 0.620 0.932 0.998 16 16 PHE A 17 0.998 0.998 0.998 0.916 17 17 LEU A 18 0.999 0.997 0.664 0.597 18 18 SER A 19 0.998 0.993 0.492 19 19 LYS A 20 0.992 0.989 0.764 1.000 1.000 1.000 20 20 GLY A 21 0.990 0.998 21 21 ASP A 22 0.996 0.997 0.998 0.987 22 22 LEU A 23 0.999 0.999 0.999 0.999 23 23 VAL A 24 0.998 1.000 1.000 24 24 GLN A 25 0.999 0.998 1.000 0.569 0.444 25 25 ALA A 26 0.999 0.999 26 26 CYS A 27 0.999 0.996 0.831 27 27 GLU A 28 0.997 0.997 0.633 0.800 0.957 28 28 LYS A 29 0.994 0.979 0.994 0.855 0.999 0.929 29 29 TYR A 30 0.995 0.984 0.336 0.400 30 30 TYR A 31 0.999 0.998 0.992 0.998 31 31 LYS A 32 0.999 0.998 0.938 0.728 0.805 0.924 32 32 ALA A 33 1.000 0.998 33 33 ALA A 34 1.000 0.998 34 34 GLU A 35 0.993 0.989 0.351 0.997 0.816 35 35 GLU A 36 0.998 0.998 0.941 0.922 0.938 36 36 ALA A 37 0.999 0.999 37 37 ILE A 38 0.999 0.998 0.999 0.465 38 38 LYS A 39 0.998 0.993 0.358 0.996 0.526 0.991 39 39 LEU A 40 0.998 0.999 0.999 0.999 40 40 LEU A 41 0.999 0.997 1.000 1.000 41 41 VAL A 42 0.993 0.999 1.000 42 42 ILE A 43 1.000 0.998 1.000 1.000 43 43 GLU A 44 0.995 0.989 0.707 0.611 0.813 44 44 ASN A 45 0.985 0.913 0.794 0.742 45 45 ASN A 46 0.860 0.985 0.644 0.794 46 LEU A 47 0.998 0.986 0.990 0.845 47 47 LYS A 48 0.997 0.996 0.872 1.000 1.000 1.000 48 48 GLU A 49 0.997 0.993 0.610 1.000 1.000 49 49 ILE A 50 0.990 0.999 0.998 0.681 50 50 THR A 51 0.991 0.985 0.506 51 51 ASN A 52 0.997 0.993 1.000 1.000 52 52 ASN A 53 0.997 0.991 1.000 0.997 53 53 VAL A 54 0.949 0.937 0.423 54 54 LYS A 55 0.985 0.992 0.518 0.999 1.000 1.000 55 55 ASN A 56 0.943 0.988 0.945 0.985 56 56 LYS A 57 0.986 0.451 0.999 0.686 0.998 0.922 GLY A 58 0.395 0.872 ARG A 59 0.959 0.962 0.693 0.611 0.861 0.726 1.000 59 59 TRP A 60 0.991 0.841 0.940 0.692 60 LYS A 61 0.832 0.420 0.552 0.635 0.999 0.999 SER A 62 0.676 0.962 0.340 GLU A 63 0.995 0.994 0.663 0.999 0.971 63 63 ASN A 64 0.997 0.995 1.000 0.990 64 64 LEU A 65 0.994 0.997 0.999 0.998 65 65 PHE A 66 0.999 0.993 0.926 0.928 66 66 LYS A 67 0.996 0.998 1.000 1.000 0.997 0.999 67 67 ALA A 68 0.999 0.992 68 68 SER A 69 0.994 0.994 0.835 69 69 LYS A 70 0.998 0.992 0.712 0.997 0.936 0.934 70 70 LEU A 71 0.985 0.562 0.804 0.717 LEU A 72 0.569 0.958 0.996 0.999 ARG A 73 0.978 0.992 0.342 0.998 0.738 0.993 1.000 73 73 SER A 74 0.999 0.999 1.000 74 74 ASN A 75 0.997 0.998 0.874 0.842 75 75 ASN A 76 0.997 0.989 0.998 0.953 76 76 THR A 77 0.988 0.997 1.000 77 77 GLU A 78 0.988 0.984 0.999 0.923 0.890 78 78 ILE A 79 0.998 0.998 1.000 1.000 79 79 PRO A 80 0.995 0.995 0.952 0.908 80 80 ILE A 81 0.994 0.999 1.000 1.000 81 81 LEU A 82 0.997 0.998 0.999 1.000 82 82 TRP A 83 0.997 0.995 0.935 0.606 83 83 LYS A 84 0.996 0.997 0.768 1.000 1.000 1.000 84 84 SER A 85 0.997 0.995 0.715 85 85 ALA A 86 0.992 0.991 86 86 TRP A 87 0.998 0.989 0.995 0.452 87 87 THR A 88 0.993 0.988 0.925 88 88 LEU A 89 0.994 0.985 0.639 0.638 89 89 HIS A 90 0.955 0.994 0.923 0.653 90 90 VAL A 91 0.990 0.981 0.856 91 91 GLU A 92 0.786 0.828 0.860 0.537 0.893 GLY A 93 0.785 0.432 PHE A 94 0.397 0.672 0.551 0.795 HIS A 95 0.432 0.594 0.483 0.193 GLU A 96 0.520 0.323 0.539 0.796 0.927 LEU A 97 0.953 0.892 0.595 0.524 97 SER A 98 0.617 0.656 0.169 LEU A 99 0.355 0.916 0.937 0.937 ASN A 100 0.930 0.973 0.653 0.916 100 100 GLU A 101 0.996 0.995 0.934 0.999 0.986 101 101 LYS A 102 0.998 0.995 0.667 1.000 1.000 1.000 102 102 GLU A 103 0.998 0.997 0.999 0.426 0.934 103 103 VAL A 104 0.999 0.994 0.917 104 104 LYS A 105 0.997 0.990 0.936 1.000 0.999 1.000 105 105 LYS A 106 0.989 0.996 0.664 0.925 0.876 0.998 106 106 LEU A 107 0.996 0.993 0.605 0.634 107 107 LYS A 108 0.997 0.983 0.660 0.918 0.868 0.617 108 108 GLU A 109 0.992 0.993 0.869 0.590 0.922 109 109 ASP A 110 0.998 0.996 1.000 1.000 110 110 VAL A 111 0.999 0.996 1.000 111 111 ARG A 112 0.998 0.997 0.999 0.880 0.424 0.587 1.000 112 112 LYS A 113 0.998 0.998 0.999 0.998 0.600 0.997 113 113 LEU A 114 0.999 0.999 0.692 0.647 114 114 VAL A 115 1.000 0.999 1.000 115 115 ILE A 116 0.996 0.995 0.837 1.000 116 116 PHE A 117 0.999 0.999 0.998 0.918 117 117 ALA A 118 0.999 0.999 118 118 VAL A 119 0.999 0.996 1.000 119 119 ASN A 120 0.997 0.997 0.942 0.956 120 120 SER A 121 0.995 0.991 0.447 121 121 LEU A 122 0.980 0.956 0.814 0.753 122 122 GLU A 123 0.641 0.707 0.868 0.701 0.893 HIS A 124 0.526 0.625 0.623 0.504 HIS A 125 0.554 0.737 0.473 0.521 HIS A 126 0.130 0.127 0.678 0.820 HIS A 127 0.551 0.596 0.407 0.528 HIS A 128 0.441 0.298 0.391 0.633 HIS A 129 0.934 0.639 0.235 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: 0.589 > 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: 0.653 > 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: 0.777 > 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: 0.749 > 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: 0.734 > 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: 0.635 > 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: 0.679 > 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: 0.724 > 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: 0.964 > 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: 0.698 > 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: 0.818 > 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: 0.543 (*) > 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: 0.815 > 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: 0.765 > 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: 0.963 > 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: 0.653 > 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: 0.652 > 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: 0.784 > 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: 0.698 > 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: 0.667 > > 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: 0.728 > Range of RMSD values to reference struct. is 0.543 to 0.964 > 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: 0.889 (*) > 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: 1.047 > 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: 1.161 > 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: 1.057 > 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: 1.134 > 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: 0.981 > 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: 0.976 > 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: 1.212 > 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: 1.320 > 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: 1.096 > 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: 1.293 > 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: 0.906 > 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: 1.173 > 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: 1.042 > 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: 1.477 > 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: 1.119 > 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: 0.937 > 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: 1.334 > 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: 1.107 > 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: 1.035 > > 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: 1.115 > Range of RMSD values to reference struct. is 0.889 to 1.477 PdbStat> PdbStat> *END* of program detected, BYE! ...