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 `HR5546A_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 122 MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET THR GLY 1 > ReadCoordsPdb(): Counting models in file `HR5546A_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 HR5546A_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 37820 ATOM records read from file > ReadCoordsPdb(): --> 37820 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 0.517 0.867 0.513 0.334 GLY A 2 0.475 0.278 HIS A 3 0.855 0.425 0.303 0.577 HIS A 4 0.815 0.559 0.165 0.257 HIS A 5 0.689 0.572 0.600 0.677 HIS A 6 0.782 0.697 0.544 0.521 HIS A 7 0.668 0.766 0.509 0.712 HIS A 8 0.783 0.727 0.651 0.432 SER A 9 0.809 0.884 0.448 9 HIS A 10 0.822 0.705 0.872 0.902 MET A 11 0.829 0.859 0.587 0.448 0.056 11 THR A 12 0.937 0.337 0.607 GLY A 13 0.042 0.645 ASN A 14 0.898 0.724 0.619 0.785 VAL A 15 0.977 0.994 1.000 15 15 CYS A 16 0.985 0.991 0.634 16 16 ILE A 17 0.988 0.988 1.000 0.951 17 17 GLU A 18 0.980 0.995 0.846 0.400 0.792 18 18 GLU A 19 0.986 0.974 0.438 0.783 0.916 19 19 ILE A 20 0.980 0.992 1.000 0.999 20 20 ASP A 21 0.993 0.991 0.996 0.981 21 21 VAL A 22 0.948 0.969 0.425 22 22 ASP A 23 0.970 0.995 0.997 0.943 23 23 GLY A 24 0.993 0.992 24 24 LYS A 25 0.968 0.979 0.998 0.861 0.931 0.999 25 25 PHE A 26 0.997 0.998 0.999 0.112 26 26 ILE A 27 0.996 0.989 1.000 0.999 27 27 ARG A 28 0.988 0.995 0.932 0.990 0.318 0.620 1.000 28 28 LEU A 29 0.997 0.988 0.975 0.798 29 29 LYS A 30 0.992 0.996 0.999 0.999 0.999 1.000 30 30 ASN A 31 0.993 0.992 0.997 0.920 31 31 THR A 32 0.989 0.877 0.927 32 SER A 33 0.832 0.985 0.869 33 GLU A 34 0.980 0.926 0.999 0.923 0.982 34 34 GLN A 35 0.955 0.983 0.475 0.463 0.802 35 35 ASP A 36 0.995 0.983 0.867 1.000 36 36 GLN A 37 0.979 0.957 0.629 0.518 0.682 37 37 PRO A 38 0.989 0.654 0.902 0.823 MET A 39 0.588 0.782 0.644 0.481 0.075 GLY A 40 0.615 0.489 GLY A 41 0.570 0.918 TRP A 42 0.920 0.976 0.995 0.827 42 42 GLU A 43 0.977 0.993 1.000 0.999 0.975 43 43 MET A 44 0.996 0.991 0.999 0.839 0.644 44 44 ILE A 45 0.988 0.989 1.000 0.959 45 45 ARG A 46 0.967 0.994 0.918 0.761 0.267 0.547 1.000 46 46 LYS A 47 0.974 0.977 0.699 0.996 0.999 0.998 47 47 ILE A 48 0.918 0.307 0.456 0.999 GLY A 49 0.422 0.326 ASP A 50 0.358 0.746 0.337 0.908 THR A 51 0.858 0.974 0.361 51 SER A 52 0.983 0.820 0.697 52 VAL A 53 0.909 0.970 0.355 53 53 SER A 54 0.932 0.971 0.368 54 54 TYR A 55 0.988 0.997 0.998 0.997 55 55 LYS A 56 0.996 0.986 0.868 0.935 0.998 0.871 56 56 TYR A 57 0.973 0.942 0.995 0.520 57 57 THR A 58 0.883 0.890 0.338 58 SER A 59 0.970 0.822 0.258 59 ARG A 60 0.907 0.970 0.824 0.603 0.662 0.574 1.000 60 60 TYR A 61 0.991 0.996 0.998 0.997 61 61 VAL A 62 0.983 0.981 0.624 62 62 LEU A 63 0.978 0.983 0.581 0.592 63 63 LYS A 64 0.991 0.987 0.754 0.999 1.000 0.926 64 64 ALA A 65 0.998 0.993 65 65 GLY A 66 0.997 0.993 66 66 GLN A 67 0.980 0.975 0.679 0.601 0.692 67 67 THR A 68 0.981 0.872 0.923 68 VAL A 69 0.842 0.988 0.847 69 THR A 70 0.995 0.993 0.687 70 70 ILE A 71 0.992 0.997 0.996 0.158 71 71 TRP A 72 0.997 0.992 0.999 0.993 72 72 ALA A 73 0.988 0.808 73 ALA A 74 0.717 0.930 ASN A 75 0.981 0.947 0.437 0.908 75 75 ALA A 76 0.960 0.963 76 76 GLY A 77 0.995 0.978 77 77 VAL A 78 0.961 0.948 0.347 78 78 THR A 79 0.981 0.953 0.640 79 79 ALA A 80 0.889 0.349 SER A 81 0.400 0.847 0.427 PRO A 82 0.992 0.258 0.919 0.859 PRO A 83 0.829 0.464 0.831 0.863 THR A 84 0.549 0.880 0.288 ASP A 85 0.839 0.927 0.672 0.931 85 LEU A 86 0.972 0.976 0.997 0.925 86 86 ILE A 87 0.985 0.992 0.996 0.367 87 87 TRP A 88 0.987 0.989 0.993 0.981 88 88 LYS A 89 0.991 0.986 0.831 1.000 1.000 1.000 89 89 ASN A 90 0.979 0.961 0.998 0.983 90 90 GLN A 91 0.960 0.982 0.723 0.670 0.821 91 91 ASN A 92 0.989 0.772 0.748 0.957 SER A 93 0.777 0.829 0.599 TRP A 94 0.808 0.202 0.994 0.996 GLY A 95 0.433 0.624 THR A 96 0.761 0.651 0.429 GLY A 97 0.520 0.783 GLU A 98 0.878 0.781 0.917 0.558 0.904 ASP A 99 0.774 0.803 0.715 0.936 VAL A 100 0.849 0.968 0.671 100 LYS A 101 0.938 0.989 1.000 0.998 0.876 0.999 101 101 VAL A 102 0.996 0.995 0.854 102 102 ILE A 103 0.995 0.998 1.000 1.000 103 103 LEU A 104 0.994 0.990 0.885 0.929 104 104 LYS A 105 0.987 0.983 1.000 0.999 0.999 1.000 105 105 ASN A 106 0.991 0.940 0.861 0.993 106 106 SER A 107 0.858 0.941 0.618 107 GLN A 108 0.990 0.949 0.995 0.851 0.970 108 108 GLY A 109 0.893 0.985 109 GLU A 110 0.970 0.990 0.859 0.938 0.899 110 110 GLU A 111 0.997 0.992 0.603 0.998 0.930 111 111 VAL A 112 0.994 0.987 0.863 112 112 ALA A 113 0.982 0.985 113 113 GLN A 114 0.970 0.935 0.485 0.998 0.818 114 114 ARG A 115 0.948 0.973 0.774 0.567 0.219 0.683 1.000 115 115 SER A 116 0.925 0.989 0.936 116 116 THR A 117 0.844 0.860 0.205 117 VAL A 118 0.921 0.956 0.866 118 118 PHE A 119 0.856 0.673 0.493 0.921 LYS A 120 0.860 0.609 0.521 0.928 0.931 0.999 THR A 121 0.673 0.657 0.526 THR A 122 0.737 0.647 Ranges: 10 from: A 15 to A 31 from: A 34 to A 37 from: A 42 to A 47 from: A 53 to A 57 from: A 60 to A 67 from: A 70 to A 72 from: A 75 to A 79 from: A 86 to A 91 from: A 101 to A 106 from: A 110 to A 116 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[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 1 is: 0.862 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 2 is: 0.566 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 3 is: 0.639 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 4 is: 0.693 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 5 is: 0.924 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 6 is: 0.754 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 7 is: 0.683 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 8 is: 0.697 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 9 is: 0.880 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 10 is: 0.789 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 11 is: 0.624 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 12 is: 0.802 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 13 is: 0.557 (*) > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 14 is: 0.728 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 15 is: 0.708 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 16 is: 0.937 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 17 is: 0.579 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 18 is: 1.030 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 19 is: 0.574 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 20 is: 0.675 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[15..31],[34..37],[42..47],[53..57],[60..67],[70..72],[75..79],[86..91],[101..106],[110..116], is: 0.735 > Range of RMSD values to reference struct. is 0.557 to 1.030 > 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[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 1 is: 1.319 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 2 is: 0.928 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 3 is: 1.119 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 4 is: 1.264 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 5 is: 1.161 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 6 is: 1.253 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 7 is: 1.211 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 8 is: 1.041 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 9 is: 1.244 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 10 is: 1.124 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 11 is: 0.946 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 12 is: 1.159 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 13 is: 0.958 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 14 is: 1.120 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 15 is: 1.074 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 16 is: 1.210 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 17 is: 0.914 (*) > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 18 is: 1.239 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 19 is: 1.053 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[53..57],A[60..67],A[70..72],A[75..79],A[86..91],A[101..106],A[110..116],for model 20 is: 1.114 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[15..31],[34..37],[42..47],[53..57],[60..67],[70..72],[75..79],[86..91],[101..106],[110..116], is: 1.123 > Range of RMSD values to reference struct. is 0.914 to 1.319 PdbStat> PdbStat> *END* of program detected, BYE! ...