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 `UUR17A_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 121 MET LEU SER GLN ALA ASN GLU ASP PHE LYS LYS ILE VAL 1 > ReadCoordsPdb(): Counting models in file `UUR17A_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 UUR17A_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 40120 ATOM records read from file > ReadCoordsPdb(): --> 40120 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 0.121 0.530 0.429 0.345 LEU A 2 0.508 0.533 0.487 0.580 SER A 3 0.637 0.385 0.424 GLN A 4 0.759 0.412 0.406 0.571 0.803 ALA A 5 0.622 0.608 ASN A 6 0.991 0.996 0.999 0.876 6 6 GLU A 7 0.998 0.999 0.837 0.999 0.956 7 7 ASP A 8 0.996 0.998 0.683 0.787 8 8 PHE A 9 0.999 0.998 0.815 0.782 9 9 LYS A 10 0.999 0.999 0.908 0.996 0.870 0.929 10 10 LYS A 11 0.999 0.998 0.999 0.948 0.952 0.999 11 11 ILE A 12 0.998 0.999 0.954 1.000 12 12 VAL A 13 0.998 0.999 1.000 13 13 ASN A 14 1.000 0.999 0.999 0.979 14 14 ASN A 15 0.999 0.999 0.908 0.993 15 15 ILE A 16 0.996 0.994 1.000 1.000 16 16 ARG A 17 0.991 0.988 0.690 0.532 0.994 0.715 0.999 17 17 LEU A 18 0.997 0.995 0.992 0.987 18 18 LYS A 19 0.974 0.990 0.530 0.997 0.999 0.855 19 19 ASP A 20 0.999 0.999 1.000 1.000 20 20 THR A 21 0.985 0.988 0.534 21 21 PHE A 22 0.999 0.996 0.999 0.998 22 22 ASP A 23 0.991 0.986 0.868 0.938 23 23 PHE A 24 0.987 0.997 0.999 0.999 24 24 LYS A 25 0.996 0.998 0.999 0.992 0.317 0.992 25 25 LEU A 26 0.999 0.997 0.988 0.988 26 26 ALA A 27 1.000 0.999 27 27 ALA A 28 0.999 0.999 28 28 PHE A 29 0.998 0.995 0.998 0.998 29 29 PRO A 30 0.997 0.985 0.982 0.967 30 30 ASN A 31 0.982 0.881 0.999 0.729 31 GLN A 32 0.940 0.945 0.595 0.563 0.858 32 32 ASN A 33 0.941 0.939 0.710 0.864 33 33 TYR A 34 0.986 0.981 0.994 0.996 34 34 ASP A 35 0.975 0.983 0.454 0.921 35 35 GLN A 36 0.981 0.929 0.997 0.549 0.922 36 36 LEU A 37 0.936 0.989 0.706 0.734 37 37 LEU A 38 0.988 0.983 0.644 0.636 38 38 PRO A 39 0.995 0.996 0.980 0.967 39 39 SER A 40 1.000 1.000 0.632 40 40 GLN A 41 1.000 1.000 0.999 0.765 0.942 41 41 ILE A 42 0.999 0.999 0.948 1.000 42 42 TYR A 43 1.000 0.999 0.998 0.973 43 43 LYS A 44 0.998 0.994 1.000 0.932 1.000 1.000 44 44 ASN A 45 0.984 0.976 0.736 0.402 45 45 TYR A 46 0.999 0.999 0.751 0.984 46 46 TYR A 47 0.998 0.987 0.143 0.887 47 47 GLN A 48 0.989 0.989 0.703 0.563 0.721 48 48 GLY A 49 0.992 0.994 49 49 ILE A 50 0.999 1.000 0.999 0.961 50 50 GLU A 51 0.998 0.999 0.537 0.999 1.000 51 51 ILE A 52 0.998 0.999 1.000 1.000 52 52 GLN A 53 0.998 0.980 0.561 0.382 0.723 53 53 GLN A 54 0.998 0.996 0.784 0.948 0.886 54 54 HIS A 55 0.992 0.896 0.864 0.451 55 LYS A 56 0.954 0.876 0.619 0.462 0.686 0.508 56 TYR A 57 0.566 0.876 0.941 0.894 GLN A 58 0.953 0.852 0.997 0.947 0.471 58 ASN A 59 0.802 0.993 0.721 0.886 59 GLU A 60 0.988 0.995 0.799 0.592 0.821 60 60 LEU A 61 0.998 0.998 0.963 0.874 61 61 ASP A 62 0.997 0.986 0.996 0.948 62 62 ILE A 63 0.989 0.999 1.000 0.999 63 63 LYS A 64 0.999 0.966 1.000 1.000 1.000 0.936 64 64 ILE A 65 0.979 0.997 1.000 1.000 65 65 ILE A 66 0.987 0.991 0.999 0.760 66 66 ASN A 67 0.983 0.997 0.645 0.848 67 67 PHE A 68 0.995 0.997 0.999 0.995 68 68 LEU A 69 0.999 0.996 1.000 1.000 69 69 TYR A 70 0.990 0.978 0.995 0.976 70 70 PRO A 71 0.986 0.406 0.912 0.861 ASP A 72 0.353 0.859 0.859 0.898 GLY A 73 0.838 0.636 ASP A 74 0.929 0.929 0.638 0.761 74 74 PHE A 75 0.995 0.997 0.998 0.301 75 75 GLY A 76 1.000 0.999 76 76 SER A 77 1.000 0.999 0.403 77 77 ALA A 78 1.000 1.000 78 78 ASN A 79 1.000 0.998 0.940 0.957 79 79 LYS A 80 0.996 0.991 0.948 0.999 1.000 0.869 80 80 ASN A 81 0.973 0.972 0.773 0.951 81 81 GLY A 82 0.991 0.984 82 82 THR A 83 0.997 0.999 0.999 83 83 LEU A 84 0.992 0.996 0.636 0.654 84 84 LYS A 85 0.999 0.996 0.999 0.993 0.868 0.995 85 85 LEU A 86 0.998 0.999 0.956 0.513 86 86 SER A 87 0.998 0.998 0.487 87 87 LEU A 88 0.997 0.997 0.997 0.926 88 88 MET A 89 0.999 0.999 0.999 1.000 0.932 89 89 LEU A 90 0.998 0.986 0.996 0.995 90 90 THR A 91 0.993 0.998 1.000 91 91 ASP A 92 0.997 0.994 0.997 0.943 92 92 LYS A 93 0.995 0.985 0.999 0.865 0.767 0.997 93 93 LYS A 94 0.975 0.985 0.681 0.454 0.999 0.996 94 94 ASN A 95 0.982 0.997 0.999 0.986 95 95 ASN A 96 0.999 0.998 1.000 0.801 96 96 GLN A 97 0.997 0.999 1.000 1.000 1.000 97 97 VAL A 98 0.991 0.999 0.597 98 98 TYR A 99 0.979 0.966 0.186 0.773 99 99 TYR A 100 0.987 0.983 0.998 0.997 100 100 LYS A 101 0.988 0.998 0.997 0.964 0.935 0.584 101 101 LEU A 102 0.998 0.999 0.999 1.000 102 102 LEU A 103 0.998 0.994 0.995 0.965 103 103 GLU A 104 0.993 0.999 0.579 1.000 1.000 104 104 VAL A 105 0.998 0.998 0.999 105 105 SER A 106 0.990 0.998 1.000 106 106 GLY A 107 0.998 0.988 107 107 PHE A 108 0.987 0.906 0.997 0.983 108 108 LYS A 109 0.880 0.844 0.719 0.526 0.924 0.860 109 SER A 110 0.894 0.954 0.731 110 ASN A 111 0.995 0.989 0.937 0.721 111 111 PRO A 112 0.999 0.942 0.999 1.000 112 112 TYR A 113 0.874 0.991 0.994 0.400 113 LEU A 114 0.982 0.965 0.999 0.997 114 114 GLU A 115 0.939 0.529 0.509 0.444 0.868 HIS A 116 0.649 0.646 0.731 0.888 HIS A 117 0.850 0.506 0.295 0.398 HIS A 118 0.768 0.607 0.444 0.714 HIS A 119 0.546 0.347 0.489 0.674 HIS A 120 0.617 0.336 0.176 0.799 HIS A 121 0.888 0.746 0.556 Ranges: 5 from: A 6 to A 30 from: A 32 to A 54 from: A 60 to A 70 from: A 74 to A 108 from: A 111 to A 112 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..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 1 is: 0.781 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 2 is: 0.657 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 3 is: 0.814 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 4 is: 0.556 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 5 is: 1.266 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 6 is: 0.661 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 7 is: 0.729 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 8 is: 0.761 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 9 is: 0.578 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 10 is: 0.781 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 11 is: 1.096 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 12 is: 0.886 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 13 is: 0.740 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 14 is: 0.625 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 15 is: 0.936 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 16 is: 0.633 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 17 is: 0.694 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 18 is: 0.658 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 19 is: 0.616 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 20 is: 0.545 (*) > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[6..30],[32..54],[60..70],[74..108],[111..112], is: 0.751 > Range of RMSD values to reference struct. is 0.545 to 1.266 > 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..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 1 is: 1.181 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 2 is: 1.075 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 3 is: 1.241 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 4 is: 0.957 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 5 is: 1.715 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 6 is: 1.128 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 7 is: 1.093 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 8 is: 1.196 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 9 is: 1.043 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 10 is: 1.264 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 11 is: 1.324 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 12 is: 1.198 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 13 is: 1.161 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 14 is: 1.058 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 15 is: 1.304 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 16 is: 1.060 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 17 is: 1.046 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 18 is: 1.120 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 19 is: 1.028 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..108],A[111..112],for model 20 is: 0.929 (*) > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[6..30],[32..54],[60..70],[74..108],[111..112], is: 1.156 > Range of RMSD values to reference struct. is 0.929 to 1.715 PdbStat> PdbStat> *END* of program detected, BYE! ...