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 `CCR55_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 116 MET THR LEU ILE TYR LYS ILE LEU SER ARG ALA GLU TRP 1 > ReadCoordsPdb(): Counting models in file `CCR55_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 CCR55_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 35440 ATOM records read from file > ReadCoordsPdb(): --> 35440 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 0.285 0.803 0.548 0.122 THR A 2 0.342 0.319 0.135 LEU A 3 0.959 0.969 0.853 0.915 3 3 ILE A 4 0.994 0.996 0.935 0.864 4 4 TYR A 5 0.996 0.985 0.999 0.997 5 5 LYS A 6 0.976 0.993 0.990 0.480 0.819 0.197 6 6 ILE A 7 0.998 0.995 1.000 0.922 7 7 LEU A 8 0.988 0.997 0.903 0.912 8 8 SER A 9 0.995 0.995 0.569 9 9 ARG A 10 0.998 0.999 0.935 0.858 0.655 0.716 1.000 10 10 ALA A 11 1.000 0.998 11 11 GLU A 12 0.996 0.999 0.996 0.763 0.936 12 12 TRP A 13 1.000 0.999 0.998 0.999 13 13 ASP A 14 1.000 0.999 1.000 1.000 14 14 ALA A 15 1.000 0.999 15 15 ALA A 16 1.000 1.000 16 16 LYS A 17 0.999 0.999 0.943 0.992 0.750 0.933 17 17 ALA A 18 0.999 0.995 18 18 GLN A 19 0.994 0.990 0.568 0.911 0.935 19 19 GLY A 20 0.998 0.984 20 20 ARG A 21 0.968 0.977 0.849 0.998 0.882 0.495 1.000 21 21 PHE A 22 0.947 0.951 0.920 0.985 22 22 GLU A 23 0.774 0.265 0.936 0.729 0.955 GLY A 24 0.438 0.624 SER A 25 0.830 0.998 0.999 25 ALA A 26 0.999 0.999 26 26 VAL A 27 0.999 1.000 1.000 27 27 ASP A 28 0.997 0.993 0.993 0.885 28 28 LEU A 29 0.998 0.999 1.000 1.000 29 29 ALA A 30 0.999 0.999 30 30 ASP A 31 0.998 0.990 0.941 0.950 31 31 GLY A 32 0.934 0.919 32 32 PHE A 33 0.704 0.977 0.575 0.920 ILE A 34 0.982 0.930 0.998 0.947 34 34 HIS A 35 0.897 0.960 0.559 0.375 35 LEU A 36 0.964 0.507 0.987 0.763 SER A 37 0.470 0.968 0.845 ALA A 38 0.924 0.850 38 GLY A 39 0.542 0.866 GLU A 40 0.993 0.997 0.717 0.931 0.999 40 40 GLN A 41 0.998 0.998 0.999 0.899 0.727 41 41 ALA A 42 1.000 0.999 42 42 GLN A 43 0.997 0.998 0.872 0.556 0.665 43 43 GLU A 44 0.999 0.999 0.760 0.921 0.984 44 44 THR A 45 0.999 0.999 1.000 45 45 ALA A 46 1.000 0.997 46 46 ALA A 47 0.995 0.999 47 47 LYS A 48 0.996 0.992 0.881 0.998 0.999 0.999 48 48 TRP A 49 0.981 0.988 0.999 0.835 49 49 PHE A 50 0.983 0.842 0.997 0.799 50 ARG A 51 0.882 0.234 0.616 0.920 0.669 0.829 1.000 GLY A 52 0.487 0.830 GLN A 53 0.831 0.740 0.921 0.812 0.843 ALA A 54 0.750 0.362 ASN A 55 0.248 0.974 0.849 0.838 LEU A 56 0.981 0.974 0.891 0.886 56 56 VAL A 57 0.992 0.997 1.000 57 57 LEU A 58 0.995 0.997 0.997 0.999 58 58 LEU A 59 0.996 0.991 0.999 1.000 59 59 ALA A 60 0.981 0.994 60 60 VAL A 61 0.996 0.996 1.000 61 61 GLU A 62 0.984 0.972 0.643 1.000 0.999 62 62 ALA A 63 0.908 0.687 GLU A 64 0.403 0.181 0.572 0.864 0.956 PRO A 65 0.982 0.546 0.899 0.827 LEU A 66 0.545 0.716 0.449 0.625 GLY A 67 0.166 0.453 GLU A 68 0.750 0.959 0.999 0.786 0.911 ASP A 69 0.966 0.920 0.858 0.944 69 69 LEU A 70 0.988 0.986 0.942 0.994 70 70 LYS A 71 0.990 0.996 0.658 0.997 1.000 0.996 71 71 TRP A 72 0.992 0.994 0.999 0.992 72 72 GLU A 73 0.981 0.991 0.926 0.878 0.952 73 73 ALA A 74 0.948 0.913 74 74 SER A 75 0.860 0.270 0.443 ARG A 76 0.318 0.206 0.575 0.863 0.801 0.887 1.000 GLY A 77 0.383 0.458 GLY A 78 0.298 0.340 ALA A 79 0.462 0.850 ARG A 80 0.955 0.988 0.614 0.997 0.473 0.862 1.000 80 80 PHE A 81 0.993 0.994 0.998 0.995 81 81 PRO A 82 1.000 0.970 0.990 0.975 82 82 HIS A 83 0.972 0.992 0.997 0.668 83 83 LEU A 84 0.995 0.991 0.931 0.935 84 84 TYR A 85 0.989 0.934 0.995 0.485 85 85 ARG A 86 0.920 0.988 0.252 0.774 0.392 0.489 1.000 86 86 PRO A 87 0.992 0.986 0.912 0.849 87 87 LEU A 88 0.975 0.983 0.931 0.945 88 88 LEU A 89 0.990 0.990 0.999 1.000 89 89 VAL A 90 0.926 0.959 0.916 90 90 SER A 91 0.922 0.981 0.920 91 91 GLU A 92 0.902 0.966 0.758 0.473 0.889 92 92 VAL A 93 0.996 0.997 0.999 93 93 THR A 94 0.987 0.998 0.999 94 94 ARG A 95 0.997 0.995 0.747 0.682 0.934 0.729 1.000 95 95 GLU A 96 0.980 0.957 0.063 0.950 0.635 96 96 ALA A 97 0.945 0.960 97 97 ASP A 98 0.985 0.947 0.777 0.965 98 98 LEU A 99 0.822 0.888 0.357 0.617 99 ASP A 100 0.901 0.636 0.474 0.963 LEU A 101 0.634 0.938 0.750 0.833 ASP A 102 0.829 0.986 0.362 0.951 102 ALA A 103 0.527 0.790 ASP A 104 0.862 0.963 0.570 0.929 104 GLY A 105 0.799 0.946 VAL A 106 0.773 0.755 0.999 PRO A 107 0.984 0.756 0.893 0.820 GLN A 108 0.876 0.852 0.770 0.725 0.649 108 LEU A 109 0.987 0.982 0.657 0.988 109 109 GLY A 110 0.999 0.994 110 110 ASP A 111 0.990 0.999 0.998 0.948 111 111 HIS A 112 0.994 0.995 0.496 0.549 112 112 LEU A 113 0.979 0.619 0.995 0.998 ALA A 114 0.433 0.497 LEU A 115 0.470 0.378 0.721 0.689 GLU A 116 0.592 0.570 0.999 1.000 Ranges: 7 from: A 3 to A 22 from: A 26 to A 32 from: A 40 to A 49 from: A 56 to A 62 from: A 69 to A 74 from: A 80 to A 98 from: A 109 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[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 1 is: 0.717 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 2 is: 1.280 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 3 is: 0.881 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 4 is: 0.989 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 5 is: 0.738 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 6 is: 0.696 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 7 is: 0.668 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 8 is: 0.898 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 9 is: 0.927 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 10 is: 0.685 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 11 is: 1.027 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 12 is: 0.991 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 13 is: 0.714 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 14 is: 1.024 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 15 is: 1.386 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 16 is: 0.761 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 17 is: 0.756 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 18 is: 1.096 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 19 is: 0.857 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 20 is: 0.664 (*) > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[3..22],[26..32],[40..49],[56..62],[69..74],[80..98],[109..112], is: 0.888 > Range of RMSD values to reference struct. is 0.664 to 1.386 > 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[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 1 is: 1.020 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 2 is: 1.551 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 3 is: 1.109 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 4 is: 1.191 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 5 is: 0.929 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 6 is: 0.890 (*) > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 7 is: 0.965 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 8 is: 1.116 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 9 is: 1.286 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 10 is: 1.082 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 11 is: 1.356 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 12 is: 1.280 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 13 is: 1.036 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 14 is: 1.194 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 15 is: 1.559 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 16 is: 1.022 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 17 is: 1.017 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 18 is: 1.444 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 19 is: 1.017 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..32],A[40..49],A[56..62],A[69..74],A[80..98],A[109..112],for model 20 is: 1.043 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[3..22],[26..32],[40..49],[56..62],[69..74],[80..98],[109..112], is: 1.155 > Range of RMSD values to reference struct. is 0.890 to 1.559 PdbStat> PdbStat> *END* of program detected, BYE! ...