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 `SR213_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 123 MET LEU SER GLN THR LEU LEU GLU MET THR GLU GLN MET 1 > ReadCoordsPdb(): Counting models in file `SR213_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 SR213_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 40520 ATOM records read from file > ReadCoordsPdb(): --> 40520 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 0.612 0.688 0.516 0.341 LEU A 2 0.766 0.720 0.566 0.579 SER A 3 0.538 0.550 0.155 GLN A 4 0.493 0.413 0.480 0.349 0.737 THR A 5 0.413 0.363 0.441 LEU A 6 0.675 0.968 0.727 0.743 LEU A 7 0.995 0.995 0.705 0.567 7 7 GLU A 8 0.997 0.998 0.612 0.788 0.936 8 8 MET A 9 0.997 0.999 1.000 0.741 0.271 9 9 THR A 10 0.999 0.999 1.000 10 10 GLU A 11 0.999 0.999 0.632 0.243 0.892 11 11 GLN A 12 1.000 1.000 0.778 0.629 0.838 12 12 MET A 13 0.999 1.000 1.000 0.999 1.000 13 13 ILE A 14 1.000 1.000 1.000 1.000 14 14 GLU A 15 0.999 0.999 0.763 1.000 1.000 15 15 VAL A 16 1.000 0.999 1.000 16 16 ALA A 17 1.000 1.000 17 17 GLU A 18 1.000 0.998 0.764 0.999 1.000 18 18 LYS A 19 0.998 0.995 1.000 1.000 0.999 1.000 19 19 GLY A 20 0.999 0.997 20 20 ALA A 21 1.000 0.999 21 21 ASP A 22 0.999 0.998 1.000 1.000 22 22 ARG A 23 0.997 0.996 0.803 0.641 0.722 0.720 1.000 23 23 TYR A 24 0.998 0.997 0.997 0.896 24 24 GLN A 25 0.997 0.992 0.936 1.000 0.999 25 25 GLU A 26 0.992 0.986 0.649 0.781 0.937 26 26 GLY A 27 0.396 0.251 LYS A 28 0.550 0.323 0.469 0.998 0.999 0.999 ASN A 29 0.694 0.257 0.564 0.803 SER A 30 0.675 0.276 0.219 ASN A 31 0.658 0.434 0.682 0.920 HIS A 32 0.771 0.648 0.474 0.382 SER A 33 0.429 0.411 0.216 TYR A 34 0.579 0.299 0.517 0.758 ASP A 35 0.631 0.533 0.763 0.873 PHE A 36 0.172 0.327 0.343 0.976 PHE A 37 0.459 0.598 0.450 0.916 GLU A 38 0.646 0.946 0.651 0.501 0.857 THR A 39 0.966 0.958 0.761 39 39 ILE A 40 0.966 0.471 0.998 0.624 LYS A 41 0.602 0.993 0.997 0.935 0.998 0.560 PRO A 42 0.989 0.984 0.894 0.812 42 42 ALA A 43 0.982 0.988 43 43 VAL A 44 0.992 0.985 0.807 44 44 GLU A 45 0.975 0.992 0.574 0.932 0.977 45 45 GLU A 46 0.992 0.997 0.872 0.923 0.983 46 46 ASN A 47 0.992 0.982 0.999 0.990 47 47 ASP A 48 0.998 0.999 1.000 1.000 48 48 GLU A 49 1.000 0.999 0.822 0.716 0.997 49 49 LEU A 50 0.999 0.999 0.928 0.932 50 50 ALA A 51 1.000 0.999 51 51 ALA A 52 1.000 0.999 52 52 ARG A 53 0.998 0.999 0.998 0.593 0.998 0.706 1.000 53 53 TRP A 54 1.000 0.999 0.999 0.999 54 54 ALA A 55 1.000 0.999 55 55 GLU A 56 0.998 0.999 0.598 0.999 0.998 56 56 GLY A 57 0.996 0.995 57 57 ALA A 58 0.998 0.998 58 58 LEU A 59 0.995 0.985 0.680 0.748 59 59 GLU A 60 0.991 0.995 0.649 0.846 0.970 60 60 LEU A 61 0.998 0.994 0.776 0.801 61 61 ILE A 62 0.972 0.971 0.590 0.999 62 62 LYS A 63 0.987 0.984 0.628 0.999 0.999 0.999 63 63 VAL A 64 0.993 0.994 1.000 64 64 ARG A 65 0.955 0.542 0.795 0.721 0.572 0.747 1.000 ARG A 66 0.521 0.976 0.261 0.999 0.788 0.935 1.000 PRO A 67 0.991 0.713 0.931 0.888 LYS A 68 0.720 0.605 0.663 0.998 0.998 0.852 TYR A 69 0.589 0.966 0.928 0.890 VAL A 70 0.951 0.968 0.306 70 70 HIS A 71 0.937 0.989 0.616 0.419 71 71 LYS A 72 0.995 0.992 0.331 0.999 0.936 0.830 72 72 GLU A 73 0.997 0.996 0.875 1.000 1.000 73 73 GLN A 74 0.995 0.998 0.942 0.767 0.671 74 74 ILE A 75 0.999 1.000 1.000 0.914 75 75 GLU A 76 0.999 0.999 1.000 0.999 1.000 76 76 ALA A 77 0.999 0.998 77 77 VAL A 78 0.999 0.996 1.000 78 78 LYS A 79 0.999 0.997 1.000 0.999 0.999 1.000 79 79 ASP A 80 0.988 0.995 0.999 0.965 80 80 ASN A 81 0.998 0.997 1.000 0.997 81 81 PHE A 82 0.999 0.997 0.999 0.999 82 82 LEU A 83 0.995 0.993 0.802 0.798 83 83 GLU A 84 0.996 0.995 0.606 0.339 0.935 84 84 LEU A 85 0.998 0.996 0.828 0.617 85 85 VAL A 86 0.994 0.992 0.844 86 86 LEU A 87 0.996 0.993 0.641 0.596 87 87 GLN A 88 0.979 0.979 0.999 0.502 0.955 88 88 SER A 89 0.997 0.987 0.938 89 89 TYR A 90 0.969 0.987 0.922 0.667 90 90 VAL A 91 0.980 0.982 0.136 91 91 HIS A 92 0.989 0.967 0.921 0.498 92 92 HIS A 93 0.961 0.782 0.607 0.436 ILE A 94 0.887 0.868 0.369 0.880 94 HIS A 95 0.832 0.207 0.638 0.443 LYS A 96 0.468 0.876 0.652 0.999 1.000 1.000 LYS A 97 0.979 0.958 0.578 0.999 0.999 0.874 97 97 ARG A 98 0.994 0.997 0.767 0.926 0.936 0.838 1.000 98 98 PHE A 99 0.996 0.995 0.994 0.994 99 99 LYS A 100 0.996 0.996 0.712 0.999 0.998 0.732 100 100 ASP A 101 0.999 0.998 1.000 1.000 101 101 ILE A 102 0.999 0.998 1.000 0.919 102 102 THR A 103 0.999 0.999 1.000 103 103 GLU A 104 0.999 0.996 0.877 0.999 1.000 104 104 SER A 105 0.987 0.985 0.533 105 105 VAL A 106 0.964 0.990 0.999 106 106 LEU A 107 0.999 0.995 0.730 0.745 107 107 TYR A 108 0.996 0.989 0.604 0.789 108 108 THR A 109 0.998 0.999 0.999 109 109 LEU A 110 0.999 0.996 1.000 0.999 110 110 HIS A 111 0.998 0.996 0.935 0.507 111 111 ALA A 112 0.994 0.998 112 112 VAL A 113 0.998 0.994 0.952 113 113 LYS A 114 1.000 0.998 0.936 0.998 0.999 0.997 114 114 ASP A 115 0.998 0.998 0.940 0.964 115 115 GLU A 116 0.994 0.985 0.855 0.544 0.816 116 116 ILE A 117 0.989 0.996 1.000 0.999 117 117 ALA A 118 0.998 0.997 118 118 ARG A 119 0.981 0.967 0.569 0.809 0.647 0.462 1.000 119 119 GLU A 120 0.988 0.957 0.458 0.222 0.889 120 120 ASP A 121 0.192 0.523 0.664 0.950 SER A 122 0.814 0.357 0.399 ARG A 123 0.556 0.752 0.696 0.792 0.883 1.000 Ranges: 4 from: A 7 to A 26 from: A 42 to A 64 from: A 70 to A 92 from: A 97 to A 120 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[7..26],A[42..64],A[70..92],A[97..120],for model 1 is: 0.471 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 2 is: 0.781 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 3 is: 0.438 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 4 is: 0.549 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 5 is: 0.438 (*) > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 6 is: 0.854 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 7 is: 0.605 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 8 is: 0.819 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 9 is: 0.977 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 10 is: 0.523 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 11 is: 0.477 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 12 is: 0.736 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 13 is: 0.776 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 14 is: 0.911 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 15 is: 0.721 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 16 is: 0.976 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 17 is: 0.730 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 18 is: 0.712 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 19 is: 0.621 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 20 is: 0.724 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[7..26],[42..64],[70..92],[97..120], is: 0.692 > Range of RMSD values to reference struct. is 0.438 to 0.977 > 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[7..26],A[42..64],A[70..92],A[97..120],for model 1 is: 1.099 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 2 is: 1.287 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 3 is: 0.934 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 4 is: 0.966 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 5 is: 0.974 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 6 is: 1.403 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 7 is: 1.097 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 8 is: 1.211 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 9 is: 1.350 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 10 is: 1.009 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 11 is: 0.878 (*) > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 12 is: 1.148 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 13 is: 1.236 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 14 is: 1.290 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 15 is: 1.250 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 16 is: 1.539 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 17 is: 1.194 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 18 is: 1.177 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 19 is: 0.985 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 20 is: 1.396 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[7..26],[42..64],[70..92],[97..120], is: 1.171 > Range of RMSD values to reference struct. is 0.878 to 1.539 PdbStat> PdbStat> *END* of program detected, BYE! ...