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_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 123 MET LEU SER GLN THR LEU LEU GLU MET THR GLU GLN MET 1 > ReadCoordsPdb(): Counting models in file `SR213_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 SR213_R3Cons_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 0.290 0.790 0.569 0.380 LEU A 2 0.596 0.567 0.474 0.567 SER A 3 0.457 0.440 0.195 GLN A 4 0.594 0.470 0.637 0.226 0.740 THR A 5 0.394 0.275 0.429 LEU A 6 0.693 0.936 0.766 0.799 LEU A 7 0.998 0.998 0.999 0.999 7 7 GLU A 8 0.999 0.999 0.709 0.999 0.999 8 8 MET A 9 1.000 0.998 0.773 0.983 0.385 9 9 THR A 10 1.000 1.000 1.000 10 10 GLU A 11 1.000 1.000 0.999 0.820 0.910 11 11 GLN A 12 1.000 1.000 1.000 0.864 0.976 12 12 MET A 13 1.000 1.000 0.797 0.927 0.441 13 13 ILE A 14 1.000 1.000 1.000 1.000 14 14 GLU A 15 1.000 1.000 1.000 0.999 0.912 15 15 VAL A 16 1.000 1.000 1.000 16 16 ALA A 17 1.000 1.000 17 17 GLU A 18 1.000 1.000 1.000 1.000 1.000 18 18 LYS A 19 1.000 0.999 0.940 0.864 0.935 0.999 19 19 GLY A 20 1.000 0.999 20 20 ALA A 21 1.000 1.000 21 21 ASP A 22 1.000 1.000 1.000 1.000 22 22 ARG A 23 1.000 1.000 0.913 0.645 0.241 0.455 1.000 23 23 TYR A 24 0.999 1.000 0.994 0.895 24 24 GLN A 25 1.000 0.999 0.940 0.688 0.944 25 25 GLU A 26 0.998 0.995 0.935 0.843 0.957 26 26 GLY A 27 0.387 0.242 LYS A 28 0.542 0.381 0.472 0.797 0.999 0.999 ASN A 29 0.695 0.199 0.497 0.833 SER A 30 0.655 0.360 0.193 ASN A 31 0.672 0.366 0.582 0.921 HIS A 32 0.750 0.568 0.392 0.845 SER A 33 0.458 0.428 0.419 TYR A 34 0.550 0.340 0.432 0.650 ASP A 35 0.625 0.502 0.727 0.816 PHE A 36 0.136 0.367 0.505 0.980 PHE A 37 0.474 0.583 0.489 0.980 GLU A 38 0.637 0.954 0.818 0.599 0.820 THR A 39 0.986 0.961 0.651 39 39 ILE A 40 0.977 0.668 0.993 0.562 LYS A 41 0.648 0.994 0.996 0.937 0.998 0.650 PRO A 42 0.991 0.993 0.909 0.822 42 42 ALA A 43 1.000 0.999 43 43 VAL A 44 1.000 1.000 1.000 44 44 GLU A 45 1.000 1.000 1.000 0.999 1.000 45 45 GLU A 46 1.000 1.000 1.000 1.000 1.000 46 46 ASN A 47 1.000 0.999 1.000 0.956 47 47 ASP A 48 1.000 1.000 1.000 1.000 48 48 GLU A 49 0.999 0.998 1.000 0.999 1.000 49 49 LEU A 50 1.000 1.000 0.918 0.921 50 50 ALA A 51 1.000 0.999 51 51 ALA A 52 1.000 1.000 52 52 ARG A 53 1.000 1.000 0.996 0.940 0.889 0.892 1.000 53 53 TRP A 54 1.000 1.000 0.999 1.000 54 54 ALA A 55 1.000 1.000 55 55 GLU A 56 1.000 1.000 0.941 0.999 1.000 56 56 GLY A 57 1.000 0.999 57 57 ALA A 58 1.000 1.000 58 58 LEU A 59 1.000 1.000 1.000 1.000 59 59 GLU A 60 1.000 1.000 1.000 1.000 1.000 60 60 LEU A 61 1.000 1.000 0.873 0.871 61 61 ILE A 62 0.993 0.985 0.834 0.999 62 62 LYS A 63 1.000 0.998 0.872 0.474 0.997 0.999 63 63 VAL A 64 0.995 0.996 1.000 64 64 ARG A 65 0.974 0.477 0.998 0.759 0.755 0.713 1.000 ARG A 66 0.502 0.984 0.402 0.999 0.727 0.937 1.000 PRO A 67 0.990 0.720 0.936 0.890 LYS A 68 0.761 0.594 0.807 0.938 0.994 0.935 TYR A 69 0.585 0.971 0.997 0.600 VAL A 70 0.954 0.992 0.753 70 70 HIS A 71 0.959 0.994 0.673 0.704 71 71 LYS A 72 1.000 0.999 0.530 1.000 0.930 1.000 72 72 GLU A 73 1.000 0.999 0.937 1.000 1.000 73 73 GLN A 74 1.000 0.999 0.999 0.699 0.635 74 74 ILE A 75 0.999 1.000 1.000 0.842 75 75 GLU A 76 1.000 1.000 1.000 1.000 1.000 76 76 ALA A 77 1.000 0.999 77 77 VAL A 78 1.000 1.000 1.000 78 78 LYS A 79 1.000 1.000 1.000 0.886 0.803 0.998 79 79 ASP A 80 1.000 1.000 1.000 1.000 80 80 ASN A 81 1.000 1.000 1.000 0.996 81 81 PHE A 82 1.000 1.000 0.997 0.998 82 82 LEU A 83 1.000 1.000 1.000 1.000 83 83 GLU A 84 1.000 1.000 0.657 0.511 0.956 84 84 LEU A 85 1.000 1.000 0.994 0.814 85 85 VAL A 86 1.000 1.000 1.000 86 86 LEU A 87 1.000 0.998 0.949 0.759 87 87 GLN A 88 0.996 0.992 0.999 0.474 0.919 88 88 SER A 89 0.999 0.996 0.392 89 89 TYR A 90 0.994 0.995 0.996 0.580 90 90 VAL A 91 0.986 0.990 0.753 91 91 HIS A 92 0.996 0.954 0.998 0.185 92 92 HIS A 93 0.958 0.773 0.592 0.349 ILE A 94 0.878 0.880 0.262 0.673 94 HIS A 95 0.847 0.201 0.865 0.194 LYS A 96 0.453 0.905 0.647 0.998 1.000 1.000 LYS A 97 1.000 0.997 0.588 1.000 0.999 0.868 97 97 ARG A 98 0.999 0.999 0.769 0.999 0.999 0.800 1.000 98 98 PHE A 99 1.000 1.000 0.999 0.893 99 99 LYS A 100 1.000 0.999 0.616 1.000 1.000 1.000 100 100 ASP A 101 1.000 0.999 0.943 0.964 101 101 ILE A 102 1.000 1.000 1.000 1.000 102 102 THR A 103 1.000 1.000 1.000 103 103 GLU A 104 1.000 1.000 0.754 0.999 0.951 104 104 SER A 105 1.000 1.000 0.403 105 105 VAL A 106 1.000 1.000 1.000 106 106 LEU A 107 1.000 1.000 1.000 1.000 107 107 TYR A 108 1.000 1.000 0.999 1.000 108 108 THR A 109 1.000 1.000 1.000 109 109 LEU A 110 1.000 1.000 1.000 1.000 110 110 HIS A 111 1.000 1.000 1.000 0.997 111 111 ALA A 112 1.000 1.000 112 112 VAL A 113 1.000 1.000 1.000 113 113 LYS A 114 1.000 0.999 1.000 0.999 0.999 0.997 114 114 ASP A 115 1.000 1.000 0.667 0.777 115 115 GLU A 116 0.999 0.999 0.726 0.540 0.813 116 116 ILE A 117 0.999 1.000 1.000 1.000 117 117 ALA A 118 0.996 0.991 118 118 ARG A 119 0.986 0.981 0.997 0.697 0.221 0.334 1.000 119 119 GLU A 120 0.996 0.974 0.621 0.372 0.847 120 120 ASP A 121 0.176 0.548 0.561 0.936 SER A 122 0.785 0.379 0.334 ARG A 123 0.560 0.792 0.933 0.868 0.733 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: 0.552 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 2 is: 0.549 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 3 is: 0.610 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 4 is: 0.409 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 5 is: 0.515 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 6 is: 0.523 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 7 is: 0.386 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 8 is: 0.638 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 9 is: 0.542 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 10 is: 0.438 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 11 is: 0.783 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 12 is: 0.476 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 13 is: 0.352 (*) > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 14 is: 0.553 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 15 is: 0.405 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 16 is: 0.378 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 17 is: 0.496 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 18 is: 0.436 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 19 is: 0.931 > Kabsch RMSD of backbone atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 20 is: 0.488 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[7..26],[42..64],[70..92],[97..120], is: 0.523 > Range of RMSD values to reference struct. is 0.352 to 0.931 > 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: 0.919 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 2 is: 0.992 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 3 is: 0.908 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 4 is: 0.844 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 5 is: 0.741 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 6 is: 0.928 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 7 is: 0.802 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 8 is: 0.892 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 9 is: 0.830 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 10 is: 0.778 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 11 is: 1.088 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 12 is: 1.018 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 13 is: 0.730 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 14 is: 0.829 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 15 is: 0.799 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 16 is: 0.862 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 17 is: 0.957 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 18 is: 0.680 (*) > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 19 is: 1.317 > Kabsch RMSD of heavy atoms in res. A[7..26],A[42..64],A[70..92],A[97..120],for model 20 is: 0.817 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[7..26],[42..64],[70..92],[97..120], is: 0.887 > Range of RMSD values to reference struct. is 0.680 to 1.317 PdbStat> PdbStat> *END* of program detected, BYE! ...