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 `STR70_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 142 MET ALA ASN ASP THR PRO PHE SER ALA LEU TRP GLN ARG 1 > ReadCoordsPdb(): Counting models in file `STR70_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 STR70_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 44980 ATOM records read from file > ReadCoordsPdb(): --> 44980 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 0.295 0.716 0.388 0.184 ALA A 2 0.423 0.383 ASN A 3 0.473 0.523 0.682 0.867 ASP A 4 0.420 0.441 0.696 0.964 THR A 5 0.170 0.842 0.767 PRO A 6 0.985 0.226 0.905 0.850 PHE A 7 0.346 0.135 0.629 0.837 SER A 8 0.376 0.460 0.417 ALA A 9 0.989 0.983 9 9 LEU A 10 0.976 0.989 0.563 0.573 10 10 TRP A 11 0.975 0.992 0.766 0.109 11 11 GLN A 12 0.997 0.990 0.724 0.801 0.960 12 12 ARG A 13 0.993 0.997 0.818 0.930 0.860 0.942 1.000 13 13 LEU A 14 0.991 0.994 0.998 0.998 14 14 LEU A 15 0.984 0.982 0.802 0.800 15 15 THR A 16 0.982 0.977 0.541 16 16 ARG A 17 0.989 0.870 0.716 0.570 0.663 0.718 1.000 17 GLY A 18 0.845 0.582 TRP A 19 0.605 0.984 0.999 0.938 GLN A 20 0.979 0.992 0.552 0.606 0.704 20 20 PRO A 21 0.998 0.995 1.000 1.000 21 21 VAL A 22 0.998 0.997 1.000 22 22 GLU A 23 0.988 0.996 0.922 0.929 0.904 23 23 ALA A 24 0.998 0.996 24 24 SER A 25 0.989 0.990 0.841 25 25 THR A 26 0.957 0.975 0.853 26 26 VAL A 27 0.995 0.993 0.851 27 27 ASP A 28 0.986 0.995 0.609 0.855 28 28 ASP A 29 0.997 0.998 0.902 0.945 29 29 TRP A 30 0.999 0.999 1.000 1.000 30 30 ILE A 31 0.998 0.996 0.945 0.937 31 31 LYS A 32 0.998 0.996 0.850 0.948 0.998 0.996 32 32 ARG A 33 0.989 0.982 0.598 0.739 0.994 0.944 1.000 33 33 VAL A 34 0.977 0.968 0.506 34 34 GLY A 35 0.991 0.988 35 35 ASP A 36 0.992 0.975 0.923 0.968 36 36 GLY A 37 0.985 0.988 37 37 VAL A 38 0.998 0.989 0.852 38 38 ILE A 39 0.993 0.997 1.000 0.999 39 39 LEU A 40 0.990 0.983 0.540 0.656 40 40 LEU A 41 0.985 0.951 0.990 0.929 41 41 SER A 42 0.962 0.351 0.281 SER A 43 0.343 0.257 0.302 ASP A 44 0.348 0.713 0.745 0.975 PRO A 45 0.986 0.287 0.944 0.911 ARG A 46 0.596 0.265 0.257 0.747 0.669 0.872 1.000 ARG A 47 0.612 0.130 0.670 0.613 0.856 0.697 1.000 THR A 48 0.167 0.657 0.576 PRO A 49 0.985 0.200 0.941 0.910 GLU A 50 0.151 0.153 0.866 0.789 0.973 VAL A 51 0.350 0.349 0.619 SER A 52 0.388 0.164 0.107 ASP A 53 0.592 0.237 0.404 0.935 ASN A 54 0.229 0.822 0.718 0.862 PRO A 55 0.974 0.552 0.880 0.821 VAL A 56 0.827 0.263 0.431 MET A 57 0.366 0.906 0.916 0.528 0.274 ILE A 58 0.975 0.985 0.751 0.396 58 58 ALA A 59 0.993 0.991 59 59 GLU A 60 0.992 0.991 0.998 0.834 0.946 60 60 LEU A 61 0.992 0.988 0.591 0.596 61 61 LEU A 62 0.988 0.986 0.911 0.629 62 62 ARG A 63 0.994 0.982 0.936 0.998 0.660 0.979 1.000 63 63 GLU A 64 0.987 0.956 0.796 0.609 0.909 64 64 PHE A 65 0.998 0.994 0.999 0.999 65 65 PRO A 66 0.999 0.799 0.999 1.000 GLN A 67 0.933 0.981 0.605 0.177 0.674 67 67 PHE A 68 0.981 0.888 0.922 0.996 68 ASP A 69 0.904 0.986 0.998 0.996 69 69 TRP A 70 0.988 0.993 0.997 0.455 70 70 GLN A 71 0.987 0.990 0.997 0.999 0.991 71 71 VAL A 72 0.993 0.997 0.926 72 72 ALA A 73 0.975 0.985 73 73 VAL A 74 0.984 0.959 0.422 74 74 ALA A 75 0.876 0.704 ASP A 76 0.688 0.513 0.746 0.849 LEU A 77 0.629 0.976 0.594 0.495 GLU A 78 0.980 0.985 0.709 0.882 0.978 78 78 GLN A 79 0.978 0.974 0.997 0.426 0.936 79 79 SER A 80 0.995 0.983 0.202 80 80 GLU A 81 0.997 0.996 0.607 0.924 0.978 81 81 ALA A 82 0.999 0.996 82 82 ILE A 83 0.999 0.999 1.000 1.000 83 83 GLY A 84 0.997 0.993 84 84 ASP A 85 0.997 0.996 0.847 0.898 85 85 ARG A 86 0.988 0.994 0.817 0.617 0.491 0.330 1.000 86 86 PHE A 87 0.994 0.991 0.999 0.898 87 87 ASN A 88 0.997 0.987 0.794 0.892 88 88 VAL A 89 0.952 0.353 0.513 ARG A 90 0.045 0.259 0.491 0.862 0.610 0.826 1.000 ARG A 91 0.482 0.382 0.726 0.792 0.717 0.715 1.000 PHE A 92 0.525 0.956 0.217 0.832 PRO A 93 0.996 0.884 0.945 0.890 93 ALA A 94 0.905 0.965 94 94 THR A 95 0.978 0.974 0.920 95 95 LEU A 96 0.987 0.995 0.993 0.927 96 96 VAL A 97 0.996 0.997 1.000 97 97 PHE A 98 0.997 0.995 0.996 0.998 98 98 THR A 99 0.986 0.992 0.296 99 99 ASP A 100 0.996 0.993 0.707 0.823 100 100 GLY A 101 0.997 0.995 101 101 LYS A 102 0.991 0.990 0.864 0.868 0.948 0.876 102 102 LEU A 103 0.989 0.995 0.999 1.000 103 103 ARG A 104 0.984 0.986 0.793 0.744 0.493 0.666 1.000 104 104 GLY A 105 0.979 0.975 105 105 ALA A 106 0.900 0.976 106 LEU A 107 0.956 0.717 0.654 0.703 SER A 108 0.641 0.612 0.206 GLY A 109 0.438 0.509 ILE A 110 0.862 0.267 0.524 0.706 HIS A 111 0.558 0.373 0.599 0.575 PRO A 112 0.973 0.363 0.878 0.819 TRP A 113 0.402 0.502 0.260 0.397 ALA A 114 0.491 0.961 GLU A 115 0.981 0.979 0.656 0.365 0.865 115 115 LEU A 116 0.982 0.976 0.620 0.501 116 116 LEU A 117 0.996 0.992 0.621 0.580 117 117 THR A 118 0.995 0.996 0.924 118 118 LEU A 119 0.993 0.983 0.639 0.650 119 119 MET A 120 0.993 0.991 0.693 0.458 0.200 120 120 ARG A 121 0.986 0.988 0.760 0.998 0.803 0.991 1.000 121 121 SER A 122 0.987 0.997 0.838 122 122 ILE A 123 0.997 0.992 0.999 1.000 123 123 VAL A 124 0.966 0.848 0.853 124 ASP A 125 0.944 0.933 0.218 0.824 125 125 THR A 126 0.264 0.921 0.695 PRO A 127 0.995 0.219 0.980 0.968 ALA A 128 0.460 0.142 ALA A 129 0.569 0.258 GLN A 130 0.440 0.441 0.508 0.398 0.789 GLU A 131 0.332 0.589 0.499 0.744 0.900 THR A 132 0.556 0.278 0.452 VAL A 133 0.712 0.593 0.715 GLN A 134 0.422 0.602 0.686 0.463 0.862 LEU A 135 0.708 0.589 0.619 0.641 GLU A 136 0.673 0.579 0.632 0.674 0.933 HIS A 137 0.621 0.471 0.476 0.706 HIS A 138 0.541 0.531 0.504 0.662 HIS A 139 0.623 0.578 0.408 0.459 HIS A 140 0.708 0.591 0.324 0.506 HIS A 141 0.836 0.317 0.559 0.406 HIS A 142 0.938 0.694 0.566 Ranges: 7 from: A 9 to A 16 from: A 20 to A 41 from: A 58 to A 65 from: A 69 to A 74 from: A 78 to A 88 from: A 94 to A 105 from: A 115 to A 123 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[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 1 is: 0.636 (*) > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 2 is: 0.765 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 3 is: 1.160 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 4 is: 1.293 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 5 is: 0.748 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 6 is: 0.794 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 7 is: 0.695 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 8 is: 0.782 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 9 is: 1.242 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 10 is: 1.126 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 11 is: 0.718 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 12 is: 1.130 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 13 is: 0.912 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 14 is: 0.998 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 15 is: 0.909 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 16 is: 0.828 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 17 is: 0.705 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 18 is: 1.204 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 19 is: 0.663 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 20 is: 0.844 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..16],[20..41],[58..65],[69..74],[78..88],[94..105],[115..123], is: 0.908 > Range of RMSD values to reference struct. is 0.636 to 1.293 > 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[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 1 is: 1.168 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 2 is: 1.123 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 3 is: 1.787 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 4 is: 1.735 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 5 is: 1.313 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 6 is: 1.197 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 7 is: 1.069 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 8 is: 1.213 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 9 is: 1.610 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 10 is: 1.469 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 11 is: 1.267 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 12 is: 1.596 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 13 is: 1.300 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 14 is: 1.400 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 15 is: 1.273 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 16 is: 1.254 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 17 is: 1.026 (*) > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 18 is: 1.644 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 19 is: 1.158 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..105],A[115..123],for model 20 is: 1.188 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..16],[20..41],[58..65],[69..74],[78..88],[94..105],[115..123], is: 1.339 > Range of RMSD values to reference struct. is 1.026 to 1.787 PdbStat> PdbStat> *END* of program detected, BYE! ...