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 `SGR209C_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 155 PRO GLN SER TYR PHE ASN ALA ALA ALA LYS ARG GLN LYS 1 > ReadCoordsPdb(): Counting models in file `SGR209C_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 SGR209C_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 50200 ATOM records read from file > ReadCoordsPdb(): --> 50200 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 ----------------------------------------------------------------------------------- PRO A 1 0.273 0.932 0.888 GLN A 2 0.480 0.217 0.251 0.448 0.761 SER A 3 0.312 0.387 0.338 TYR A 4 0.426 0.442 0.382 0.983 PHE A 5 0.639 0.243 0.401 0.907 ASN A 6 0.236 0.459 0.492 0.741 ALA A 7 0.681 0.475 ALA A 8 0.701 0.329 ALA A 9 0.474 0.328 LYS A 10 0.262 0.262 0.738 0.801 0.872 0.925 ARG A 11 0.367 0.509 0.569 0.598 0.862 0.627 1.000 GLN A 12 0.534 0.647 0.385 0.543 0.856 LYS A 13 0.626 0.827 0.918 0.524 0.996 0.863 TYR A 14 0.949 0.975 0.997 0.721 14 14 ALA A 15 0.981 0.995 15 15 MET A 16 0.990 0.957 0.878 0.401 0.217 16 16 LYS A 17 0.945 0.998 0.535 0.999 0.598 1.000 17 17 PRO A 18 0.995 0.879 0.909 0.823 18 GLY A 19 0.853 0.931 19 LEU A 20 0.969 0.996 0.828 0.831 20 20 SER A 21 0.999 0.997 0.855 21 21 ALA A 22 1.000 0.999 22 22 LEU A 23 0.999 1.000 1.000 1.000 23 23 GLU A 24 1.000 0.999 0.941 0.996 0.929 24 24 LYS A 25 1.000 0.999 0.895 0.996 0.868 0.998 25 25 ASN A 26 1.000 1.000 0.891 0.916 26 26 ALA A 27 1.000 1.000 27 27 VAL A 28 0.999 0.999 1.000 28 28 ILE A 29 1.000 0.999 1.000 0.839 29 29 LYS A 30 1.000 0.999 0.721 1.000 1.000 1.000 30 30 ALA A 31 1.000 0.999 31 31 ALA A 32 1.000 0.999 32 32 TYR A 33 0.999 0.996 0.996 0.381 33 33 ARG A 34 0.999 0.992 0.685 0.730 0.652 0.830 1.000 34 34 GLN A 35 0.993 0.997 0.865 0.768 0.819 35 35 ILE A 36 0.997 0.992 0.999 0.767 36 36 PHE A 37 0.994 0.977 0.999 0.896 37 37 GLU A 38 0.998 0.994 0.999 1.000 0.922 38 38 ARG A 39 0.549 0.595 0.315 0.681 0.223 0.639 1.000 ASP A 40 0.650 0.457 0.636 0.953 ILE A 41 0.675 0.847 0.936 0.999 THR A 42 0.685 0.784 0.046 LYS A 43 0.554 0.334 0.692 0.930 0.827 0.935 ALA A 44 0.275 0.846 TYR A 45 0.681 0.288 0.620 0.406 SER A 46 0.290 0.373 0.596 GLN A 47 0.457 0.884 0.932 0.668 0.941 SER A 48 0.997 0.995 0.454 48 48 ILE A 49 0.998 0.999 0.999 0.463 49 49 SER A 50 0.999 0.998 0.604 50 50 TYR A 51 1.000 0.997 0.998 0.999 51 51 LEU A 52 0.999 0.999 1.000 1.000 52 52 GLU A 53 0.999 0.998 0.933 0.998 0.871 53 53 SER A 54 0.999 0.998 1.000 54 54 GLN A 55 1.000 0.999 0.999 0.586 0.806 55 55 VAL A 56 0.998 0.999 0.999 56 56 ARG A 57 0.999 0.998 0.792 0.994 0.313 0.740 1.000 57 57 ASN A 58 0.997 0.992 1.000 0.999 58 58 GLY A 59 0.992 0.997 59 59 ASP A 60 0.997 0.999 0.999 0.971 60 60 ILE A 61 0.999 0.997 1.000 1.000 61 61 SER A 62 0.993 0.993 0.916 62 62 MET A 63 0.997 0.992 0.674 0.610 0.488 63 63 LYS A 64 0.998 0.996 0.816 0.894 0.590 0.790 64 64 GLU A 65 0.999 0.999 0.583 0.314 0.900 65 65 PHE A 66 0.999 0.998 0.996 0.958 66 66 VAL A 67 0.999 0.999 1.000 67 67 ARG A 68 0.998 0.995 0.797 0.998 0.664 0.597 1.000 68 68 ARG A 69 0.999 0.999 0.998 0.742 0.929 0.658 1.000 69 69 LEU A 70 0.999 0.998 0.999 0.999 70 70 ALA A 71 0.999 0.997 71 71 LYS A 72 0.990 0.981 0.712 0.922 0.445 0.768 72 72 SER A 73 0.998 0.996 0.363 73 73 PRO A 74 0.999 0.999 0.972 0.941 74 74 LEU A 75 0.999 0.996 0.903 0.862 75 75 TYR A 76 0.995 0.996 0.996 0.996 76 76 ARG A 77 0.997 0.997 0.505 0.930 0.769 0.694 1.000 77 77 LYS A 78 0.995 0.990 0.672 0.929 1.000 1.000 78 78 GLN A 79 0.985 0.061 0.998 0.999 0.997 PHE A 80 0.128 0.756 0.938 0.890 PHE A 81 0.800 0.983 0.997 0.998 GLU A 82 0.905 0.902 0.571 1.000 0.956 82 82 PRO A 83 0.990 0.934 0.961 0.939 83 83 PHE A 84 0.986 0.886 0.999 0.998 84 ILE A 85 0.891 0.987 0.845 0.935 85 ASN A 86 0.999 0.998 0.920 0.996 86 86 SER A 87 0.999 0.997 0.526 87 87 ARG A 88 0.997 0.999 0.869 0.715 0.931 0.887 1.000 88 88 ALA A 89 1.000 1.000 89 89 LEU A 90 0.999 0.999 0.999 1.000 90 90 GLU A 91 0.999 0.999 0.772 0.998 0.937 91 91 LEU A 92 1.000 0.997 0.946 0.999 92 92 ALA A 93 1.000 0.999 93 93 PHE A 94 0.999 0.996 0.931 0.486 94 94 ARG A 95 0.998 0.997 0.640 0.993 0.536 0.504 1.000 95 95 HIS A 96 0.986 0.985 0.613 0.313 96 96 ILE A 97 0.988 0.995 0.999 0.964 97 97 LEU A 98 0.992 0.982 0.992 0.868 98 98 GLY A 99 0.982 0.952 99 99 ARG A 100 0.932 0.316 0.284 0.597 0.425 0.567 1.000 GLY A 101 0.225 0.979 PRO A 102 0.992 0.934 0.911 0.837 102 102 SER A 103 0.953 0.969 0.485 103 103 SER A 104 0.895 0.977 0.549 104 ARG A 105 1.000 0.997 0.936 0.992 0.576 0.695 1.000 105 105 GLU A 106 0.999 0.999 0.874 1.000 1.000 106 106 GLU A 107 0.999 0.999 0.879 0.944 0.797 107 107 VAL A 108 1.000 0.999 1.000 108 108 GLN A 109 1.000 0.999 1.000 0.998 0.928 109 109 LYS A 110 0.999 0.999 0.999 0.998 1.000 0.999 110 110 TYR A 111 0.997 1.000 0.997 0.662 111 111 PHE A 112 1.000 1.000 0.999 1.000 112 112 SER A 113 0.999 0.999 0.756 113 113 ILE A 114 0.999 1.000 1.000 1.000 114 114 VAL A 115 0.999 1.000 1.000 115 115 SER A 116 0.999 0.998 0.934 116 116 SER A 117 0.999 0.993 0.720 117 117 GLY A 118 0.983 0.918 118 118 GLY A 119 0.918 0.994 119 119 LEU A 120 0.999 0.999 0.999 0.999 120 120 PRO A 121 0.999 0.998 0.954 0.891 121 121 ALA A 122 1.000 1.000 122 122 LEU A 123 1.000 1.000 1.000 1.000 123 123 VAL A 124 1.000 0.999 1.000 124 124 ASP A 125 0.999 0.999 0.948 0.925 125 125 ALA A 126 1.000 0.999 126 126 LEU A 127 0.999 0.999 0.999 0.999 127 127 VAL A 128 0.998 0.998 0.999 128 128 ASP A 129 0.989 0.967 0.998 0.986 129 129 SER A 130 0.991 0.988 0.859 130 130 GLN A 131 0.999 0.997 0.819 0.708 0.800 131 131 GLU A 132 0.999 0.998 0.760 0.812 0.982 132 132 TYR A 133 0.997 0.996 0.596 0.717 133 133 ALA A 134 0.997 0.994 134 134 ASP A 135 0.996 0.996 0.930 0.952 135 135 TYR A 136 0.982 0.987 0.601 0.623 136 136 PHE A 137 0.962 0.970 0.586 0.847 137 137 GLY A 138 0.964 0.953 138 138 GLU A 139 0.983 0.986 0.338 0.894 0.908 139 139 GLU A 140 0.984 0.989 0.999 0.823 0.944 140 140 THR A 141 0.996 0.998 0.999 141 141 VAL A 142 0.990 0.996 0.999 142 142 PRO A 143 0.978 0.896 0.904 0.852 143 TYR A 144 0.902 0.653 0.331 0.836 LEU A 145 0.868 0.562 0.898 0.856 ARG A 146 0.468 0.230 0.416 0.601 0.423 0.584 1.000 GLY A 147 0.264 0.345 LEU A 148 0.333 0.412 0.649 0.677 GLU A 149 0.729 0.408 0.843 0.734 0.921 HIS A 150 0.692 0.474 0.513 0.476 HIS A 151 0.522 0.185 0.338 0.291 HIS A 152 0.715 0.537 0.588 0.512 HIS A 153 0.691 0.209 0.445 0.469 HIS A 154 0.544 0.337 0.232 0.377 HIS A 155 0.783 0.550 0.277 Ranges: 7 from: A 14 to A 17 from: A 20 to A 38 from: A 48 to A 78 from: A 82 to A 83 from: A 86 to A 99 from: A 102 to A 103 from: A 105 to A 142 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[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 1 is: 1.109 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 2 is: 0.945 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 3 is: 0.963 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 4 is: 0.697 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 5 is: 1.157 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 6 is: 0.862 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 7 is: 1.044 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 8 is: 1.158 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 9 is: 0.821 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 10 is: 0.773 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 11 is: 0.910 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 12 is: 0.671 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 13 is: 0.742 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 14 is: 1.167 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 15 is: 0.667 (*) > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 16 is: 0.769 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 17 is: 1.003 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 18 is: 1.038 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 19 is: 0.803 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 20 is: 0.697 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[14..17],[20..38],[48..78],[82..83],[86..99],[102..103],[105..142], is: 0.900 > Range of RMSD values to reference struct. is 0.667 to 1.167 > 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[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 1 is: 1.450 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 2 is: 1.544 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 3 is: 1.360 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 4 is: 1.102 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 5 is: 1.503 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 6 is: 1.248 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 7 is: 1.370 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 8 is: 1.523 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 9 is: 1.173 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 10 is: 1.176 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 11 is: 1.292 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 12 is: 1.011 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 13 is: 1.185 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 14 is: 1.466 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 15 is: 0.976 (*) > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 16 is: 1.117 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 17 is: 1.364 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 18 is: 1.335 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 19 is: 1.369 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[82..83],A[86..99],A[102..103],A[105..142],for model 20 is: 1.079 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[14..17],[20..38],[48..78],[82..83],[86..99],[102..103],[105..142], is: 1.282 > Range of RMSD values to reference struct. is 0.976 to 1.544 PdbStat> PdbStat> *END* of program detected, BYE! ...