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 `DHR8C_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 ASP ASN ARG GLN PHE LEU SER LEU THR GLY VAL SER 1 > ReadCoordsPdb(): Counting models in file `DHR8C_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 DHR8C_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 45520 ATOM records read from file > ReadCoordsPdb(): --> 45520 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 M 1 0.151 0.796 0.514 0.154 ASP M 2 0.563 0.410 0.497 0.917 ASN M 3 0.583 0.683 0.690 0.837 ARG M 4 0.732 0.947 0.714 0.992 0.480 0.701 1.000 GLN M 5 0.967 0.983 0.996 0.620 0.575 5 5 PHE M 6 0.991 0.986 0.997 0.980 6 6 LEU M 7 0.982 0.992 0.992 0.949 7 7 SER M 8 0.990 0.982 0.999 8 8 LEU M 9 0.981 0.993 0.773 0.875 9 9 THR M 10 0.984 0.934 0.452 10 10 GLY M 11 0.956 0.985 11 11 VAL M 12 0.986 0.995 1.000 12 12 SER M 13 0.980 0.976 0.249 13 13 LYS M 14 0.991 0.976 0.375 0.999 0.999 0.999 14 14 VAL M 15 0.988 0.996 1.000 15 15 GLN M 16 0.998 0.986 0.936 0.542 0.936 16 16 SER M 17 0.982 0.981 1.000 17 17 PHE M 18 0.963 0.951 0.772 0.959 18 18 ASP M 19 0.952 0.986 0.720 0.994 19 19 PRO M 20 0.994 0.995 0.956 0.912 20 20 LYS M 21 0.974 0.973 0.803 0.999 1.000 0.999 21 21 GLU M 22 0.993 0.988 0.934 0.999 0.980 22 22 ILE M 23 0.990 0.995 1.000 0.958 23 23 LEU M 24 0.996 0.996 0.852 0.861 24 24 LEU M 25 0.995 0.965 0.999 0.998 25 25 GLU M 26 0.974 0.996 0.999 0.999 0.879 26 26 THR M 27 0.945 0.972 0.567 27 27 ILE M 28 0.826 0.131 0.733 0.704 GLN M 29 0.129 0.953 0.915 0.753 0.736 GLY M 30 0.908 0.984 30 30 VAL M 31 0.995 0.977 0.786 31 31 LEU M 32 0.961 0.993 0.920 0.926 32 32 SER M 33 0.992 0.999 0.923 33 33 ILE M 34 0.996 0.997 1.000 1.000 34 34 LYS M 35 0.996 0.998 0.921 0.927 0.997 0.618 35 35 GLY M 36 0.995 0.991 36 36 GLU M 37 0.975 0.991 0.510 0.999 1.000 37 37 LYS M 38 0.998 0.997 0.999 0.999 1.000 1.000 38 38 LEU M 39 0.997 0.971 0.999 0.999 39 39 GLY M 40 0.913 0.907 40 40 ILE M 41 0.671 0.430 0.805 0.843 LYS M 42 0.494 0.374 0.512 0.780 0.997 0.999 HIS M 43 0.574 0.553 0.435 0.062 LEU M 44 0.716 0.208 0.499 0.574 ASP M 45 0.573 0.293 0.452 0.935 LEU M 46 0.313 0.471 0.544 0.468 LYS M 47 0.420 0.813 0.580 0.999 1.000 0.999 ALA M 48 0.786 0.727 GLY M 49 0.691 0.941 GLN M 50 0.926 0.969 0.442 0.998 0.650 50 50 VAL M 51 0.990 0.994 0.933 51 51 GLU M 52 0.992 0.963 0.994 0.989 0.790 52 52 VAL M 53 0.965 0.968 0.705 53 53 GLU M 54 0.976 0.996 0.998 0.999 0.852 54 54 GLY M 55 0.995 0.996 55 55 LEU M 56 0.996 0.976 0.769 0.732 56 56 ILE M 57 0.983 0.999 1.000 1.000 57 57 ASP M 58 0.996 0.994 0.883 0.923 58 58 ALA M 59 0.991 0.986 59 59 LEU M 60 0.971 0.961 0.999 0.997 60 60 VAL M 61 0.966 0.984 1.000 61 61 TYR M 62 0.973 0.961 0.902 0.392 62 62 PRO M 63 0.984 0.762 0.903 0.826 LEU M 64 0.696 0.341 0.632 0.610 GLU M 65 0.251 0.043 0.526 0.738 0.943 HIS M 66 0.400 0.386 0.599 0.319 HIS M 67 0.751 0.498 0.419 0.411 HIS M 68 0.464 0.140 0.510 0.652 HIS M 69 0.624 0.249 0.276 0.801 HIS M 70 0.358 0.505 0.318 0.418 HIS M 71 0.837 0.285 0.638 0.350 MET M 82 0.085 0.151 0.796 0.514 0.154 ASP M 83 0.563 0.410 0.497 0.917 ASN M 84 0.583 0.683 0.690 0.837 ARG M 85 0.732 0.948 0.714 0.992 0.480 0.701 1.000 GLN M 86 0.967 0.983 0.996 0.620 0.575 86 86 PHE M 87 0.991 0.986 0.997 0.980 87 87 LEU M 88 0.982 0.992 0.991 0.949 88 88 SER M 89 0.990 0.982 0.999 89 89 LEU M 90 0.981 0.993 0.773 0.875 90 90 THR M 91 0.984 0.934 0.452 91 91 GLY M 92 0.956 0.985 92 92 VAL M 93 0.986 0.995 1.000 93 93 SER M 94 0.980 0.976 0.249 94 94 LYS M 95 0.991 0.976 0.375 0.999 0.999 0.999 95 95 VAL M 96 0.988 0.996 1.000 96 96 GLN M 97 0.998 0.986 0.936 0.542 0.936 97 97 SER M 98 0.982 0.981 1.000 98 98 PHE M 99 0.963 0.951 0.772 0.959 99 99 ASP M 100 0.952 0.986 0.720 0.994 100 100 PRO M 101 0.994 0.995 0.956 0.912 101 101 LYS M 102 0.974 0.973 0.803 0.999 1.000 0.999 102 102 GLU M 103 0.993 0.988 0.934 0.999 0.980 103 103 ILE M 104 0.990 0.995 1.000 0.957 104 104 LEU M 105 0.996 0.996 0.852 0.861 105 105 LEU M 106 0.995 0.965 0.999 0.998 106 106 GLU M 107 0.974 0.996 0.999 0.999 0.879 107 107 THR M 108 0.945 0.972 0.567 108 108 ILE M 109 0.826 0.131 0.733 0.704 GLN M 110 0.129 0.952 0.915 0.753 0.736 GLY M 111 0.908 0.984 111 111 VAL M 112 0.995 0.977 0.787 112 112 LEU M 113 0.961 0.993 0.920 0.926 113 113 SER M 114 0.992 0.999 0.923 114 114 ILE M 115 0.996 0.997 1.000 1.000 115 115 LYS M 116 0.996 0.998 0.921 0.927 0.997 0.618 116 116 GLY M 117 0.995 0.991 117 117 GLU M 118 0.975 0.991 0.510 0.999 1.000 118 118 LYS M 119 0.998 0.997 0.999 0.999 1.000 1.000 119 119 LEU M 120 0.997 0.971 0.999 0.999 120 120 GLY M 121 0.913 0.907 121 121 ILE M 122 0.671 0.430 0.805 0.843 LYS M 123 0.494 0.374 0.512 0.780 0.997 0.999 HIS M 124 0.574 0.553 0.434 0.062 LEU M 125 0.716 0.208 0.499 0.573 ASP M 126 0.573 0.294 0.452 0.935 LEU M 127 0.313 0.471 0.544 0.468 LYS M 128 0.420 0.812 0.580 0.999 1.000 0.999 ALA M 129 0.786 0.727 GLY M 130 0.691 0.940 GLN M 131 0.926 0.969 0.442 0.998 0.650 131 131 VAL M 132 0.990 0.994 0.933 132 132 GLU M 133 0.992 0.963 0.994 0.989 0.790 133 133 VAL M 134 0.965 0.969 0.705 134 134 GLU M 135 0.977 0.996 0.998 0.999 0.852 135 135 GLY M 136 0.995 0.996 136 136 LEU M 137 0.996 0.976 0.769 0.732 137 137 ILE M 138 0.983 0.999 1.000 1.000 138 138 ASP M 139 0.996 0.994 0.883 0.923 139 139 ALA M 140 0.991 0.986 140 140 LEU M 141 0.971 0.960 0.999 0.997 141 141 VAL M 142 0.966 0.984 1.000 142 142 TYR M 143 0.973 0.961 0.902 0.392 143 143 PRO M 144 0.984 0.762 0.903 0.826 LEU M 145 0.696 0.340 0.632 0.610 GLU M 146 0.251 0.043 0.526 0.738 0.943 HIS M 147 0.401 0.386 0.599 0.319 HIS M 148 0.751 0.497 0.419 0.411 HIS M 149 0.464 0.140 0.510 0.652 HIS M 150 0.624 0.249 0.276 0.801 HIS M 151 0.358 0.504 0.318 0.418 HIS M 152 0.837 0.638 0.350 Ranges: 6 from: M 5 to M 27 from: M 30 to M 40 from: M 50 to M 62 from: M 86 to M 108 from: M 111 to M 121 from: M 131 to M 143 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. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 1 is: 0.950 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 2 is: 0.415 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 3 is: 0.485 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 4 is: 0.610 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 5 is: 0.409 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 6 is: 0.477 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 7 is: 0.437 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 8 is: 0.562 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 9 is: 1.119 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 10 is: 0.386 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 11 is: 0.487 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 12 is: 0.518 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 13 is: 0.498 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 14 is: 0.433 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 15 is: 0.410 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 16 is: 0.391 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 17 is: 0.384 (*) > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 18 is: 0.563 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 19 is: 0.463 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 20 is: 0.533 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[5..27],[30..40],[50..62],[86..108],[111..121],[131..143], is: 0.527 > Range of RMSD values to reference struct. is 0.384 to 1.119 > 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. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 1 is: 1.127 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 2 is: 0.590 (*) > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 3 is: 0.841 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 4 is: 0.935 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 5 is: 0.733 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 6 is: 0.851 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 7 is: 0.644 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 8 is: 0.812 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 9 is: 1.384 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 10 is: 0.601 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 11 is: 0.794 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 12 is: 0.817 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 13 is: 0.725 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 14 is: 0.924 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 15 is: 0.948 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 16 is: 0.654 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 17 is: 0.756 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 18 is: 1.057 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 19 is: 0.977 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..40],M[50..62],M[86..108],M[111..121],M[131..143],for model 20 is: 0.860 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[5..27],[30..40],[50..62],[86..108],[111..121],[131..143], is: 0.852 > Range of RMSD values to reference struct. is 0.590 to 1.384 PdbStat> PdbStat> *END* of program detected, BYE! ...