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_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 27-MAY-10 2KYI > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF DSY0195(21-82) PROTEIN FROM > ReadCoordsPdb(): >> TITLE 2 DESULFITOBACTERIUM HAFNIENSE. NORTHEAST STRUCTURAL GENOMICS > ReadCoordsPdb(): >> TITLE 3 CONSORTIUM TARGET DHR8C > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `DHR8C_NMR_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_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 45800 ATOM records read from file > ReadCoordsPdb(): --> 45800 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 0.049 0.513 0.284 0.271 ASP M 2 0.570 0.346 0.318 0.521 ASN M 3 0.577 0.703 0.561 0.336 ARG M 4 0.727 0.948 0.450 0.983 0.173 0.742 0.997 GLN M 5 0.986 0.986 0.921 0.874 0.509 5 5 PHE M 6 0.989 0.994 0.754 0.384 6 6 LEU M 7 0.990 0.988 0.999 1.000 7 7 SER M 8 0.991 0.987 0.427 8 8 LEU M 9 0.985 0.985 0.997 0.999 9 9 THR M 10 0.985 0.919 0.659 10 10 GLY M 11 0.919 0.967 11 11 VAL M 12 0.971 0.992 1.000 12 12 SER M 13 0.988 0.981 0.304 13 13 LYS M 14 0.990 0.987 0.586 0.855 0.546 0.076 14 14 VAL M 15 0.994 0.986 0.128 15 15 GLN M 16 0.990 0.987 0.987 0.741 0.715 16 16 SER M 17 0.982 0.986 0.373 17 17 PHE M 18 0.984 1.000 0.995 0.700 18 18 ASP M 19 0.998 0.996 0.664 0.316 19 19 PRO M 20 0.994 0.981 0.954 0.881 20 20 LYS M 21 0.980 0.975 0.764 0.766 0.463 0.338 21 21 GLU M 22 0.993 0.981 0.901 0.769 0.393 22 22 ILE M 23 0.986 0.996 0.999 0.790 23 23 LEU M 24 0.996 0.997 0.998 0.998 24 24 LEU M 25 0.994 0.993 0.999 0.999 25 25 GLU M 26 0.994 0.994 0.991 0.749 0.595 26 26 THR M 27 0.982 0.954 0.383 27 27 ILE M 28 0.797 0.149 0.792 0.780 GLN M 29 0.180 0.940 0.325 0.709 0.244 GLY M 30 0.938 0.940 30 30 VAL M 31 0.961 0.986 0.999 31 31 LEU M 32 0.985 0.995 0.999 0.999 32 32 SER M 33 0.997 0.995 0.565 33 33 ILE M 34 0.993 0.998 0.997 0.594 34 34 LYS M 35 0.991 0.996 0.606 0.883 0.394 0.193 35 35 GLY M 36 0.995 0.992 36 36 GLU M 37 0.973 0.992 0.444 0.588 0.373 37 37 LYS M 38 0.998 0.968 0.666 0.541 0.643 0.050 38 38 LEU M 39 0.983 1.000 0.936 0.998 39 39 GLY M 40 0.938 0.866 40 ILE M 41 0.603 0.443 0.272 0.426 LYS M 42 0.482 0.249 0.521 0.595 0.544 0.364 HIS M 43 0.511 0.703 0.253 0.184 LEU M 44 0.754 0.210 0.269 0.545 ASP M 45 0.596 0.326 0.358 0.243 LEU M 46 0.231 0.441 0.590 0.564 LYS M 47 0.381 0.835 0.308 0.588 0.634 0.080 ALA M 48 0.770 0.696 GLY M 49 0.719 0.861 GLN M 50 0.927 0.970 0.164 0.927 0.296 50 50 VAL M 51 0.977 0.987 0.586 51 51 GLU M 52 0.986 0.981 0.424 0.729 0.379 52 52 VAL M 53 0.986 0.976 0.349 53 53 GLU M 54 0.989 0.975 0.476 0.612 0.410 54 54 GLY M 55 0.981 0.990 55 55 LEU M 56 0.994 0.984 0.992 0.656 56 56 ILE M 57 0.990 0.977 0.998 0.999 57 57 ASP M 58 0.985 0.991 0.656 0.618 58 58 ALA M 59 0.980 0.987 59 59 LEU M 60 0.993 0.992 0.961 0.722 60 60 VAL M 61 0.993 0.992 1.000 61 61 TYR M 62 0.981 0.966 0.925 0.913 62 62 PRO M 63 0.983 0.737 0.937 0.890 LEU M 64 0.723 0.329 0.139 0.459 GLU M 65 0.261 0.153 0.515 0.399 0.334 HIS M 66 0.431 0.416 0.391 0.304 HIS M 67 0.682 0.425 0.254 0.203 HIS M 68 0.416 0.102 0.326 0.427 HIS M 69 0.617 0.228 0.268 0.045 HIS M 70 0.311 0.352 0.489 0.183 HIS M 71 0.812 0.459 0.330 0.243 MET M 82 0.454 0.354 0.338 0.298 0.508 ASP M 83 0.406 0.320 0.292 0.472 ASN M 84 0.716 0.846 0.352 0.071 ARG M 85 0.895 0.948 0.612 0.986 0.433 0.806 0.998 85 GLN M 86 0.973 0.994 0.932 0.932 0.394 86 86 PHE M 87 0.998 0.997 0.991 0.267 87 87 LEU M 88 0.996 0.994 1.000 0.999 88 88 SER M 89 0.994 0.993 0.373 89 89 LEU M 90 0.984 0.986 0.993 0.957 90 90 THR M 91 0.989 0.814 0.612 91 GLY M 92 0.848 0.971 92 VAL M 93 0.974 0.979 0.999 93 93 SER M 94 0.982 0.988 0.269 94 94 LYS M 95 0.982 0.981 0.620 0.921 0.569 0.185 95 95 VAL M 96 0.996 0.977 0.102 96 96 GLN M 97 0.984 0.980 0.992 0.755 0.539 97 97 SER M 98 0.973 0.991 0.400 98 98 PHE M 99 0.983 0.999 0.992 0.706 99 99 ASP M 100 0.999 0.993 0.614 0.150 100 100 PRO M 101 0.994 0.961 0.967 0.929 101 101 LYS M 102 0.954 0.984 0.840 0.800 0.622 0.194 102 102 GLU M 103 0.983 0.997 0.928 0.606 0.357 103 103 ILE M 104 0.986 0.995 0.999 0.854 104 104 LEU M 105 0.994 0.994 0.998 0.999 105 105 LEU M 106 0.983 0.983 0.919 0.917 106 106 GLU M 107 0.987 0.989 0.991 0.736 0.708 107 107 THR M 108 0.973 0.975 0.565 108 108 ILE M 109 0.873 0.331 0.879 0.915 GLN M 110 0.356 0.972 0.373 0.772 0.089 GLY M 111 0.963 0.972 111 111 VAL M 112 0.979 0.988 0.999 112 112 LEU M 113 0.987 0.988 0.927 0.812 113 113 SER M 114 0.993 0.994 0.581 114 114 ILE M 115 0.995 0.997 0.994 0.565 115 115 LYS M 116 0.992 0.993 0.706 0.799 0.268 0.226 116 116 GLY M 117 0.993 0.990 117 117 GLU M 118 0.971 0.987 0.044 0.369 0.399 118 118 LYS M 119 0.996 0.966 0.619 0.635 0.731 0.165 119 119 LEU M 120 0.992 1.000 0.997 0.997 120 120 GLY M 121 0.882 0.821 121 ILE M 122 0.140 0.464 0.443 0.323 LYS M 123 0.445 0.161 0.259 0.771 0.770 0.053 HIS M 124 0.707 0.702 0.220 0.198 LEU M 125 0.733 0.273 0.409 0.517 ASP M 126 0.644 0.528 0.391 0.327 LEU M 127 0.624 0.551 0.436 0.458 LYS M 128 0.572 0.375 0.407 0.348 0.668 0.151 ALA M 129 0.318 0.794 GLY M 130 0.789 0.837 GLN M 131 0.964 0.970 0.222 0.933 0.361 131 131 VAL M 132 0.970 0.988 0.803 132 132 GLU M 133 0.975 0.989 0.480 0.760 0.385 133 133 VAL M 134 0.985 0.983 0.154 134 134 GLU M 135 0.992 0.993 0.346 0.804 0.396 135 135 GLY M 136 0.989 0.985 136 136 LEU M 137 0.989 0.987 0.995 0.559 137 137 ILE M 138 0.992 0.981 0.999 0.999 138 138 ASP M 139 0.980 0.987 0.523 0.274 139 139 ALA M 140 0.989 0.988 140 140 LEU M 141 0.990 0.993 0.976 0.468 141 141 VAL M 142 0.994 0.994 1.000 142 142 TYR M 143 0.984 0.967 0.965 0.750 143 143 PRO M 144 0.969 0.782 0.941 0.888 LEU M 145 0.564 0.096 0.534 0.456 GLU M 146 0.657 0.251 0.492 0.340 0.306 HIS M 147 0.770 0.466 0.221 0.181 HIS M 148 0.632 0.565 0.160 0.527 HIS M 149 0.585 0.215 0.281 0.284 HIS M 150 0.338 0.313 0.354 0.195 HIS M 151 0.483 0.323 0.234 0.161 HIS M 152 0.652 0.491 0.335 Ranges: 7 from: M 5 to M 27 from: M 30 to M 39 from: M 50 to M 62 from: M 86 to M 90 from: M 93 to M 108 from: M 111 to M 120 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..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 1 is: 0.459 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 2 is: 0.481 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 3 is: 0.526 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 4 is: 0.365 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 5 is: 0.544 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 6 is: 0.385 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 7 is: 0.416 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 8 is: 0.465 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 9 is: 0.382 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 10 is: 0.488 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 11 is: 0.446 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 12 is: 0.421 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 13 is: 0.500 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 14 is: 0.411 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 15 is: 0.477 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 16 is: 0.455 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 17 is: 0.504 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 18 is: 0.349 (*) > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 19 is: 0.478 > Kabsch RMSD of backbone atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 20 is: 0.397 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[5..27],[30..39],[50..62],[86..90],[93..108],[111..120],[131..143], is: 0.447 > Range of RMSD values to reference struct. is 0.349 to 0.544 > 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..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 1 is: 0.916 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 2 is: 0.890 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 3 is: 0.993 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 4 is: 0.798 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 5 is: 1.048 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 6 is: 0.774 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 7 is: 0.846 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 8 is: 0.934 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 9 is: 0.821 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 10 is: 0.956 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 11 is: 0.857 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 12 is: 0.843 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 13 is: 0.909 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 14 is: 0.931 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 15 is: 0.937 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 16 is: 0.885 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 17 is: 0.882 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 18 is: 0.757 (*) > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 19 is: 0.891 > Kabsch RMSD of heavy atoms in res. M[5..27],M[30..39],M[50..62],M[86..90],M[93..108],M[111..120],M[131..143],for model 20 is: 0.869 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[5..27],[30..39],[50..62],[86..90],[93..108],[111..120],[131..143], is: 0.887 > Range of RMSD values to reference struct. is 0.757 to 1.048 PdbStat> PdbStat> *END* of program detected, BYE! ...