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 `HR3646E_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER SIGNALING PROTEIN 09-APR-09 2KHN > ReadCoordsPdb(): >> TITLE NMR SOLUTION STRUCTURE OF THE EH 1 DOMAIN FROM HUMAN > ReadCoordsPdb(): >> TITLE 2 INTERSECTIN-1 PROTEIN. NORTHEAST STRUCTURAL GENOMICS > ReadCoordsPdb(): >> TITLE 3 CONSORTIUM TARGET HR3646E. > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `HR3646E_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 HR3646E_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 38060 ATOM records read from file > ReadCoordsPdb(): --> 38060 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 0.660 0.410 0.505 0.299 GLY A 2 0.423 0.233 HIS A 3 0.561 0.620 0.618 0.352 HIS A 4 0.662 0.661 0.447 0.266 HIS A 5 0.792 0.707 0.294 0.134 HIS A 6 0.601 0.645 0.404 0.249 HIS A 7 0.767 0.657 0.398 0.522 HIS A 8 0.486 0.731 0.254 0.413 SER A 9 0.815 0.813 0.463 9 HIS A 10 0.933 0.703 0.663 0.554 MET A 11 0.624 0.762 0.280 0.536 0.334 ALA A 12 0.734 0.615 GLN A 13 0.735 0.647 0.531 0.483 0.347 PHE A 14 0.843 0.920 0.091 0.185 14 PRO A 15 0.985 0.929 0.951 0.891 15 15 THR A 16 0.898 0.744 0.159 PRO A 17 0.977 0.756 0.925 0.879 PHE A 18 0.562 0.712 0.456 0.606 GLY A 19 0.423 0.251 GLY A 20 0.337 0.302 SER A 21 0.831 0.493 0.750 LEU A 22 0.538 0.253 0.544 0.609 ASP A 23 0.303 0.781 0.318 0.584 THR A 24 0.921 0.982 0.962 24 24 TRP A 25 0.978 0.959 0.992 0.980 25 25 ALA A 26 0.933 0.951 26 26 ILE A 27 0.978 0.982 0.997 0.921 27 27 THR A 28 0.971 0.988 0.887 28 28 VAL A 29 0.996 0.991 0.537 29 29 GLU A 30 0.997 0.993 0.546 0.704 0.289 30 30 GLU A 31 0.994 0.996 0.983 0.746 0.199 31 31 ARG A 32 0.997 0.994 0.790 0.407 0.219 0.744 0.999 32 32 ALA A 33 0.991 0.991 33 33 LYS A 34 0.998 0.988 0.637 0.384 0.757 0.457 34 34 HIS A 35 0.993 0.993 0.759 0.396 35 35 ASP A 36 0.996 0.997 0.843 0.357 36 36 GLN A 37 0.996 0.995 0.577 0.592 0.359 37 37 GLN A 38 0.996 0.995 0.877 0.189 0.427 38 38 PHE A 39 0.998 0.998 0.969 0.506 39 39 HIS A 40 0.996 0.998 0.903 0.624 40 40 SER A 41 1.000 1.000 0.612 41 41 LEU A 42 0.994 0.990 0.783 0.630 42 42 LYS A 43 0.998 0.995 0.849 0.354 0.730 0.373 43 43 PRO A 44 0.993 0.986 0.960 0.931 44 44 ILE A 45 0.967 0.400 0.665 0.439 SER A 46 0.383 0.654 0.484 GLY A 47 0.613 0.959 PHE A 48 0.980 0.988 0.702 0.250 48 48 ILE A 49 0.984 0.990 0.987 0.366 49 49 THR A 50 0.985 0.992 0.395 50 50 GLY A 51 0.997 0.993 51 51 ASP A 52 0.998 0.995 0.822 0.529 52 52 GLN A 53 0.996 0.996 0.776 0.179 0.197 53 53 ALA A 54 0.998 0.995 54 54 ARG A 55 0.998 0.995 0.074 0.671 0.578 0.786 0.998 55 55 ASN A 56 0.994 0.992 0.834 0.359 56 56 PHE A 57 0.998 0.997 0.999 0.115 57 57 PHE A 58 0.987 0.983 0.693 0.715 58 58 PHE A 59 0.999 0.996 0.968 0.905 59 59 GLN A 60 0.995 0.980 0.676 0.336 0.214 60 60 SER A 61 0.991 0.976 0.549 61 61 GLY A 62 0.987 0.966 62 62 LEU A 63 0.962 0.997 0.998 0.999 63 63 PRO A 64 0.993 0.995 0.952 0.900 64 64 GLN A 65 0.999 0.999 0.663 0.588 0.477 65 65 PRO A 66 0.999 0.992 0.942 0.857 66 66 VAL A 67 0.987 0.998 0.997 67 67 LEU A 68 0.998 0.999 0.919 0.947 68 68 ALA A 69 0.999 0.998 69 69 GLN A 70 0.998 0.998 0.873 0.688 0.400 70 70 ILE A 71 0.997 0.998 0.996 0.938 71 71 TRP A 72 0.999 0.997 0.997 0.999 72 72 ALA A 73 0.998 0.990 73 73 LEU A 74 0.992 0.993 0.970 0.884 74 74 ALA A 75 0.996 0.975 75 75 ASP A 76 0.997 0.990 0.454 0.776 76 76 MET A 77 0.995 0.993 0.839 0.870 0.672 77 77 ASN A 78 0.994 0.999 0.473 0.564 78 78 ASN A 79 0.997 0.989 0.997 0.832 79 79 ASP A 80 0.988 0.990 0.791 0.547 80 80 GLY A 81 0.983 0.943 81 81 ARG A 82 0.945 0.889 0.578 0.609 0.124 0.659 0.998 82 MET A 83 0.899 0.843 0.486 0.989 0.485 83 ASP A 84 0.901 0.988 0.868 0.586 84 84 GLN A 85 0.994 0.993 0.855 0.387 0.189 85 85 VAL A 86 0.998 0.993 0.709 86 86 GLU A 87 0.999 0.997 0.976 0.650 0.419 87 87 PHE A 88 0.998 0.997 0.984 0.811 88 88 SER A 89 0.997 0.987 0.535 89 89 ILE A 90 0.981 0.993 0.996 0.998 90 90 ALA A 91 0.986 0.991 91 91 MET A 92 0.994 0.988 0.340 0.170 0.524 92 92 LYS A 93 0.976 0.978 0.281 0.388 0.463 0.034 93 93 LEU A 94 0.995 0.995 0.940 0.999 94 94 ILE A 95 0.998 0.997 0.993 0.444 95 95 LYS A 96 0.996 0.995 0.813 0.508 0.995 0.780 96 96 LEU A 97 0.989 0.989 0.566 0.563 97 97 LYS A 98 0.997 0.993 0.767 0.548 0.502 0.104 98 98 LEU A 99 0.997 0.991 0.998 0.999 99 99 GLN A 100 0.994 0.987 0.554 0.091 0.352 100 100 GLY A 101 0.969 0.915 101 101 TYR A 102 0.923 0.991 0.798 0.247 102 102 GLN A 103 0.923 0.572 0.185 0.539 0.431 LEU A 104 0.606 0.940 0.461 0.378 PRO A 105 0.985 0.988 0.946 0.914 105 105 SER A 106 0.979 0.990 0.611 106 106 ALA A 107 0.958 0.971 107 107 LEU A 108 0.990 0.994 0.515 0.422 108 108 PRO A 109 0.995 1.000 0.959 0.896 109 109 PRO A 110 0.995 0.990 0.942 0.864 110 110 VAL A 111 0.993 0.994 0.914 111 111 MET A 112 0.987 0.986 0.932 0.773 0.711 112 112 LYS A 113 0.980 0.982 0.894 0.753 0.160 0.441 113 113 GLN A 114 0.924 0.753 0.924 0.867 0.378 GLN A 115 0.604 0.796 0.672 0.751 0.260 PRO A 116 0.978 0.877 0.930 0.881 116 VAL A 117 0.952 0.937 0.656 117 117 ALA A 118 0.560 0.565 ILE A 119 0.730 0.505 0.488 0.510 SER A 120 0.877 0.406 0.599 SER A 121 0.790 0.279 Ranges: 4 from: A 24 to A 44 from: A 48 to A 81 from: A 84 to A 102 from: A 105 to A 113 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[24..44],A[48..81],A[84..102],A[105..113],for model 1 is: 0.733 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 2 is: 1.312 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 3 is: 0.724 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 4 is: 0.701 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 5 is: 0.892 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 6 is: 0.822 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 7 is: 1.211 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 8 is: 0.690 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 9 is: 0.814 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 10 is: 0.758 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 11 is: 0.907 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 12 is: 0.611 (*) > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 13 is: 0.617 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 14 is: 0.936 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 15 is: 0.935 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 16 is: 0.785 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 17 is: 1.006 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 18 is: 0.871 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 19 is: 0.855 > Kabsch RMSD of backbone atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 20 is: 0.655 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[24..44],[48..81],[84..102],[105..113], is: 0.842 > Range of RMSD values to reference struct. is 0.611 to 1.312 > 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[24..44],A[48..81],A[84..102],A[105..113],for model 1 is: 1.109 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 2 is: 1.627 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 3 is: 1.217 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 4 is: 1.194 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 5 is: 1.320 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 6 is: 1.217 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 7 is: 1.629 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 8 is: 1.174 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 9 is: 1.276 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 10 is: 1.145 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 11 is: 1.390 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 12 is: 1.035 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 13 is: 0.995 (*) > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 14 is: 1.357 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 15 is: 1.239 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 16 is: 1.228 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 17 is: 1.408 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 18 is: 1.285 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 19 is: 1.361 > Kabsch RMSD of heavy atoms in res. A[24..44],A[48..81],A[84..102],A[105..113],for model 20 is: 1.004 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[24..44],[48..81],[84..102],[105..113], is: 1.261 > Range of RMSD values to reference struct. is 0.995 to 1.629 PdbStat> PdbStat> *END* of program detected, BYE! ...