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 `RPR324_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 101 MET THR SER THR PHE ASP ARG VAL ALA THR ILE ILE ALA 1 > ReadCoordsPdb(): Counting models in file `RPR324_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 RPR324_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 31500 ATOM records read from file > ReadCoordsPdb(): --> 31500 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 0.141 0.739 0.506 0.328 THR A 2 0.946 0.953 0.728 2 2 SER A 3 0.918 0.989 0.940 3 3 THR A 4 0.997 0.994 0.924 4 4 PHE A 5 0.998 0.998 0.998 0.996 5 5 ASP A 6 0.997 0.998 0.939 0.933 6 6 ARG A 7 0.999 0.997 0.930 0.926 0.559 0.532 1.000 7 7 VAL A 8 0.997 0.999 1.000 8 8 ALA A 9 0.999 0.999 9 9 THR A 10 0.992 0.996 0.924 10 10 ILE A 11 0.999 0.999 1.000 1.000 11 11 ILE A 12 0.997 0.994 0.916 1.000 12 12 ALA A 13 0.996 0.982 13 13 GLU A 14 0.980 0.998 0.999 1.000 1.000 14 14 THR A 15 0.987 0.999 1.000 15 15 CYS A 16 0.992 0.988 0.916 16 16 ASP A 17 0.997 0.990 0.679 0.865 17 17 ILE A 18 0.976 0.999 0.999 0.447 18 18 PRO A 19 0.996 0.992 0.942 0.888 19 19 ARG A 20 0.997 0.990 0.112 0.997 0.440 0.675 1.000 20 20 GLU A 21 0.995 0.999 1.000 1.000 1.000 21 21 THR A 22 0.993 0.983 0.922 22 22 ILE A 23 0.965 0.992 0.999 1.000 23 23 THR A 24 0.991 0.979 0.711 24 24 PRO A 25 0.999 0.998 0.945 0.885 25 25 GLU A 26 0.984 0.977 1.000 1.000 1.000 26 26 SER A 27 0.995 0.973 0.999 27 27 HIS A 28 0.994 0.992 1.000 0.997 28 28 ALA A 29 0.996 0.998 29 29 ILE A 30 0.996 1.000 1.000 1.000 30 30 ASP A 31 0.999 1.000 1.000 1.000 31 31 ASP A 32 0.999 1.000 0.999 0.959 32 32 LEU A 33 0.998 0.987 0.971 0.609 33 33 GLY A 34 0.987 0.999 34 34 ILE A 35 0.994 0.996 1.000 1.000 35 35 ASP A 36 0.995 0.980 0.836 0.938 36 36 SER A 37 0.995 0.998 1.000 37 37 LEU A 38 0.992 0.998 1.000 1.000 38 38 ASP A 39 0.998 0.999 0.999 0.992 39 39 PHE A 40 0.999 0.999 0.998 0.697 40 40 LEU A 41 0.997 0.999 0.883 0.872 41 41 ASP A 42 1.000 1.000 1.000 1.000 42 42 ILE A 43 1.000 0.999 1.000 1.000 43 43 ALA A 44 1.000 0.999 44 44 PHE A 45 0.999 0.999 0.932 0.947 45 45 ALA A 46 1.000 1.000 46 46 ILE A 47 1.000 1.000 1.000 1.000 47 47 ASP A 48 1.000 0.999 0.897 0.934 48 48 LYS A 49 0.999 0.998 1.000 1.000 0.998 1.000 49 49 ALA A 50 1.000 0.996 50 50 PHE A 51 0.991 0.998 0.999 0.997 51 51 GLY A 52 0.999 0.998 52 52 ILE A 53 0.998 0.995 1.000 1.000 53 53 LYS A 54 0.992 0.988 0.557 0.998 1.000 0.998 54 54 LEU A 55 0.968 0.989 0.998 0.657 55 55 PRO A 56 1.000 0.998 1.000 1.000 56 56 LEU A 57 0.995 0.997 0.999 0.999 57 57 GLU A 58 0.999 0.998 0.935 1.000 1.000 58 58 LYS A 59 0.988 0.987 0.625 0.999 0.998 0.698 59 59 TRP A 60 0.995 0.993 0.999 0.982 60 60 THR A 61 0.978 0.983 0.649 61 61 GLN A 62 0.998 0.997 0.634 0.586 0.903 62 62 GLU A 63 0.998 0.996 0.879 0.779 0.916 63 63 VAL A 64 0.997 0.999 1.000 64 64 ASN A 65 0.999 0.999 1.000 1.000 65 65 ASP A 66 0.998 0.999 0.999 0.980 66 66 GLY A 67 0.998 0.997 67 67 LYS A 68 0.993 0.975 1.000 1.000 1.000 0.999 68 68 ALA A 69 0.963 0.994 69 69 THR A 70 0.996 0.998 0.999 70 70 THR A 71 0.997 0.999 0.999 71 71 GLU A 72 1.000 0.999 1.000 1.000 1.000 72 72 GLN A 73 0.992 0.987 0.869 0.395 0.789 73 73 TYR A 74 0.997 0.953 0.999 0.995 74 74 PHE A 75 0.960 0.994 0.999 0.994 75 75 VAL A 76 0.991 0.998 0.936 76 76 LEU A 77 0.993 0.990 0.644 0.491 77 77 LYS A 78 0.998 0.999 1.000 1.000 1.000 1.000 78 78 ASN A 79 0.999 0.999 1.000 0.999 79 79 LEU A 80 0.999 0.999 1.000 1.000 80 80 ALA A 81 0.999 0.999 81 81 ALA A 82 0.999 0.999 82 82 ARG A 83 0.999 0.999 0.931 0.599 0.926 0.670 1.000 83 83 ILE A 84 1.000 0.999 1.000 1.000 84 84 ASP A 85 0.999 0.999 0.747 0.828 85 85 GLU A 86 0.998 0.998 0.820 1.000 1.000 86 86 LEU A 87 1.000 0.998 1.000 1.000 87 87 VAL A 88 0.998 0.996 0.896 88 88 ALA A 89 0.999 0.999 89 89 ALA A 90 1.000 0.995 90 90 LYS A 91 0.992 0.990 0.588 0.227 0.931 0.924 91 91 GLY A 92 0.997 0.996 92 92 ALA A 93 0.994 0.999 93 93 LEU A 94 0.985 0.970 0.684 0.703 94 94 GLU A 95 0.798 0.367 0.580 0.932 0.998 HIS A 96 0.812 0.734 0.393 0.604 HIS A 97 0.461 0.484 0.499 0.735 HIS A 98 0.566 0.585 0.425 0.501 HIS A 99 0.870 0.660 0.549 0.653 HIS A 100 0.688 0.541 0.656 0.717 HIS A 101 0.715 0.752 0.752 Ranges: 1 from: A 2 to A 94 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[2..94],for model 1 is: 0.398 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 2 is: 0.571 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 3 is: 0.554 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 4 is: 0.564 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 5 is: 0.401 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 6 is: 0.718 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 7 is: 0.311 (*) > Kabsch RMSD of backbone atoms in res. A[2..94],for model 8 is: 0.885 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 9 is: 0.543 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 10 is: 0.661 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 11 is: 0.528 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 12 is: 0.383 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 13 is: 0.600 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 14 is: 0.628 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 15 is: 0.510 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 16 is: 0.535 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 17 is: 0.464 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 18 is: 0.665 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 19 is: 0.521 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 20 is: 0.408 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..94], is: 0.542 > Range of RMSD values to reference struct. is 0.311 to 0.885 > 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[2..94],for model 1 is: 0.705 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 2 is: 0.795 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 3 is: 0.850 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 4 is: 0.875 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 5 is: 0.646 (*) > Kabsch RMSD of heavy atoms in res. A[2..94],for model 6 is: 1.073 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 7 is: 0.772 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 8 is: 1.091 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 9 is: 0.755 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 10 is: 0.939 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 11 is: 0.763 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 12 is: 0.687 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 13 is: 0.835 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 14 is: 0.902 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 15 is: 0.843 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 16 is: 0.849 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 17 is: 0.691 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 18 is: 0.932 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 19 is: 0.787 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 20 is: 0.700 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..94], is: 0.825 > Range of RMSD values to reference struct. is 0.646 to 1.091 PdbStat> PdbStat> *END* of program detected, BYE! ...