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 `GMR137_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER BIOSYNTHETIC PROTEIN 30-JUN-08 2K5P > ReadCoordsPdb(): >> TITLE NMR SOLUTION STRUCTURE OF A THIAMINE BIOSYNTHESIS PROTEIN > ReadCoordsPdb(): >> TITLE 2 FROM GEOBACTER METALLIREDUCENS: NORTHEAST STRUCTURAL > ReadCoordsPdb(): >> TITLE 3 GENOMICS CONSORTIUM TARGET GMR137 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `GMR137_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 GMR137_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 23600 ATOM records read from file > ReadCoordsPdb(): --> 23600 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 0.979 0.998 0.804 0.516 ASN A 2 0.990 0.991 0.997 0.572 2 2 LEU A 3 0.987 0.931 0.994 0.538 3 3 THR A 4 0.926 0.953 0.997 4 4 VAL A 5 0.950 0.992 0.253 5 5 ASN A 6 0.999 0.990 0.939 0.371 6 6 GLY A 7 0.983 0.986 7 7 LYS A 8 0.985 0.976 0.993 0.502 0.498 0.066 8 8 PRO A 9 0.990 0.941 0.913 0.845 9 9 SER A 10 0.953 0.871 0.555 10 THR A 11 0.865 0.971 0.700 11 VAL A 12 0.984 0.971 0.999 12 12 ASP A 13 0.880 0.962 0.987 0.688 13 GLY A 14 0.883 0.791 ALA A 15 0.721 0.951 GLU A 16 0.943 0.486 0.188 0.668 0.447 SER A 17 0.430 0.909 0.509 LEU A 18 0.930 0.982 0.637 0.618 18 18 ASN A 19 0.980 0.995 0.601 0.716 19 19 VAL A 20 0.997 0.998 0.999 20 20 THR A 21 0.998 0.997 0.997 21 21 GLU A 22 0.996 0.995 0.937 0.528 0.395 22 22 LEU A 23 0.998 0.996 0.871 0.545 23 23 LEU A 24 0.999 0.996 0.665 0.507 24 24 SER A 25 0.995 0.987 0.641 25 25 ALA A 26 0.995 0.994 26 26 LEU A 27 0.994 0.982 0.572 0.362 27 27 LYS A 28 0.997 0.916 0.594 0.707 0.417 0.282 28 28 VAL A 29 0.950 0.952 0.510 29 29 ALA A 30 0.986 0.359 GLN A 31 0.400 0.784 0.994 0.334 0.281 ALA A 32 0.904 0.965 32 32 GLU A 33 0.942 0.978 0.253 0.193 0.296 33 33 TYR A 34 0.951 0.940 0.994 0.436 34 34 VAL A 35 0.966 0.939 0.847 35 35 THR A 36 0.955 0.974 0.998 36 36 VAL A 37 0.967 0.960 0.998 37 37 GLU A 38 0.975 0.951 0.996 0.763 0.335 38 38 LEU A 39 0.938 0.979 0.306 0.252 39 39 ASN A 40 0.999 0.985 0.930 0.427 40 40 GLY A 41 0.951 0.916 41 41 GLU A 42 0.917 0.987 0.843 0.587 0.205 42 42 VAL A 43 0.986 0.994 0.999 43 43 LEU A 44 0.993 0.976 0.992 0.662 44 44 GLU A 45 0.986 0.993 0.634 0.314 0.514 45 45 ARG A 46 0.994 0.986 0.327 0.752 0.334 0.633 0.999 46 46 GLU A 47 0.959 0.936 0.102 0.844 0.616 47 47 ALA A 48 0.957 0.985 48 48 PHE A 49 0.995 0.993 0.994 0.753 49 49 ASP A 50 0.995 0.990 0.482 0.260 50 50 ALA A 51 0.984 0.932 51 51 THR A 52 0.933 0.991 0.999 52 52 THR A 53 0.993 0.976 0.532 53 53 VAL A 54 0.971 0.978 0.999 54 54 LYS A 55 0.983 0.939 0.557 0.867 0.352 0.434 55 55 ASP A 56 0.912 0.917 0.991 0.352 56 56 GLY A 57 0.900 0.956 57 ASP A 58 0.949 0.947 0.759 0.383 58 58 ALA A 59 0.936 0.927 59 59 VAL A 60 0.948 0.971 0.726 60 60 GLU A 61 0.980 0.983 0.864 0.774 0.759 61 61 PHE A 62 0.975 0.965 0.779 0.245 62 62 LEU A 63 0.865 0.943 0.548 0.984 63 TYR A 64 0.225 0.929 0.539 0.506 PHE A 65 0.627 0.462 0.612 0.435 MET A 66 0.455 0.610 0.498 0.389 0.347 GLY A 67 0.751 0.729 GLY A 68 0.113 0.131 GLY A 69 0.360 0.573 LYS A 70 0.408 0.856 0.365 0.723 0.567 0.322 LEU A 71 0.635 0.596 0.358 0.428 GLU A 72 0.704 0.399 0.324 0.500 0.506 HIS A 73 0.527 0.407 0.374 0.661 HIS A 74 0.534 0.547 0.368 0.191 HIS A 75 0.648 0.792 0.365 0.606 HIS A 76 0.669 0.773 0.440 0.222 HIS A 77 0.898 0.921 0.288 0.078 77 HIS A 78 0.916 0.433 0.103 Ranges: 4 from: A 2 to A 9 from: A 18 to A 29 from: A 32 to A 56 from: A 58 to A 62 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..9],A[18..29],A[32..56],A[58..62],for model 1 is: 0.859 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 2 is: 0.714 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 3 is: 0.616 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 4 is: 0.510 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 5 is: 0.768 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 6 is: 0.594 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 7 is: 0.554 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 8 is: 0.631 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 9 is: 0.786 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 10 is: 0.643 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 11 is: 0.653 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 12 is: 0.602 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 13 is: 0.608 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 14 is: 0.489 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 15 is: 0.901 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 16 is: 0.543 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 17 is: 0.404 (*) > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 18 is: 0.907 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 19 is: 0.818 > Kabsch RMSD of backbone atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 20 is: 0.614 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..9],[18..29],[32..56],[58..62], is: 0.661 > Range of RMSD values to reference struct. is 0.404 to 0.907 > 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..9],A[18..29],A[32..56],A[58..62],for model 1 is: 1.348 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 2 is: 1.205 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 3 is: 1.263 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 4 is: 1.130 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 5 is: 1.246 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 6 is: 1.304 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 7 is: 1.047 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 8 is: 1.140 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 9 is: 1.190 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 10 is: 1.123 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 11 is: 1.124 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 12 is: 1.042 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 13 is: 1.087 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 14 is: 0.982 (*) > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 15 is: 1.369 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 16 is: 1.080 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 17 is: 1.025 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 18 is: 1.208 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 19 is: 1.369 > Kabsch RMSD of heavy atoms in res. A[2..9],A[18..29],A[32..56],A[58..62],for model 20 is: 1.145 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..9],[18..29],[32..56],[58..62], is: 1.171 > Range of RMSD values to reference struct. is 0.982 to 1.369 PdbStat> PdbStat> *END* of program detected, BYE! ...