Running PDBSTAT from Linux Ayuda is on: /farm/software/PdbStat/PdbStat-5.9 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2013 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.9-exp mar may 14 00:20:00 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 ...) 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 `XCR50_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 09-OCT-04 1XPV > ReadCoordsPdb(): >> TITLE SOLUTION STRUCTURE OF NORTHEAST STRUCTURAL GENOMICS TARGET > ReadCoordsPdb(): >> TITLE 2 PROTEIN XCR50 FROM X. CAMPESTRIS > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): >> COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN XCC2852; > ReadCoordsPdb(): Counting models in file `XCR50_NMR_em_bcr3.pdb'; Model: > 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 XCR50_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 23880 ATOM records read from file > ReadCoordsPdb(): --> 23880 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 0.191 0.392 0.652 0.734 ALA A 2 0.853 0.905 2 LEU A 3 0.936 0.999 0.917 0.973 3 3 THR A 4 0.995 0.993 0.993 4 4 LEU A 5 0.997 0.994 0.999 0.998 5 5 TYR A 6 0.995 0.999 0.994 0.988 6 6 GLN A 7 0.970 0.985 0.920 0.829 0.471 7 7 ARG A 8 0.950 0.769 0.449 0.618 0.679 0.519 1.000 ASP A 9 0.626 0.419 0.776 0.581 ASP A 10 0.501 0.916 0.764 0.623 CYS A 11 0.913 0.551 0.230 HIS A 12 0.584 0.978 0.777 0.376 LEU A 13 0.983 0.997 0.973 0.933 13 13 CYS A 14 0.994 0.993 0.271 14 14 ASP A 15 0.998 0.994 0.729 0.741 15 15 GLN A 16 0.998 0.997 0.998 0.988 0.958 16 16 ALA A 17 0.997 0.999 17 17 VAL A 18 0.999 1.000 0.997 18 18 GLU A 19 1.000 1.000 0.999 0.666 0.481 19 19 ALA A 20 1.000 1.000 20 20 LEU A 21 0.999 1.000 0.999 0.989 21 21 ALA A 22 0.999 1.000 22 22 GLN A 23 1.000 0.998 0.999 1.000 0.805 23 23 ALA A 24 0.998 0.997 24 24 ARG A 25 0.997 1.000 0.989 0.892 0.991 0.535 1.000 25 25 ALA A 26 0.999 0.993 26 26 GLY A 27 0.992 0.999 27 27 ALA A 28 0.998 1.000 28 28 PHE A 29 0.998 0.999 0.999 0.994 29 29 PHE A 30 0.997 0.994 0.993 0.563 30 30 SER A 31 0.988 0.992 0.549 31 31 VAL A 32 0.991 0.998 0.998 32 32 PHE A 33 0.996 0.997 0.997 0.603 33 33 ILE A 34 0.996 0.997 1.000 0.994 34 34 ASP A 35 0.983 0.809 0.586 0.670 35 ASP A 36 0.687 0.738 0.786 0.834 ASP A 37 0.710 0.994 0.905 0.616 ALA A 38 0.993 0.999 38 38 ALA A 39 0.999 0.999 39 39 LEU A 40 0.999 0.999 0.999 0.994 40 40 GLU A 41 0.999 1.000 0.999 0.971 0.851 41 41 SER A 42 1.000 1.000 1.000 42 42 ALA A 43 0.999 0.999 43 43 TYR A 44 0.998 0.999 0.996 0.990 44 44 GLY A 45 0.998 0.995 45 45 LEU A 46 0.991 0.998 0.985 0.998 46 46 ARG A 47 1.000 1.000 0.996 0.996 0.991 0.401 1.000 47 47 VAL A 48 0.998 1.000 0.957 48 48 PRO A 49 1.000 0.997 1.000 1.000 49 49 VAL A 50 0.998 0.998 0.999 50 50 LEU A 51 0.994 0.995 0.954 0.510 51 51 ARG A 52 0.990 0.991 0.519 0.782 0.659 0.628 1.000 52 52 ASP A 53 0.992 0.998 0.454 0.395 53 53 PRO A 54 1.000 0.985 1.000 1.000 54 54 MET A 55 0.928 0.988 0.701 0.382 0.346 55 55 GLY A 56 0.697 0.933 ARG A 57 0.734 0.980 0.946 0.979 0.612 0.615 1.000 GLU A 58 0.983 0.984 0.605 0.351 0.617 58 58 LEU A 59 0.986 1.000 0.983 0.839 59 59 ASP A 60 0.998 0.988 0.609 0.717 60 60 TRP A 61 0.989 1.000 1.000 1.000 61 61 PRO A 62 1.000 0.997 1.000 1.000 62 62 PHE A 63 0.997 0.996 1.000 0.999 63 63 ASP A 64 0.994 0.999 1.000 0.926 64 64 ALA A 65 0.999 1.000 65 65 PRO A 66 1.000 1.000 1.000 1.000 66 66 ARG A 67 1.000 1.000 1.000 0.994 0.994 0.655 1.000 67 67 LEU A 68 1.000 1.000 1.000 0.998 68 68 ARG A 69 0.999 1.000 0.982 0.486 0.796 0.453 1.000 69 69 ALA A 70 1.000 1.000 70 70 TRP A 71 0.999 0.999 0.999 0.999 71 71 LEU A 72 0.997 0.998 0.992 0.832 72 72 ASP A 73 0.990 0.972 0.907 0.701 73 73 ALA A 74 0.934 0.995 74 74 ALA A 75 0.461 0.218 PRO A 76 1.000 0.992 1.000 1.000 76 76 HIS A 77 0.528 0.108 0.577 0.457 ALA A 78 0.505 Ranges: 4 from: A 3 to A 7 from: A 13 to A 34 from: A 38 to A 55 from: A 58 to A 74 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[3..7],A[13..34],A[38..55],A[58..74],for model 1 is: 0.243 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 2 is: 0.560 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 3 is: 0.305 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 4 is: 0.410 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 5 is: 0.319 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 6 is: 0.327 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 7 is: 0.348 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 8 is: 0.365 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 9 is: 0.414 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 10 is: 0.252 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 11 is: 0.449 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 12 is: 0.515 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 13 is: 0.377 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 14 is: 0.489 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 15 is: 0.586 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 16 is: 0.579 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 17 is: 0.335 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 18 is: 0.236 (*) > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 19 is: 0.366 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 20 is: 0.560 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[3..7],[13..34],[38..55],[58..74], is: 0.402 > Range of RMSD values to reference struct. is 0.236 to 0.586 > 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[3..7],A[13..34],A[38..55],A[58..74],for model 1 is: 0.617 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 2 is: 0.769 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 3 is: 0.592 (*) > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 4 is: 0.751 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 5 is: 0.632 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 6 is: 0.727 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 7 is: 0.669 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 8 is: 0.691 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 9 is: 0.714 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 10 is: 0.596 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 11 is: 0.677 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 12 is: 0.783 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 13 is: 0.635 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 14 is: 0.711 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 15 is: 0.957 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 16 is: 0.855 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 17 is: 0.643 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 18 is: 0.643 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 19 is: 0.870 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 20 is: 0.824 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[3..7],[13..34],[38..55],[58..74], is: 0.718 > Range of RMSD values to reference struct. is 0.592 to 0.957 PdbStat> PdbStat> *END* of program detected, BYE! ...