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_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 78 MET ALA LEU THR LEU TYR GLN ARG ASP ASP CYS HIS LEU > ReadCoordsPdb(): Counting models in file `XCR50_R3Cons_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_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 23940 ATOM records read from file > ReadCoordsPdb(): --> 23940 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 0.290 0.747 0.564 0.355 ALA A 2 0.803 0.951 2 LEU A 3 0.976 0.998 0.999 0.999 3 3 THR A 4 0.999 0.999 1.000 4 4 LEU A 5 0.999 0.999 0.999 1.000 5 5 TYR A 6 0.999 0.999 0.999 0.791 6 6 GLN A 7 0.997 0.996 0.920 0.999 0.666 7 7 ARG A 8 0.939 0.784 0.651 0.697 0.861 0.565 1.000 ASP A 9 0.604 0.401 0.579 0.967 ASP A 10 0.543 0.871 0.989 0.973 CYS A 11 0.882 0.557 0.423 HIS A 12 0.679 0.938 0.777 0.583 LEU A 13 1.000 0.999 1.000 1.000 13 13 CYS A 14 1.000 1.000 0.998 14 14 ASP A 15 1.000 1.000 0.772 0.848 15 15 GLN A 16 1.000 1.000 1.000 0.997 0.999 16 16 ALA A 17 1.000 1.000 17 17 VAL A 18 1.000 1.000 1.000 18 18 GLU A 19 1.000 1.000 1.000 1.000 1.000 19 19 ALA A 20 1.000 1.000 20 20 LEU A 21 1.000 1.000 1.000 1.000 21 21 ALA A 22 1.000 1.000 22 22 GLN A 23 1.000 1.000 1.000 1.000 0.866 23 23 ALA A 24 0.997 0.986 24 24 ARG A 25 0.995 0.999 1.000 1.000 0.999 0.999 1.000 25 25 ALA A 26 0.999 0.988 26 26 GLY A 27 0.975 0.996 27 27 ALA A 28 0.999 0.999 28 28 PHE A 29 1.000 0.999 1.000 1.000 29 29 PHE A 30 0.999 1.000 1.000 0.999 30 30 SER A 31 0.995 0.999 0.563 31 31 VAL A 32 0.999 1.000 1.000 32 32 PHE A 33 0.995 0.995 0.997 0.993 33 33 ILE A 34 0.997 0.995 1.000 0.966 34 34 ASP A 35 0.993 0.806 0.893 0.742 35 ASP A 36 0.693 0.779 0.564 0.879 ASP A 37 0.824 0.993 1.000 0.999 37 ALA A 38 1.000 1.000 38 38 ALA A 39 1.000 1.000 39 39 LEU A 40 1.000 1.000 1.000 1.000 40 40 GLU A 41 1.000 1.000 1.000 0.998 0.964 41 41 SER A 42 1.000 1.000 1.000 42 42 ALA A 43 1.000 1.000 43 43 TYR A 44 0.991 1.000 1.000 0.851 44 44 GLY A 45 0.999 0.993 45 45 LEU A 46 0.992 0.998 0.884 0.993 46 46 ARG A 47 0.999 0.993 1.000 0.998 0.997 0.782 1.000 47 47 VAL A 48 0.998 1.000 1.000 48 48 PRO A 49 0.999 0.999 1.000 1.000 49 49 VAL A 50 0.995 1.000 0.999 50 50 LEU A 51 0.998 0.999 0.876 1.000 51 51 ARG A 52 0.997 0.995 0.474 0.991 0.220 0.665 1.000 52 52 ASP A 53 0.980 0.983 0.783 0.815 53 53 PRO A 54 0.993 0.988 0.916 0.851 54 54 MET A 55 0.976 0.995 1.000 0.555 0.315 55 55 GLY A 56 0.708 0.984 ARG A 57 0.674 0.970 0.995 0.755 0.326 0.815 1.000 GLU A 58 0.984 1.000 0.925 0.999 0.803 58 58 LEU A 59 0.995 1.000 1.000 1.000 59 59 ASP A 60 0.999 0.996 0.879 0.999 60 60 TRP A 61 1.000 1.000 0.999 1.000 61 61 PRO A 62 1.000 1.000 1.000 1.000 62 62 PHE A 63 0.999 0.999 1.000 0.998 63 63 ASP A 64 0.998 1.000 1.000 0.975 64 64 ALA A 65 1.000 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 1.000 1.000 1.000 1.000 67 67 LEU A 68 1.000 1.000 0.999 1.000 68 68 ARG A 69 1.000 1.000 0.999 0.995 0.830 0.751 1.000 69 69 ALA A 70 1.000 1.000 70 70 TRP A 71 1.000 1.000 1.000 0.999 71 71 LEU A 72 1.000 1.000 1.000 1.000 72 72 ASP A 73 0.999 0.999 1.000 1.000 73 73 ALA A 74 0.977 0.982 74 74 ALA A 75 0.511 0.200 PRO A 76 0.997 0.996 0.983 0.970 76 76 HIS A 77 0.525 0.165 0.424 0.230 ALA A 78 0.628 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: 0.707 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 2 is: 0.901 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 3 is: 0.329 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 4 is: 0.320 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 5 is: 0.829 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 6 is: 0.287 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 7 is: 0.389 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 8 is: 0.280 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 9 is: 0.398 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 10 is: 0.281 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 11 is: 0.329 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 12 is: 0.274 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 13 is: 0.355 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 14 is: 0.407 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 15 is: 0.718 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 16 is: 0.412 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 17 is: 0.352 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 18 is: 0.267 (*) > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 19 is: 0.427 > Kabsch RMSD of backbone atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 20 is: 0.394 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[3..7],[13..34],[38..55],[58..74], is: 0.433 > Range of RMSD values to reference struct. is 0.267 to 0.901 > 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: 0.821 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 2 is: 0.962 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 3 is: 0.496 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 4 is: 0.502 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 5 is: 0.962 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 6 is: 0.472 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 7 is: 0.579 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 8 is: 0.453 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 9 is: 0.596 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 10 is: 0.478 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 11 is: 0.488 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 12 is: 0.498 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 13 is: 0.576 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 14 is: 0.565 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 15 is: 0.851 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 16 is: 0.570 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 17 is: 0.508 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 18 is: 0.421 (*) > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 19 is: 0.606 > Kabsch RMSD of heavy atoms in res. A[3..7],A[13..34],A[38..55],A[58..74],for model 20 is: 0.574 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[3..7],[13..34],[38..55],[58..74], is: 0.599 > Range of RMSD values to reference struct. is 0.421 to 0.962 PdbStat> PdbStat> *END* of program detected, BYE! ...