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 `SGR42_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 66 MET ILE PHE PRO GLY ALA THR VAL ARG VAL THR ASN VAL 1 > ReadCoordsPdb(): Counting models in file `SGR42_R3Cons_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 SGR42_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 21320 ATOM records read from file > ReadCoordsPdb(): --> 21320 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 0.529 0.610 0.473 0.163 ILE A 2 0.682 0.995 1.000 1.000 PHE A 3 0.974 0.999 0.486 0.999 3 3 PRO A 4 0.998 0.991 0.936 0.873 4 4 GLY A 5 0.997 0.991 5 5 ALA A 6 0.988 0.998 6 6 THR A 7 0.999 0.999 0.999 7 7 VAL A 8 1.000 0.990 1.000 8 8 ARG A 9 0.979 0.996 0.730 0.996 0.174 0.996 1.000 9 9 VAL A 10 0.998 0.999 1.000 10 10 THR A 11 0.994 0.983 0.999 11 11 ASN A 12 0.989 0.999 1.000 0.967 12 12 VAL A 13 0.997 0.990 0.681 13 13 ASP A 14 0.986 0.912 0.861 0.946 14 14 ASP A 15 0.967 0.989 0.953 0.813 15 15 THR A 16 0.985 0.990 0.515 16 16 TYR A 17 0.998 0.999 0.997 0.899 17 17 TYR A 18 0.995 0.928 0.999 0.996 18 18 ARG A 19 0.749 0.922 0.652 1.000 0.720 0.999 1.000 PHE A 20 0.982 0.998 0.999 0.715 20 20 GLU A 21 0.991 0.983 0.999 0.998 0.984 21 21 GLY A 22 0.978 0.999 22 22 LEU A 23 0.999 0.998 0.722 0.755 23 23 VAL A 24 0.999 0.998 1.000 24 24 GLN A 25 0.994 0.999 1.000 1.000 1.000 25 25 ARG A 26 0.998 0.985 0.511 0.998 0.217 0.978 1.000 26 26 VAL A 27 0.990 0.998 1.000 27 27 SER A 28 0.905 0.628 0.362 ASP A 29 0.469 0.732 0.618 0.900 GLY A 30 0.716 0.954 LYS A 31 0.999 0.999 1.000 0.999 1.000 1.000 31 31 ALA A 32 0.997 0.999 32 32 ALA A 33 0.999 0.992 33 33 VAL A 34 0.993 0.999 1.000 34 34 LEU A 35 1.000 0.997 1.000 1.000 35 35 PHE A 36 0.992 0.998 0.998 0.299 36 36 GLU A 37 0.983 0.704 0.742 0.999 1.000 ASN A 38 0.692 0.672 0.788 0.922 GLY A 39 0.859 0.687 ASN A 40 0.723 0.909 0.857 0.946 TRP A 41 0.911 0.996 1.000 0.994 41 41 ASP A 42 0.995 0.986 0.511 0.575 42 42 LYS A 43 0.998 0.999 0.999 0.790 1.000 1.000 43 43 LEU A 44 0.999 0.999 1.000 1.000 44 44 VAL A 45 0.999 0.999 1.000 45 45 THR A 46 1.000 1.000 1.000 46 46 PHE A 47 1.000 0.999 0.999 0.699 47 47 ARG A 48 1.000 0.999 1.000 0.997 0.934 0.999 1.000 48 48 LEU A 49 0.999 0.997 1.000 1.000 49 49 SER A 50 0.998 1.000 1.000 50 50 GLU A 51 0.997 0.998 0.998 0.992 0.878 51 51 LEU A 52 0.999 0.995 1.000 1.000 52 52 GLU A 53 0.993 0.985 0.798 0.999 0.998 53 53 ALA A 54 0.994 0.995 54 54 VAL A 55 0.960 0.970 0.561 55 55 LYS A 56 0.678 0.972 0.582 0.999 1.000 0.931 PRO A 57 0.989 0.987 0.901 0.824 57 57 ILE A 58 0.985 0.977 0.156 1.000 58 58 LEU A 59 0.671 0.791 0.598 0.643 GLU A 60 0.741 0.634 0.488 0.999 0.999 HIS A 61 0.744 0.647 0.302 0.273 HIS A 62 0.899 0.615 0.461 0.686 HIS A 63 0.422 0.726 0.418 0.324 HIS A 64 0.686 0.587 0.474 0.460 HIS A 65 0.703 0.606 0.460 0.651 HIS A 66 0.883 0.633 0.533 Ranges: 5 from: A 3 to A 18 from: A 20 to A 27 from: A 31 to A 36 from: A 41 to A 55 from: A 57 to A 58 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..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 1 is: 0.998 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 2 is: 1.423 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 3 is: 0.395 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 4 is: 0.387 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 5 is: 0.614 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 6 is: 0.505 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 7 is: 1.545 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 8 is: 1.221 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 9 is: 1.187 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 10 is: 1.097 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 11 is: 0.859 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 12 is: 0.271 (*) > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 13 is: 0.579 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 14 is: 0.343 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 15 is: 0.384 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 16 is: 0.782 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 17 is: 0.489 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 18 is: 0.513 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 19 is: 0.879 > Kabsch RMSD of backbone atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 20 is: 0.354 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[3..18],[20..27],[31..36],[41..55],[57..58], is: 0.741 > Range of RMSD values to reference struct. is 0.271 to 1.545 > 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..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 1 is: 1.149 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 2 is: 1.802 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 3 is: 0.697 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 4 is: 0.742 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 5 is: 0.843 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 6 is: 0.930 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 7 is: 1.848 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 8 is: 1.425 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 9 is: 1.562 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 10 is: 1.282 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 11 is: 1.137 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 12 is: 0.657 (*) > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 13 is: 0.872 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 14 is: 0.709 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 15 is: 0.729 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 16 is: 1.029 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 17 is: 0.890 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 18 is: 0.810 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 19 is: 1.142 > Kabsch RMSD of heavy atoms in res. A[3..18],A[20..27],A[31..36],A[41..55],A[57..58],for model 20 is: 0.763 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[3..18],[20..27],[31..36],[41..55],[57..58], is: 1.051 > Range of RMSD values to reference struct. is 0.657 to 1.848 PdbStat> PdbStat> *END* of program detected, BYE! ...