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_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 22-DEC-07 2JZ2 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF SSL0352 PROTEIN FROM SYNECHOCYSTIS SP. PCC > ReadCoordsPdb(): >> TITLE 2 6803. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SGR42 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): >> COMPND 2 MOLECULE: SSL0352 PROTEIN; 1 > ReadCoordsPdb(): Counting models in file `SGR42_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 SGR42_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 21440 ATOM records read from file > ReadCoordsPdb(): --> 21440 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 0.611 0.418 0.390 0.282 ILE A 2 0.656 0.997 0.999 1.000 PHE A 3 0.975 0.991 0.791 0.897 3 3 PRO A 4 0.997 0.988 0.980 0.954 4 4 GLY A 5 0.990 0.987 5 5 ALA A 6 0.985 0.991 6 6 THR A 7 0.996 0.998 0.999 7 7 VAL A 8 0.999 0.996 0.999 8 8 ARG A 9 0.989 0.993 0.990 0.981 0.244 0.790 0.998 9 9 VAL A 10 0.994 0.993 1.000 10 10 THR A 11 0.988 0.972 0.784 11 11 ASN A 12 0.991 0.998 0.937 0.737 12 12 VAL A 13 0.989 0.984 0.712 13 13 ASP A 14 0.977 0.902 0.992 0.975 14 14 ASP A 15 0.967 0.990 0.993 0.247 15 15 THR A 16 0.983 0.993 0.957 16 16 TYR A 17 0.991 0.994 0.992 0.502 17 17 TYR A 18 0.996 0.919 0.994 0.911 18 18 ARG A 19 0.772 0.957 0.275 0.977 0.358 0.794 0.997 PHE A 20 0.988 0.998 0.996 0.214 20 20 GLU A 21 0.991 0.988 0.995 0.866 0.370 21 21 GLY A 22 0.980 0.988 22 22 LEU A 23 0.990 0.991 0.697 0.581 23 23 VAL A 24 0.994 0.997 1.000 24 24 GLN A 25 0.992 0.998 0.887 0.621 0.627 25 25 ARG A 26 0.994 0.989 0.905 0.910 0.161 0.777 0.998 26 26 VAL A 27 0.993 0.973 0.999 27 27 SER A 28 0.959 0.570 0.374 ASP A 29 0.481 0.685 0.528 0.263 GLY A 30 0.725 0.958 LYS A 31 0.987 0.993 0.913 0.927 0.175 0.719 31 31 ALA A 32 0.980 0.993 32 32 ALA A 33 0.996 0.996 33 33 VAL A 34 0.997 0.998 0.999 34 34 LEU A 35 0.998 0.994 1.000 1.000 35 35 PHE A 36 0.988 0.997 0.998 0.999 36 36 GLU A 37 0.983 0.691 0.987 0.647 0.613 ASN A 38 0.703 0.661 0.991 0.298 GLY A 39 0.841 0.713 ASN A 40 0.720 0.912 0.810 0.340 TRP A 41 0.919 0.988 0.997 0.991 41 41 ASP A 42 0.988 0.994 0.595 0.134 42 42 LYS A 43 0.994 0.982 0.957 0.524 0.721 0.284 43 43 LEU A 44 0.992 0.998 0.999 0.900 44 44 VAL A 45 0.993 0.997 0.999 45 45 THR A 46 0.997 0.995 0.995 46 46 PHE A 47 0.995 0.994 0.996 0.902 47 47 ARG A 48 0.992 0.993 0.994 0.643 0.480 0.713 0.998 48 48 LEU A 49 0.996 0.998 0.996 0.868 49 49 SER A 50 0.994 0.997 0.753 50 50 GLU A 51 0.989 0.987 0.876 0.378 0.389 51 51 LEU A 52 0.996 0.979 0.998 0.998 52 52 GLU A 53 0.963 0.967 0.556 0.761 0.312 53 53 ALA A 54 0.990 0.986 54 54 VAL A 55 0.985 0.993 0.998 55 55 LYS A 56 0.669 0.974 0.238 0.614 0.729 0.430 PRO A 57 0.991 0.948 0.933 0.862 57 57 ILE A 58 0.993 0.993 0.995 0.609 58 58 LEU A 59 0.648 0.778 0.224 0.494 GLU A 60 0.732 0.589 0.220 0.533 0.431 HIS A 61 0.734 0.644 0.468 0.193 HIS A 62 0.898 0.663 0.181 0.207 HIS A 63 0.436 0.757 0.187 0.408 HIS A 64 0.680 0.577 0.322 0.353 HIS A 65 0.702 0.609 0.135 0.200 HIS A 66 0.835 0.229 0.246 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: 0.652 > 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: 0.743 > 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: 0.680 > 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: 0.761 > 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: 0.456 (*) > 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: 1.466 > 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: 1.233 > 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: 0.991 > 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: 0.813 > 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: 1.517 > 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: 0.588 > 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: 0.570 > 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: 0.556 > 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: 0.567 > 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: 0.544 > 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: 0.671 > 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: 0.625 > 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: 0.619 > 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: 0.659 > 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: 1.016 > > 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: 0.786 > Range of RMSD values to reference struct. is 0.456 to 1.517 > 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: 0.934 > 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: 1.071 > 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: 1.023 > 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: 1.095 > 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: 0.993 > 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: 1.801 > 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: 1.646 > 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: 1.324 > 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: 1.046 > 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: 1.941 > 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: 0.943 > 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: 0.951 > 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: 0.915 > 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: 0.902 > 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: 0.880 (*) > 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: 1.067 > 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: 0.931 > 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: 1.041 > 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: 0.988 > 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: 1.290 > > 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: 1.139 > Range of RMSD values to reference struct. is 0.880 to 1.941 PdbStat> PdbStat> *END* of program detected, BYE! ...