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 `RPR324_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER TRANSFERASE 30-MAR-10 2KW2 > ReadCoordsPdb(): >> TITLE SOLUTION NMR OF THE SPECIALIZED ACYL CARRIER PROTEIN (RPA2022) FROM > ReadCoordsPdb(): >> TITLE 2 RHODOPSEUDOMONAS PALUSTRIS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM > ReadCoordsPdb(): >> TITLE 3 TARGET RPR324 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `RPR324_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 RPR324_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 31620 ATOM records read from file > ReadCoordsPdb(): --> 31620 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 0.094 0.258 0.638 0.213 THR A 2 0.940 0.968 0.714 2 2 SER A 3 0.913 0.953 0.298 3 3 THR A 4 0.998 0.995 0.997 4 4 PHE A 5 0.998 0.993 0.998 0.999 5 5 ASP A 6 0.997 0.995 0.670 0.898 6 6 ARG A 7 0.997 0.996 0.994 0.922 0.414 0.719 0.998 7 7 VAL A 8 0.999 0.999 0.999 8 8 ALA A 9 0.999 0.999 9 9 THR A 10 0.993 0.989 0.692 10 10 ILE A 11 0.999 0.998 0.999 0.835 11 11 ILE A 12 0.999 0.998 0.999 0.999 12 12 ALA A 13 0.999 0.999 13 13 GLU A 14 0.997 0.986 0.924 0.473 0.312 14 14 THR A 15 0.996 0.996 0.764 15 15 CYS A 16 0.996 0.993 0.503 16 16 ASP A 17 0.998 0.920 0.603 0.649 17 17 ILE A 18 0.926 0.994 0.997 0.999 18 18 PRO A 19 0.996 0.986 0.931 0.843 19 19 ARG A 20 0.998 0.997 0.591 0.359 0.532 0.384 0.996 20 20 GLU A 21 0.999 0.995 0.999 0.994 0.518 21 21 THR A 22 0.989 0.980 0.998 22 22 ILE A 23 0.976 0.991 0.998 0.999 23 23 THR A 24 0.979 0.995 0.994 24 24 PRO A 25 0.997 0.996 0.916 0.823 25 25 GLU A 26 0.996 0.990 0.508 0.915 0.270 26 26 SER A 27 0.997 0.975 0.212 27 27 HIS A 28 0.982 0.999 0.999 0.997 28 28 ALA A 29 1.000 0.998 29 29 ILE A 30 0.999 0.990 0.998 0.999 30 30 ASP A 31 0.994 0.985 0.928 0.903 31 31 ASP A 32 0.980 0.997 0.869 0.409 32 32 LEU A 33 0.996 0.992 0.999 0.999 33 33 GLY A 34 0.985 0.973 34 34 ILE A 35 0.986 0.978 0.997 0.999 35 35 ASP A 36 0.986 0.995 0.582 0.269 36 36 SER A 37 0.992 0.994 0.219 37 37 LEU A 38 0.995 0.995 0.997 0.998 38 38 ASP A 39 0.998 0.997 0.996 0.684 39 39 PHE A 40 0.998 1.000 0.999 0.216 40 40 LEU A 41 1.000 0.998 0.997 0.998 41 41 ASP A 42 0.997 0.998 0.593 0.375 42 42 ILE A 43 0.999 0.998 0.999 0.999 43 43 ALA A 44 0.999 0.999 44 44 PHE A 45 0.998 0.998 0.994 0.794 45 45 ALA A 46 0.999 0.999 46 46 ILE A 47 0.998 1.000 0.999 1.000 47 47 ASP A 48 0.999 0.998 0.761 0.684 48 48 LYS A 49 0.997 0.990 0.999 0.996 0.767 0.496 49 49 ALA A 50 0.994 0.998 50 50 PHE A 51 0.999 0.996 0.999 0.800 51 51 GLY A 52 0.997 0.984 52 52 ILE A 53 0.985 0.988 0.999 1.000 53 53 LYS A 54 0.980 0.992 0.997 0.991 0.078 0.712 54 54 LEU A 55 0.986 0.996 0.999 0.998 55 55 PRO A 56 0.999 1.000 1.000 1.000 56 56 LEU A 57 0.999 0.998 0.999 0.999 57 57 GLU A 58 0.999 0.999 0.999 0.993 0.213 58 58 LYS A 59 0.996 0.995 0.985 0.993 0.597 0.545 59 59 TRP A 60 0.998 0.998 0.999 0.994 60 60 THR A 61 0.996 0.996 0.999 61 61 GLN A 62 0.998 0.997 0.994 0.997 0.125 62 62 GLU A 63 0.997 0.996 0.995 0.513 0.705 63 63 VAL A 64 0.999 0.999 0.998 64 64 ASN A 65 0.996 0.989 0.995 0.912 65 65 ASP A 66 0.995 0.995 0.752 0.547 66 66 GLY A 67 0.995 0.995 67 67 LYS A 68 0.990 0.975 0.995 0.993 0.425 0.420 68 68 ALA A 69 0.949 0.998 69 69 THR A 70 0.998 0.998 0.466 70 70 THR A 71 0.998 0.999 0.808 71 71 GLU A 72 0.998 0.997 0.998 0.906 0.235 72 72 GLN A 73 0.998 0.998 0.997 0.944 0.596 73 73 TYR A 74 0.993 0.860 0.997 0.993 74 PHE A 75 0.869 0.996 0.998 0.996 75 VAL A 76 0.999 0.999 0.999 76 76 LEU A 77 0.999 0.999 0.998 0.998 77 77 LYS A 78 0.998 0.999 0.999 0.939 0.998 0.497 78 78 ASN A 79 0.998 0.999 0.997 0.878 79 79 LEU A 80 1.000 0.999 0.997 0.999 80 80 ALA A 81 0.999 0.998 81 81 ALA A 82 0.999 0.999 82 82 ARG A 83 0.998 0.996 0.998 0.998 0.998 0.865 0.998 83 83 ILE A 84 0.999 0.999 0.999 0.999 84 84 ASP A 85 0.999 0.999 0.998 0.992 85 85 GLU A 86 0.997 0.998 0.947 0.432 0.396 86 86 LEU A 87 0.999 0.999 0.998 0.998 87 87 VAL A 88 0.999 0.998 1.000 88 88 ALA A 89 0.998 0.994 89 89 ALA A 90 0.998 0.997 90 90 LYS A 91 0.997 0.999 0.989 0.995 0.806 0.504 91 91 GLY A 92 0.998 0.989 92 92 ALA A 93 0.990 0.994 93 93 LEU A 94 0.976 0.971 0.996 0.999 94 94 GLU A 95 0.807 0.458 0.504 0.209 0.274 HIS A 96 0.806 0.723 0.256 0.330 HIS A 97 0.512 0.485 0.165 0.146 HIS A 98 0.577 0.634 0.378 0.291 HIS A 99 0.891 0.684 0.374 0.462 HIS A 100 0.610 0.464 0.356 0.313 HIS A 101 0.654 0.347 0.321 Ranges: 2 from: A 2 to A 73 from: A 76 to A 94 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..73],A[76..94],for model 1 is: 0.475 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 2 is: 0.499 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 3 is: 0.539 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 4 is: 0.695 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 5 is: 0.400 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 6 is: 0.433 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 7 is: 0.393 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 8 is: 0.504 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 9 is: 0.538 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 10 is: 0.344 (*) > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 11 is: 0.432 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 12 is: 0.385 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 13 is: 0.405 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 14 is: 0.358 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 15 is: 0.474 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 16 is: 0.593 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 17 is: 0.590 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 18 is: 0.475 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 19 is: 0.505 > Kabsch RMSD of backbone atoms in res. A[2..73],A[76..94],for model 20 is: 0.486 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..73],[76..94], is: 0.476 > Range of RMSD values to reference struct. is 0.344 to 0.695 > 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..73],A[76..94],for model 1 is: 0.777 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 2 is: 0.809 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 3 is: 0.798 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 4 is: 0.874 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 5 is: 0.672 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 6 is: 0.718 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 7 is: 0.689 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 8 is: 0.779 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 9 is: 0.859 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 10 is: 0.743 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 11 is: 0.682 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 12 is: 0.681 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 13 is: 0.699 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 14 is: 0.643 (*) > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 15 is: 0.673 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 16 is: 0.832 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 17 is: 0.790 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 18 is: 0.706 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 19 is: 0.728 > Kabsch RMSD of heavy atoms in res. A[2..73],A[76..94],for model 20 is: 0.697 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..73],[76..94], is: 0.742 > Range of RMSD values to reference struct. is 0.643 to 0.874 PdbStat> PdbStat> *END* of program detected, BYE! ...