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 `MRR110B_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER DNA BINDING PROTEIN 30-JUN-08 2K5V > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE SECOND OB-FOLD DOMAIN OF > ReadCoordsPdb(): >> TITLE 2 REPLICATION PROTEIN A FROM METHANOCOCCUS MARIPALUDIS. > ReadCoordsPdb(): >> TITLE 3 NORTHEAST STRUCTURAL GENOMICS TARGET MRR110B. > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `MRR110B_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 MRR110B_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 30540 ATOM records read from file > ReadCoordsPdb(): --> 30540 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 0.968 0.262 0.124 0.484 ASN A 2 0.980 0.975 0.362 0.410 2 2 TYR A 3 0.959 0.983 0.995 0.220 3 3 LYS A 4 0.987 0.993 0.835 0.504 0.742 0.265 4 4 ILE A 5 0.995 0.995 0.998 0.930 5 5 SER A 6 0.996 0.988 0.568 6 6 GLU A 7 0.991 0.988 0.589 0.148 0.318 7 7 LEU A 8 0.993 0.946 0.999 1.000 8 8 MET A 9 0.946 0.999 0.861 0.998 0.797 9 9 PRO A 10 0.999 0.993 0.943 0.860 10 10 ASN A 11 0.999 0.985 0.869 0.781 11 11 LEU A 12 0.973 0.982 0.998 0.860 12 12 SER A 13 0.976 0.979 0.446 13 13 GLY A 14 0.978 0.990 14 14 THR A 15 0.989 0.984 0.999 15 15 ILE A 16 0.980 0.991 0.999 1.000 16 16 ASN A 17 0.992 0.993 0.933 0.688 17 17 ALA A 18 0.989 0.995 18 18 GLU A 19 0.993 0.992 0.230 0.892 0.273 19 19 VAL A 20 0.998 0.990 1.000 20 20 VAL A 21 0.989 0.985 0.999 21 21 ALA A 22 0.986 0.983 22 22 ALA A 23 0.970 0.991 23 23 TYR A 24 0.986 0.983 0.998 0.244 24 24 PRO A 25 0.990 0.975 0.908 0.831 25 25 LYS A 26 0.984 0.953 0.996 0.993 0.371 0.050 26 26 LYS A 27 0.934 0.984 0.996 0.755 0.585 0.126 27 27 GLU A 28 0.977 0.976 0.575 0.998 0.210 28 28 PHE A 29 0.975 0.982 0.997 0.698 29 29 SER A 30 0.981 0.981 0.457 30 30 ARG A 31 0.964 0.944 0.990 0.511 0.144 0.753 0.998 31 31 LYS A 32 0.995 0.989 0.188 0.311 0.783 0.230 32 32 ASP A 33 0.959 0.895 0.533 0.640 33 GLY A 34 0.877 0.895 34 THR A 35 0.882 0.962 0.995 35 LYS A 36 0.662 0.675 0.495 0.830 0.478 0.068 GLY A 37 0.823 0.925 37 GLN A 38 0.963 0.979 0.866 0.993 0.580 38 38 LEU A 39 0.977 0.969 0.998 1.000 39 39 LYS A 40 0.965 0.979 0.995 0.731 0.690 0.080 40 40 SER A 41 0.981 0.976 0.445 41 41 LEU A 42 0.991 0.963 0.997 0.998 42 42 PHE A 43 0.950 0.990 0.999 0.405 43 43 LEU A 44 0.993 0.991 0.999 1.000 44 44 LYS A 45 0.979 0.986 0.994 0.996 0.602 0.221 45 45 ASP A 46 0.951 0.982 0.671 0.396 46 46 ASP A 47 0.987 0.982 0.555 0.217 47 47 THR A 48 0.985 0.977 0.922 48 48 GLY A 49 0.978 0.999 49 49 SER A 50 0.995 0.978 0.663 50 50 ILE A 51 0.991 0.997 0.999 0.635 51 51 ARG A 52 0.992 0.985 0.478 0.630 0.180 0.731 0.998 52 52 GLY A 53 0.973 0.950 53 53 THR A 54 0.957 0.989 0.999 54 54 LEU A 55 0.993 0.987 0.998 0.999 55 55 TRP A 56 0.990 0.992 0.998 0.996 56 56 ASN A 57 0.998 0.991 0.675 0.798 57 57 GLU A 58 0.993 0.985 0.773 0.685 0.223 58 58 LEU A 59 0.993 0.996 0.999 0.999 59 59 ALA A 60 0.999 0.980 60 60 ASP A 61 0.982 0.985 0.465 0.316 61 61 PHE A 62 0.992 0.985 0.998 0.997 62 62 GLU A 63 0.994 0.973 0.998 0.938 0.235 63 63 VAL A 64 0.971 0.970 0.998 64 64 LYS A 65 0.977 0.975 0.748 0.732 0.144 0.163 65 65 LYS A 66 0.987 0.971 0.996 0.801 0.457 0.339 66 66 GLY A 67 0.946 0.946 67 67 ASP A 68 0.956 0.967 0.553 0.610 68 68 ILE A 69 0.990 0.985 0.999 1.000 69 69 ALA A 70 0.975 0.986 70 70 GLU A 71 0.986 0.991 0.999 0.991 0.160 71 71 VAL A 72 0.993 0.990 1.000 72 72 SER A 73 0.987 0.989 0.477 73 73 GLY A 74 0.985 0.980 74 74 TYR A 75 0.988 0.994 0.997 0.801 75 75 VAL A 76 0.996 0.991 1.000 76 76 LYS A 77 0.982 0.983 0.542 0.937 0.240 0.477 77 77 GLN A 78 0.977 0.984 0.999 0.993 1.000 78 78 GLY A 79 0.878 0.863 79 TYR A 80 0.950 0.380 0.805 0.349 SER A 81 0.351 0.847 0.490 GLY A 82 0.802 0.868 82 LEU A 83 0.961 0.957 0.999 0.946 83 83 GLU A 84 0.980 0.954 0.662 0.608 0.299 84 84 ILE A 85 0.967 0.990 1.000 1.000 85 85 SER A 86 0.992 0.993 0.462 86 86 VAL A 87 0.993 0.990 1.000 87 87 ASP A 88 0.991 0.982 0.563 0.630 88 88 ASN A 89 0.988 0.991 0.811 0.356 89 89 ILE A 90 0.989 0.993 1.000 1.000 90 90 GLY A 91 0.989 0.990 91 91 ILE A 92 0.995 0.986 0.998 0.568 92 92 ILE A 93 0.989 0.987 0.998 0.855 93 93 GLU A 94 0.919 0.885 0.627 0.641 0.457 94 LYS A 95 0.926 0.717 0.693 0.590 0.215 0.148 SER A 96 0.811 0.839 0.181 96 LEU A 97 0.828 0.233 0.621 0.607 GLU A 98 0.891 0.553 0.406 0.286 Ranges: 3 from: A 2 to A 32 from: A 38 to A 78 from: A 83 to A 93 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..32],A[38..78],A[83..93],for model 1 is: 0.548 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 2 is: 0.535 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 3 is: 0.516 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 4 is: 0.602 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 5 is: 0.652 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 6 is: 0.466 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 7 is: 0.685 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 8 is: 0.518 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 9 is: 0.545 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 10 is: 0.408 (*) > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 11 is: 0.486 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 12 is: 0.574 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 13 is: 0.578 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 14 is: 0.496 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 15 is: 0.438 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 16 is: 0.500 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 17 is: 0.613 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 18 is: 0.535 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 19 is: 0.837 > Kabsch RMSD of backbone atoms in res. A[2..32],A[38..78],A[83..93],for model 20 is: 0.522 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..32],[38..78],[83..93], is: 0.553 > Range of RMSD values to reference struct. is 0.408 to 0.837 > 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..32],A[38..78],A[83..93],for model 1 is: 1.019 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 2 is: 1.050 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 3 is: 0.945 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 4 is: 1.034 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 5 is: 1.244 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 6 is: 1.011 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 7 is: 1.032 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 8 is: 0.948 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 9 is: 0.968 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 10 is: 0.814 (*) > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 11 is: 0.942 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 12 is: 0.944 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 13 is: 0.973 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 14 is: 1.004 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 15 is: 0.844 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 16 is: 0.905 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 17 is: 1.019 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 18 is: 0.954 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 19 is: 1.229 > Kabsch RMSD of heavy atoms in res. A[2..32],A[38..78],A[83..93],for model 20 is: 0.889 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..32],[38..78],[83..93], is: 0.988 > Range of RMSD values to reference struct. is 0.814 to 1.244 PdbStat> PdbStat> *END* of program detected, BYE! ...