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 `HR4694F_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER TRANSFERASE 30-JUN-10 2L05 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE RAS-BINDING DOMAIN OF SERINE/THREONINE- > ReadCoordsPdb(): >> TITLE 2 PROTEIN KINASE B-RAF FROM HOMO SAPIENS, NORTHEAST STRUCTURAL GENOMICS > ReadCoordsPdb(): >> TITLE 3 CONSORTIUM TARGET HR4694F > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `HR4694F_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 HR4694F_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 27960 ATOM records read from file > ReadCoordsPdb(): --> 27960 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 ----------------------------------------------------------------------------------- HIS A 1 0.335 0.447 0.217 MET A 2 0.267 0.935 0.493 0.415 0.087 PRO A 3 0.984 0.864 0.935 0.866 3 LYS A 4 0.918 0.703 0.554 0.666 0.193 0.332 SER A 5 0.565 0.919 0.046 PRO A 6 0.985 0.736 0.928 0.868 GLN A 7 0.881 0.733 0.176 0.852 0.568 LYS A 8 0.945 0.993 0.782 0.252 0.578 0.498 8 8 PRO A 9 0.996 0.985 0.998 1.000 9 9 ILE A 10 0.992 0.998 0.998 0.724 10 10 VAL A 11 0.998 0.997 1.000 11 11 ARG A 12 0.994 0.988 0.992 0.890 0.709 0.774 0.999 12 12 VAL A 13 0.989 0.991 1.000 13 13 PHE A 14 0.991 0.991 0.997 0.233 14 14 LEU A 15 0.984 0.995 0.999 1.000 15 15 PRO A 16 0.997 0.986 0.937 0.868 16 16 ASN A 17 0.996 0.978 0.731 0.774 17 17 LYS A 18 0.998 0.975 0.917 0.498 0.493 0.243 18 18 GLN A 19 0.965 0.976 0.998 0.946 0.958 19 19 ARG A 20 0.965 0.988 0.508 0.401 0.416 0.766 0.999 20 20 THR A 21 0.995 0.980 0.998 21 21 VAL A 22 0.984 0.997 0.999 22 22 VAL A 23 0.997 0.995 0.999 23 23 PRO A 24 0.996 0.990 0.927 0.853 24 24 ALA A 25 0.981 0.975 25 25 ARG A 26 0.964 0.977 0.882 0.990 0.724 0.729 0.999 26 26 CYS A 27 0.985 0.977 0.999 27 27 GLY A 28 0.971 0.945 28 28 VAL A 29 0.954 0.990 0.999 29 29 THR A 30 0.996 0.997 0.998 30 30 VAL A 31 0.999 0.998 1.000 31 31 ARG A 32 0.997 0.986 0.996 0.884 0.269 0.724 0.999 32 32 ASP A 33 0.992 0.981 0.634 0.326 33 33 SER A 34 0.986 0.991 0.257 34 34 LEU A 35 0.986 0.986 0.999 0.999 35 35 LYS A 36 0.998 0.988 0.996 0.991 0.191 0.302 36 36 LYS A 37 0.996 0.991 0.513 0.855 0.273 0.241 37 37 ALA A 38 0.997 0.995 38 38 LEU A 39 0.992 0.991 1.000 1.000 39 39 MET A 40 0.999 0.997 0.998 0.482 0.423 40 40 MET A 41 0.999 0.992 0.999 0.998 0.043 41 41 ARG A 42 0.983 0.986 0.995 0.692 0.115 0.779 0.999 42 42 GLY A 43 0.981 0.982 43 43 LEU A 44 0.982 0.984 0.999 0.947 44 44 ILE A 45 0.970 0.995 0.999 1.000 45 45 PRO A 46 0.998 0.989 0.940 0.868 46 46 GLU A 47 0.991 0.982 0.537 0.342 0.372 47 47 CYS A 48 0.987 0.980 0.998 48 48 CYS A 49 0.993 0.970 0.999 49 49 ALA A 50 0.983 0.991 50 50 VAL A 51 0.992 0.993 0.999 51 51 TYR A 52 0.993 0.995 0.997 0.403 52 52 ARG A 53 0.987 0.979 0.911 0.987 0.585 0.658 0.999 53 53 ILE A 54 0.979 0.973 1.000 1.000 54 54 GLN A 55 0.952 0.977 0.841 0.611 0.278 55 55 ASP A 56 0.999 0.995 0.643 0.341 56 56 GLY A 57 0.983 0.979 57 57 GLU A 58 0.970 0.966 0.682 0.737 0.416 58 58 LYS A 59 0.983 0.965 0.998 0.992 0.556 0.799 59 59 LYS A 60 0.976 0.991 0.678 0.263 0.949 0.073 60 60 PRO A 61 0.997 0.974 0.954 0.902 61 61 ILE A 62 0.975 0.988 0.999 0.890 62 62 GLY A 63 0.982 0.994 63 63 TRP A 64 0.998 0.994 0.998 0.997 64 64 ASP A 65 0.996 0.975 0.534 0.607 65 65 THR A 66 0.987 0.998 0.997 66 66 ASP A 67 0.997 0.996 0.761 0.777 67 67 ILE A 68 0.997 1.000 0.999 0.542 68 68 SER A 69 0.998 0.996 0.524 69 69 TRP A 70 0.996 0.994 0.999 0.984 70 70 LEU A 71 0.996 0.994 0.999 0.999 71 71 THR A 72 0.997 0.994 0.999 72 72 GLY A 73 0.989 0.963 73 73 GLU A 74 0.979 0.994 0.462 0.545 0.323 74 74 GLU A 75 0.994 0.984 0.861 0.520 0.514 75 75 LEU A 76 0.991 0.973 0.999 0.999 76 76 HIS A 77 0.982 0.985 0.996 0.987 77 77 VAL A 78 0.993 0.987 0.999 78 78 GLU A 79 0.959 0.981 0.500 0.573 0.306 79 79 VAL A 80 0.991 0.981 0.999 80 80 LEU A 81 0.972 0.979 0.997 0.999 81 81 GLU A 82 0.908 0.909 0.544 0.692 0.292 82 82 ASN A 83 0.952 0.768 0.286 0.336 VAL A 84 0.753 0.925 0.383 PRO A 85 0.990 0.865 0.953 0.905 85 LEU A 86 0.905 0.390 0.387 Ranges: 1 from: A 8 to A 82 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[8..82],for model 1 is: 0.513 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 2 is: 0.536 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 3 is: 0.586 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 4 is: 0.507 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 5 is: 0.485 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 6 is: 0.417 (*) > Kabsch RMSD of backbone atoms in res. A[8..82],for model 7 is: 0.735 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 8 is: 0.455 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 9 is: 0.683 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 10 is: 0.509 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 11 is: 0.485 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 12 is: 0.524 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 13 is: 0.551 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 14 is: 0.552 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 15 is: 0.727 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 16 is: 0.615 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 17 is: 0.576 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 18 is: 0.446 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 19 is: 0.505 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 20 is: 0.640 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[8..82], is: 0.552 > Range of RMSD values to reference struct. is 0.417 to 0.735 > 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[8..82],for model 1 is: 1.042 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 2 is: 1.014 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 3 is: 1.066 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 4 is: 1.016 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 5 is: 0.888 (*) > Kabsch RMSD of heavy atoms in res. A[8..82],for model 6 is: 0.963 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 7 is: 1.190 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 8 is: 0.892 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 9 is: 1.063 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 10 is: 0.918 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 11 is: 1.038 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 12 is: 1.055 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 13 is: 0.922 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 14 is: 1.004 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 15 is: 1.139 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 16 is: 1.094 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 17 is: 1.030 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 18 is: 0.937 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 19 is: 0.948 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 20 is: 0.985 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[8..82], is: 1.010 > Range of RMSD values to reference struct. is 0.888 to 1.190 PdbStat> PdbStat> *END* of program detected, BYE! ...