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 `PFR193A_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 30-JUN-09 2KL6 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE CARDB DOMAIN OF PF1109 FROM > ReadCoordsPdb(): >> TITLE 2 PYROCOCCUS FURIOSUS. NORTHEAST STRUCTURAL GENOMICS > ReadCoordsPdb(): >> TITLE 3 CONSORTIUM TARGET PFR193A > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `PFR193A_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 PFR193A_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 33780 ATOM records read from file > ReadCoordsPdb(): --> 33780 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 0.959 0.507 0.329 0.558 GLU A 2 0.994 0.985 0.995 0.997 0.981 2 2 PHE A 3 0.997 0.992 0.996 0.898 3 3 PRO A 4 0.998 1.000 0.973 0.939 4 4 ASP A 5 0.992 0.992 0.997 0.524 5 5 LEU A 6 0.993 0.966 0.999 0.999 6 6 THR A 7 0.970 0.996 0.998 7 7 VAL A 8 0.996 1.000 0.999 8 8 GLU A 9 0.997 0.990 0.994 0.938 0.316 9 9 ILE A 10 0.991 0.995 1.000 1.000 10 10 LYS A 11 0.997 0.995 0.880 0.562 0.993 0.320 11 11 GLY A 12 0.997 0.997 12 12 PRO A 13 0.999 0.992 0.988 0.976 13 13 ASP A 14 0.994 0.970 0.523 0.240 14 14 VAL A 15 0.993 0.997 1.000 15 15 VAL A 16 0.998 0.999 1.000 16 16 GLY A 17 0.998 0.996 17 17 VAL A 18 0.999 0.999 0.999 18 18 ASN A 19 0.999 0.997 0.996 0.914 19 19 LYS A 20 0.994 0.985 0.997 0.999 1.000 0.925 20 20 LEU A 21 0.991 0.992 0.999 1.000 21 21 ALA A 22 0.992 0.998 22 22 GLU A 23 0.994 0.997 0.998 0.997 0.230 23 23 TYR A 24 0.999 0.997 0.999 0.996 24 24 GLU A 25 1.000 1.000 0.996 0.890 0.522 25 25 VAL A 26 0.997 0.998 1.000 26 26 HIS A 27 0.998 0.999 0.998 0.991 27 27 VAL A 28 0.998 0.998 0.999 28 28 LYS A 29 0.997 0.998 0.999 0.995 0.945 0.216 29 29 ASN A 30 0.997 0.999 1.000 1.000 30 30 LEU A 31 0.998 0.986 0.999 0.999 31 31 GLY A 32 0.987 0.998 32 32 GLY A 33 0.998 0.999 33 33 ILE A 34 1.000 0.998 0.997 0.999 34 34 GLY A 35 0.998 0.996 35 35 VAL A 36 0.999 0.999 1.000 36 36 PRO A 37 0.999 1.000 0.996 0.986 37 37 SER A 38 0.999 1.000 0.414 38 38 THR A 39 1.000 0.992 0.999 39 39 LYS A 40 0.993 0.998 0.997 0.996 0.875 0.567 40 40 VAL A 41 0.997 0.994 1.000 41 41 ARG A 42 0.995 0.997 0.923 0.991 0.738 0.811 0.999 42 42 VAL A 43 1.000 0.997 0.999 43 43 TYR A 44 0.997 0.999 0.997 0.211 44 44 ILE A 45 0.997 0.999 1.000 1.000 45 45 ASN A 46 0.999 1.000 0.941 0.924 46 46 GLY A 47 0.996 0.980 47 47 THR A 48 0.988 0.997 0.999 48 48 LEU A 49 0.999 0.996 1.000 1.000 49 49 TYR A 50 0.992 1.000 0.995 0.997 50 50 LYS A 51 0.993 0.998 0.995 0.890 0.539 0.535 51 51 ASN A 52 0.993 0.996 0.989 0.782 52 52 TRP A 53 0.999 0.998 0.998 0.995 53 53 THR A 54 0.996 1.000 0.999 54 54 VAL A 55 0.999 1.000 1.000 55 55 SER A 56 0.997 0.999 0.852 56 56 LEU A 57 0.999 1.000 0.999 0.999 57 57 GLY A 58 0.999 0.998 58 58 PRO A 59 0.999 0.996 0.990 0.974 59 59 LYS A 60 0.999 0.984 0.999 0.591 0.988 0.208 60 60 GLU A 61 0.986 0.999 0.996 0.756 0.207 61 61 GLU A 62 0.999 0.996 0.997 0.993 0.427 62 62 LYS A 63 0.991 0.993 0.984 0.748 0.593 0.583 63 63 VAL A 64 0.995 0.999 1.000 64 64 LEU A 65 0.998 0.990 0.998 1.000 65 65 THR A 66 0.991 0.998 0.997 66 66 PHE A 67 0.998 1.000 0.999 0.800 67 67 SER A 68 0.999 0.994 0.861 68 68 TRP A 69 0.989 1.000 0.999 0.997 69 69 THR A 70 0.997 0.999 0.999 70 70 PRO A 71 0.998 0.989 1.000 1.000 71 71 THR A 72 0.994 0.975 0.996 72 72 GLN A 73 0.967 0.995 0.766 0.520 0.411 73 73 GLU A 74 0.992 0.998 0.981 0.599 0.679 74 74 GLY A 75 0.997 0.996 75 75 MET A 76 0.996 0.992 0.639 0.295 0.339 76 76 TYR A 77 0.992 0.968 0.998 0.799 77 77 ARG A 78 0.976 0.998 0.989 0.919 0.426 0.766 0.998 78 78 ILE A 79 0.999 0.997 1.000 1.000 79 79 ASN A 80 0.997 0.993 0.998 0.954 80 80 ALA A 81 0.993 0.997 81 81 THR A 82 0.998 0.994 0.997 82 82 VAL A 83 0.987 0.998 0.999 83 83 ASP A 84 0.994 0.986 0.947 0.818 84 84 GLU A 85 0.998 0.998 0.927 0.567 0.484 85 85 GLU A 86 0.997 0.993 0.871 0.524 0.274 86 86 ASN A 87 0.997 0.972 0.624 0.129 87 87 THR A 88 0.948 0.978 0.998 88 88 VAL A 89 0.975 1.000 0.999 89 89 VAL A 90 0.997 0.998 1.000 90 90 GLU A 91 0.991 0.988 0.994 0.482 0.292 91 91 LEU A 92 0.992 0.996 0.999 1.000 92 92 ASN A 93 0.983 0.948 0.843 0.759 93 93 GLU A 94 0.962 0.966 0.209 0.500 0.288 94 94 ASN A 95 0.982 0.978 0.518 0.209 95 95 ASN A 96 0.989 0.986 0.571 0.853 96 96 ASN A 97 0.994 0.976 0.994 0.880 97 97 VAL A 98 0.990 0.996 1.000 98 98 ALA A 99 0.993 0.998 99 99 THR A 100 0.993 0.996 0.998 100 100 PHE A 101 0.995 0.992 0.999 0.702 101 101 ASP A 102 0.995 0.995 0.393 0.248 102 102 VAL A 103 0.996 0.995 1.000 103 103 SER A 104 0.994 0.997 0.999 104 104 VAL A 105 0.998 0.998 0.999 105 105 VAL A 106 0.994 0.998 0.999 106 106 LEU A 107 0.995 0.959 0.999 0.999 107 107 GLU A 108 0.792 0.930 0.991 0.354 Ranges: 1 from: A 2 to A 107 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..107],for model 1 is: 0.244 (*) > Kabsch RMSD of backbone atoms in res. A[2..107],for model 2 is: 0.358 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 3 is: 0.441 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 4 is: 0.423 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 5 is: 0.473 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 6 is: 0.401 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 7 is: 0.411 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 8 is: 0.438 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 9 is: 0.387 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 10 is: 0.287 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 11 is: 0.382 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 12 is: 0.342 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 13 is: 0.464 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 14 is: 0.321 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 15 is: 0.323 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 16 is: 0.395 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 17 is: 0.341 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 18 is: 0.292 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 19 is: 0.392 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 20 is: 0.375 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..107], is: 0.375 > Range of RMSD values to reference struct. is 0.244 to 0.473 > 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..107],for model 1 is: 0.555 (*) > Kabsch RMSD of heavy atoms in res. A[2..107],for model 2 is: 0.627 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 3 is: 0.676 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 4 is: 0.730 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 5 is: 0.695 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 6 is: 0.643 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 7 is: 0.611 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 8 is: 0.728 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 9 is: 0.640 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 10 is: 0.632 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 11 is: 0.673 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 12 is: 0.667 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 13 is: 0.758 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 14 is: 0.621 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 15 is: 0.653 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 16 is: 0.744 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 17 is: 0.709 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 18 is: 0.564 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 19 is: 0.623 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 20 is: 0.673 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..107], is: 0.661 > Range of RMSD values to reference struct. is 0.555 to 0.758 PdbStat> PdbStat> *END* of program detected, BYE! ...