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 `DHR29B_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 96 SER SER GLN THR LEU ASP ARG ASP PRO THR LEU THR LEU 1 > ReadCoordsPdb(): Counting models in file `DHR29B_R3Cons_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 DHR29B_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 30300 ATOM records read from file > ReadCoordsPdb(): --> 30300 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 ----------------------------------------------------------------------------------- SER A 1 0.186 0.406 SER A 2 0.882 0.148 0.288 GLN A 3 0.591 0.177 0.415 0.155 0.782 THR A 4 0.824 0.224 0.372 LEU A 5 0.927 0.234 0.816 0.867 ASP A 6 0.801 0.346 0.434 0.899 ARG A 7 0.768 0.466 0.378 0.993 0.374 0.773 1.000 ASP A 8 0.658 0.970 0.529 0.892 PRO A 9 0.992 0.989 0.940 0.887 9 9 THR A 10 0.995 0.998 1.000 10 10 LEU A 11 0.997 0.996 0.907 0.741 11 11 THR A 12 0.997 0.996 1.000 12 12 LEU A 13 0.999 0.985 0.999 1.000 13 13 SER A 14 0.988 0.998 0.571 14 14 LEU A 15 0.998 0.998 0.999 0.957 15 15 ILE A 16 0.999 0.998 1.000 1.000 16 16 ALA A 17 0.990 0.987 17 17 LYS A 18 0.961 0.515 0.936 0.601 0.994 0.689 ASN A 19 0.512 0.878 0.675 0.906 THR A 20 0.872 0.991 0.870 20 PRO A 21 0.987 0.992 0.898 0.822 21 21 ALA A 22 0.993 0.520 ASN A 23 0.524 0.952 0.947 0.881 SER A 24 0.978 0.974 0.322 24 24 MET A 25 0.992 0.999 1.000 0.999 0.929 25 25 ILE A 26 0.999 0.997 1.000 1.000 26 26 MET A 27 0.992 0.987 0.603 0.488 0.393 27 27 THR A 28 0.992 0.978 0.930 28 28 LYS A 29 0.988 0.992 0.871 1.000 1.000 1.000 29 29 LEU A 30 0.993 0.998 0.992 0.858 30 30 PRO A 31 0.993 0.988 0.939 0.892 31 31 SER A 32 0.983 0.988 0.509 32 32 VAL A 33 0.982 0.996 0.495 33 33 ARG A 34 0.994 0.985 0.712 0.996 0.552 0.943 1.000 34 34 VAL A 35 0.995 0.971 0.556 35 35 LYS A 36 0.992 0.999 0.932 0.994 0.466 0.999 36 36 THR A 37 0.997 0.994 1.000 37 37 GLU A 38 0.988 0.991 0.575 0.999 0.956 38 38 GLY A 39 0.989 0.973 39 39 TYR A 40 0.968 0.974 0.588 0.988 40 40 ASN A 41 0.939 0.946 0.492 0.485 41 41 PRO A 42 0.997 0.953 0.979 0.950 42 42 SER A 43 0.928 0.702 0.557 ILE A 44 0.758 0.990 0.999 0.563 ASN A 45 0.975 0.870 0.621 0.944 45 VAL A 46 0.993 0.990 0.395 46 46 ASN A 47 0.998 0.996 1.000 1.000 47 47 GLU A 48 0.992 0.993 0.931 0.707 0.894 48 48 LEU A 49 0.998 0.996 1.000 1.000 49 49 PHE A 50 0.999 0.989 1.000 0.999 50 50 ALA A 51 0.999 0.997 51 51 TYR A 52 0.994 0.997 0.860 1.000 52 52 VAL A 53 0.997 0.994 0.997 53 53 ASP A 54 0.994 0.997 0.935 0.964 54 54 LEU A 55 0.993 0.926 0.956 0.453 55 55 SER A 56 0.990 0.457 0.070 GLY A 57 0.379 0.535 SER A 58 0.746 0.635 0.319 GLU A 59 0.912 0.980 0.593 0.999 0.976 59 59 PRO A 60 0.988 0.969 0.905 0.835 60 60 GLY A 61 0.924 0.995 61 61 GLU A 62 0.997 0.995 0.702 0.999 1.000 62 62 HIS A 63 0.997 0.994 0.934 0.899 63 63 ASP A 64 0.998 0.999 1.000 1.000 64 64 TYR A 65 0.998 0.994 0.999 0.999 65 65 GLU A 66 0.994 0.997 0.930 1.000 1.000 66 66 VAL A 67 0.997 0.995 1.000 67 67 LYS A 68 0.997 0.967 1.000 0.999 0.999 0.999 68 68 VAL A 69 0.983 0.998 1.000 69 69 GLU A 70 0.996 0.993 0.637 0.935 0.871 70 70 PRO A 71 0.991 0.988 0.939 0.889 71 71 ILE A 72 0.992 0.998 0.999 0.957 72 72 PRO A 73 0.983 0.693 0.897 0.826 ASN A 74 0.614 0.951 0.937 0.906 ILE A 75 0.984 0.999 0.999 0.466 75 75 LYS A 76 0.998 0.987 0.863 1.000 1.000 1.000 76 76 ILE A 77 0.979 0.999 0.999 0.999 77 77 VAL A 78 0.999 0.999 1.000 78 78 GLU A 79 0.980 0.987 0.581 0.926 0.974 79 79 ILE A 80 0.977 0.808 0.858 0.955 80 SER A 81 0.860 0.996 1.000 81 PRO A 82 0.999 0.987 1.000 1.000 82 82 ARG A 83 0.985 0.990 0.942 0.999 0.995 0.997 1.000 83 83 VAL A 84 0.999 1.000 1.000 84 84 VAL A 85 1.000 0.999 1.000 85 85 THR A 86 0.999 0.999 1.000 86 86 LEU A 87 0.999 0.998 1.000 1.000 87 87 GLN A 88 0.999 0.998 1.000 1.000 0.999 88 88 LEU A 89 0.997 0.994 0.997 0.999 89 89 GLU A 90 0.996 0.988 0.926 0.870 0.966 90 90 HIS A 91 0.994 0.979 0.585 0.743 91 91 HIS A 92 0.951 0.307 0.860 0.189 HIS A 93 0.915 0.547 0.507 0.543 HIS A 94 0.686 0.244 0.437 0.672 HIS A 95 0.864 0.164 0.409 0.357 HIS A 96 0.619 0.632 0.399 Ranges: 6 from: A 9 to A 17 from: A 24 to A 42 from: A 46 to A 55 from: A 59 to A 72 from: A 75 to A 79 from: A 82 to A 91 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[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 1 is: 0.486 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 2 is: 0.435 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 3 is: 0.492 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 4 is: 0.512 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 5 is: 0.560 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 6 is: 0.574 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 7 is: 0.475 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 8 is: 0.478 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 9 is: 0.385 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 10 is: 0.498 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 11 is: 0.379 (*) > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 12 is: 0.437 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 13 is: 0.452 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 14 is: 0.504 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 15 is: 0.586 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 16 is: 0.842 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 17 is: 0.391 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 18 is: 0.520 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 19 is: 0.399 > Kabsch RMSD of backbone atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 20 is: 0.461 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..17],[24..42],[46..55],[59..72],[75..79],[82..91], is: 0.493 > Range of RMSD values to reference struct. is 0.379 to 0.842 > 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[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 1 is: 0.967 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 2 is: 0.903 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 3 is: 0.751 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 4 is: 0.777 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 5 is: 0.912 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 6 is: 0.970 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 7 is: 0.814 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 8 is: 0.813 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 9 is: 0.747 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 10 is: 0.956 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 11 is: 0.747 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 12 is: 0.902 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 13 is: 0.780 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 14 is: 0.827 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 15 is: 0.777 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 16 is: 1.076 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 17 is: 0.669 (*) > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 18 is: 0.875 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 19 is: 0.754 > Kabsch RMSD of heavy atoms in res. A[9..17],A[24..42],A[46..55],A[59..72],A[75..79],A[82..91],for model 20 is: 0.786 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..17],[24..42],[46..55],[59..72],[75..79],[82..91], is: 0.840 > Range of RMSD values to reference struct. is 0.669 to 1.076 PdbStat> PdbStat> *END* of program detected, BYE! ...