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 `LKR112_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 114 MET LYS ASN THR GLY ASP GLU VAL VAL ALA ILE ILE SER 1 > ReadCoordsPdb(): Counting models in file `LKR112_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 LKR112_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 35900 ATOM records read from file > ReadCoordsPdb(): --> 35900 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 0.491 0.729 0.539 0.346 LYS A 2 0.568 0.389 0.554 0.999 0.999 0.999 ASN A 3 0.789 0.892 0.808 0.665 THR A 4 0.886 0.788 0.793 GLY A 5 0.812 0.761 ASP A 6 0.887 0.798 0.610 0.975 GLU A 7 0.937 0.990 0.997 0.999 0.955 7 7 VAL A 8 0.999 0.999 1.000 8 8 VAL A 9 1.000 1.000 1.000 9 9 ALA A 10 0.999 1.000 10 10 ILE A 11 1.000 1.000 1.000 1.000 11 11 ILE A 12 1.000 1.000 1.000 1.000 12 12 SER A 13 1.000 0.999 0.641 13 13 GLN A 14 0.997 0.999 1.000 0.996 0.906 14 14 ASN A 15 1.000 0.999 1.000 0.993 15 15 GLY A 16 0.998 0.991 16 16 LYS A 17 0.991 1.000 0.999 1.000 0.927 1.000 17 17 VAL A 18 1.000 1.000 1.000 18 18 ILE A 19 1.000 1.000 1.000 1.000 19 19 ARG A 20 1.000 1.000 1.000 1.000 0.930 0.879 1.000 20 20 GLU A 21 0.999 1.000 1.000 1.000 1.000 21 21 ILE A 22 1.000 0.999 1.000 1.000 22 22 PRO A 23 1.000 0.982 1.000 1.000 23 23 LEU A 24 0.983 0.999 0.999 1.000 24 24 THR A 25 0.996 0.998 1.000 25 25 GLY A 26 0.995 0.988 26 26 HIS A 27 0.998 0.947 0.999 0.996 27 27 LYS A 28 0.965 0.918 0.930 0.793 0.999 1.000 28 28 GLY A 29 0.912 0.995 29 29 ASN A 30 0.999 1.000 1.000 0.999 30 30 GLU A 31 0.998 0.999 0.999 0.936 0.867 31 31 GLN A 32 0.999 1.000 1.000 1.000 0.997 32 32 PHE A 33 1.000 1.000 1.000 1.000 33 33 THR A 34 1.000 1.000 1.000 34 34 ILE A 35 0.999 0.998 1.000 1.000 35 35 LYS A 36 0.995 0.994 1.000 1.000 1.000 1.000 36 36 GLY A 37 0.988 0.876 37 LYS A 38 0.884 0.867 0.698 0.805 0.998 1.000 38 GLY A 39 0.861 0.709 ALA A 40 0.704 0.940 GLN A 41 0.952 0.887 0.997 0.925 0.760 41 TYR A 42 0.950 0.998 0.999 0.999 42 42 ASN A 43 0.999 0.994 0.999 0.999 43 43 LEU A 44 0.995 1.000 1.000 1.000 44 44 MET A 45 0.999 0.999 1.000 1.000 0.999 45 45 GLU A 46 0.999 1.000 0.998 0.998 0.964 46 46 VAL A 47 1.000 0.998 1.000 47 47 ASP A 48 0.994 0.938 0.991 0.872 48 48 GLY A 49 0.888 0.317 GLU A 50 0.327 0.991 0.997 0.998 0.687 ARG A 51 0.983 1.000 0.999 0.998 0.998 0.998 1.000 51 51 ILE A 52 0.999 1.000 1.000 1.000 52 52 ARG A 53 0.994 1.000 0.996 0.832 0.997 0.877 0.999 53 53 ILE A 54 0.998 0.999 1.000 1.000 54 54 LYS A 55 1.000 1.000 0.999 0.999 0.997 0.893 55 55 GLU A 56 0.998 0.998 0.994 0.780 0.794 56 56 ASP A 57 0.997 0.985 0.950 0.891 57 57 ASN A 58 0.992 0.971 0.320 0.913 58 58 SER A 59 0.956 0.993 0.699 59 59 PRO A 60 0.996 0.997 0.981 0.968 60 60 ASP A 61 0.997 0.991 0.999 0.987 61 61 GLN A 62 0.998 0.991 0.999 0.926 0.979 62 62 VAL A 63 1.000 0.999 1.000 63 63 GLY A 64 0.999 0.999 64 64 VAL A 65 1.000 1.000 1.000 65 65 LYS A 66 1.000 0.999 1.000 0.999 1.000 0.997 66 66 MET A 67 0.999 0.999 0.999 0.925 0.933 67 67 GLY A 68 0.997 0.990 68 68 TRP A 69 0.996 0.999 1.000 1.000 69 69 LYS A 70 0.998 0.998 0.999 1.000 0.996 0.932 70 70 SER A 71 0.989 0.955 0.935 71 71 LYS A 72 0.979 0.996 1.000 0.932 1.000 1.000 72 72 ALA A 73 0.994 0.942 73 73 GLY A 74 0.957 0.985 74 74 ASP A 75 0.998 0.998 1.000 0.999 75 75 THR A 76 1.000 1.000 1.000 76 76 ILE A 77 1.000 1.000 1.000 1.000 77 77 VAL A 78 1.000 0.999 1.000 78 78 CYS A 79 0.996 0.999 0.549 79 79 LEU A 80 0.999 0.996 0.999 1.000 80 80 PRO A 81 0.993 0.991 0.938 0.881 81 81 HIS A 82 0.996 0.997 0.999 0.995 82 82 LYS A 83 0.999 0.999 1.000 0.999 1.000 1.000 83 83 VAL A 84 0.999 1.000 1.000 84 84 PHE A 85 0.999 1.000 1.000 0.999 85 85 VAL A 86 1.000 1.000 1.000 86 86 GLU A 87 0.999 0.998 0.849 1.000 0.979 87 87 ILE A 88 0.999 1.000 1.000 1.000 88 88 LYS A 89 0.998 0.996 0.998 0.991 0.924 0.518 89 89 SER A 90 0.998 0.994 0.623 90 90 THR A 91 0.994 0.994 0.935 91 91 GLN A 92 0.974 0.836 0.998 0.786 0.950 92 LYS A 93 0.830 0.847 0.565 0.707 0.931 0.999 93 ASP A 94 0.769 0.832 0.358 0.922 SER A 95 0.832 0.545 0.400 LYS A 96 0.945 0.865 0.919 0.806 0.998 0.872 96 ASP A 97 0.975 0.953 0.638 0.980 97 97 PRO A 98 0.988 0.870 0.895 0.812 98 ASP A 99 0.821 0.664 0.482 0.967 THR A 100 0.896 0.439 0.312 ASP A 101 0.666 0.741 0.518 0.965 LEU A 102 0.822 0.920 0.482 0.986 102 ILE A 103 0.956 0.698 0.999 0.690 VAL A 104 0.865 0.977 0.926 104 PRO A 105 0.987 0.932 0.897 0.817 105 105 ASN A 106 0.810 0.658 0.295 0.854 LEU A 107 0.955 0.777 0.611 0.648 GLU A 108 0.946 0.776 0.542 0.999 0.933 HIS A 109 0.861 0.742 0.484 0.515 HIS A 110 0.859 0.485 0.268 0.267 HIS A 111 0.518 0.492 0.596 0.498 HIS A 112 0.845 0.715 0.471 0.464 HIS A 113 0.865 0.423 0.389 0.454 HIS A 114 0.749 0.649 0.602 Ranges: 3 from: A 7 to A 36 from: A 42 to A 48 from: A 51 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[7..36],A[42..48],A[51..91],for model 1 is: 0.198 (*) > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 2 is: 0.403 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 3 is: 0.263 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 4 is: 0.228 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 5 is: 0.337 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 6 is: 0.231 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 7 is: 0.254 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 8 is: 0.324 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 9 is: 0.251 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 10 is: 0.248 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 11 is: 0.319 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 12 is: 0.307 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 13 is: 0.411 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 14 is: 0.592 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 15 is: 0.337 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 16 is: 0.311 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 17 is: 0.240 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 18 is: 0.269 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 19 is: 0.301 > Kabsch RMSD of backbone atoms in res. A[7..36],A[42..48],A[51..91],for model 20 is: 0.385 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[7..36],[42..48],[51..91], is: 0.310 > Range of RMSD values to reference struct. is 0.198 to 0.592 > 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[7..36],A[42..48],A[51..91],for model 1 is: 0.373 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 2 is: 0.741 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 3 is: 0.366 (*) > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 4 is: 0.418 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 5 is: 0.559 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 6 is: 0.482 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 7 is: 0.400 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 8 is: 0.519 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 9 is: 0.430 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 10 is: 0.465 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 11 is: 0.441 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 12 is: 0.433 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 13 is: 0.532 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 14 is: 0.667 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 15 is: 0.487 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 16 is: 0.411 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 17 is: 0.385 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 18 is: 0.462 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 19 is: 0.420 > Kabsch RMSD of heavy atoms in res. A[7..36],A[42..48],A[51..91],for model 20 is: 0.516 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[7..36],[42..48],[51..91], is: 0.475 > Range of RMSD values to reference struct. is 0.366 to 0.741 PdbStat> PdbStat> *END* of program detected, BYE! ...