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 `PSR293_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 125 MET ASN ARG GLN GLN PHE ILE ASP TYR ALA GLN LYS LYS 1 > ReadCoordsPdb(): Counting models in file `PSR293_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 PSR293_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 41420 ATOM records read from file > ReadCoordsPdb(): --> 41420 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 0.911 0.860 0.868 0.189 ASN A 2 0.931 0.938 0.324 0.906 2 2 ARG A 3 0.997 0.995 0.715 0.985 0.193 0.606 1.000 3 3 GLN A 4 0.999 0.998 0.998 1.000 0.998 4 4 GLN A 5 0.999 0.998 0.999 0.481 0.953 5 5 PHE A 6 1.000 0.999 0.998 0.796 6 6 ILE A 7 0.999 0.999 1.000 0.999 7 7 ASP A 8 1.000 0.999 0.939 0.966 8 8 TYR A 9 0.999 0.999 0.992 0.998 9 9 ALA A 10 1.000 1.000 10 10 GLN A 11 0.997 0.998 0.998 0.849 0.915 11 11 LYS A 12 0.998 0.999 0.764 1.000 0.999 1.000 12 12 LYS A 13 0.998 0.998 0.614 0.226 0.927 0.937 13 13 TYR A 14 0.991 0.989 0.937 0.419 14 14 ASP A 15 0.996 0.996 0.891 0.947 15 15 THR A 16 0.993 0.988 0.796 16 16 LYS A 17 0.991 0.987 0.555 1.000 1.000 1.000 17 17 PRO A 18 0.997 0.991 0.967 0.937 18 18 ASP A 19 0.979 0.969 0.715 0.960 19 19 HIS A 20 0.982 0.953 0.350 0.416 20 20 PRO A 21 0.989 0.977 0.898 0.825 21 21 TRP A 22 0.996 0.993 0.998 0.736 22 22 GLU A 23 0.999 0.998 1.000 0.726 1.000 23 23 LYS A 24 0.994 0.997 1.000 0.927 0.422 0.997 24 24 PHE A 25 0.996 0.998 1.000 1.000 25 25 PRO A 26 0.999 0.998 0.957 0.909 26 26 ASP A 27 0.998 0.995 0.836 0.998 27 27 TYR A 28 0.994 0.985 0.998 0.962 28 28 ALA A 29 0.985 0.994 29 29 VAL A 30 0.996 0.999 0.999 30 30 PHE A 31 0.995 0.987 0.997 0.104 31 31 ARG A 32 0.991 0.986 0.220 0.926 0.799 0.806 1.000 32 32 HIS A 33 0.986 0.987 0.834 0.519 33 33 SER A 34 0.995 0.992 0.921 34 34 ASP A 35 0.985 0.988 0.998 0.952 35 35 ASN A 36 0.986 0.932 0.511 0.338 36 36 ASP A 37 0.841 0.388 0.757 0.921 LYS A 38 0.511 0.168 0.930 0.930 0.999 0.921 TRP A 39 0.452 0.851 0.424 0.614 TYR A 40 0.940 0.989 0.676 0.991 40 40 ALA A 41 0.989 0.989 41 41 LEU A 42 0.976 0.975 0.298 0.561 42 42 LEU A 43 0.994 0.988 0.961 0.953 43 43 MET A 44 0.993 0.992 0.904 0.691 0.909 44 44 ASP A 45 0.998 0.988 0.795 0.921 45 45 ILE A 46 0.999 0.999 1.000 1.000 46 46 PRO A 47 0.998 0.998 0.958 0.916 47 47 ALA A 48 0.999 0.999 48 48 GLU A 49 1.000 0.999 0.427 0.999 0.951 49 49 LYS A 50 1.000 1.000 0.999 0.864 1.000 1.000 50 50 ILE A 51 0.996 0.999 1.000 1.000 51 51 GLY A 52 0.999 0.999 52 52 ILE A 53 0.999 0.997 0.999 0.999 53 53 ASN A 54 0.783 0.427 0.637 0.944 GLY A 55 0.518 0.539 ASP A 56 0.414 0.968 0.519 0.988 LYS A 57 0.912 0.986 0.309 0.603 0.999 0.999 57 57 ARG A 58 0.995 0.991 0.996 0.629 0.533 0.631 1.000 58 58 VAL A 59 0.999 0.999 1.000 59 59 ASP A 60 0.996 0.999 0.998 0.945 60 60 VAL A 61 1.000 0.999 1.000 61 61 ILE A 62 0.999 0.995 1.000 1.000 62 62 ASP A 63 0.979 0.982 0.654 0.909 63 63 LEU A 64 0.976 0.976 0.433 0.414 64 64 LYS A 65 0.998 0.997 0.874 0.919 0.708 0.752 65 65 VAL A 66 1.000 0.999 0.999 66 66 GLN A 67 0.998 0.998 0.998 0.927 0.800 67 67 PRO A 68 0.999 0.999 0.930 0.844 68 68 GLU A 69 0.997 0.998 0.678 0.674 0.917 69 69 LEU A 70 0.999 0.998 1.000 1.000 70 70 VAL A 71 0.999 1.000 0.999 71 71 GLY A 72 0.999 0.997 72 72 SER A 73 0.999 0.994 0.690 73 73 LEU A 74 0.988 0.986 0.677 0.827 74 74 ARG A 75 0.999 0.997 0.814 0.994 0.647 0.734 1.000 75 75 LYS A 76 0.995 0.997 0.986 0.670 0.997 0.997 76 76 LYS A 77 0.998 0.996 0.998 0.613 0.999 0.893 77 77 PRO A 78 0.998 0.998 0.918 0.820 78 78 GLY A 79 0.998 0.993 79 79 ILE A 80 0.996 0.999 0.996 0.505 80 80 TYR A 81 0.999 0.996 0.999 0.899 81 81 PRO A 82 0.998 0.995 0.929 0.843 82 82 ALA A 83 0.994 0.970 83 83 TYR A 84 0.885 0.411 0.527 0.657 HIS A 85 0.432 0.486 0.376 0.731 MET A 86 0.682 0.119 0.766 0.415 0.346 ASN A 87 0.215 0.161 0.934 0.885 LYS A 88 0.314 0.673 0.996 0.998 0.238 0.997 GLU A 89 0.778 0.952 0.220 0.750 0.975 HIS A 90 0.974 0.968 0.998 0.817 90 90 TRP A 91 0.996 0.996 0.995 0.697 91 91 ILE A 92 0.999 0.999 0.999 0.925 92 92 THR A 93 0.996 0.996 0.859 93 93 VAL A 94 0.998 0.999 1.000 94 94 LEU A 95 1.000 1.000 0.999 1.000 95 95 LEU A 96 0.999 0.998 0.999 0.998 96 96 ASN A 97 0.999 0.997 0.999 0.988 97 97 GLY A 98 0.997 0.987 98 98 PRO A 99 0.993 0.925 0.967 0.939 99 99 LEU A 100 0.901 0.797 0.371 0.251 GLY A 101 0.826 0.990 101 ALA A 102 1.000 0.998 102 102 LYS A 103 1.000 0.999 1.000 1.000 1.000 1.000 103 103 GLU A 104 1.000 0.999 0.999 0.389 0.908 104 104 ILE A 105 0.999 0.999 1.000 1.000 105 105 HIS A 106 0.999 0.999 1.000 0.998 106 106 SER A 107 1.000 1.000 0.568 107 107 LEU A 108 0.999 0.999 1.000 0.998 108 108 ILE A 109 1.000 0.999 1.000 1.000 109 109 GLU A 110 1.000 0.999 0.999 0.705 0.941 110 110 ASP A 111 1.000 1.000 1.000 1.000 111 111 SER A 112 0.999 0.998 0.183 112 112 PHE A 113 0.999 0.998 0.867 0.883 113 113 GLN A 114 0.999 0.999 1.000 0.782 0.972 114 114 LEU A 115 0.998 0.997 0.995 0.909 115 115 THR A 116 0.997 0.994 1.000 116 116 ARG A 117 0.988 0.849 0.811 0.999 0.684 0.771 1.000 117 LEU A 118 0.770 0.841 0.725 0.872 GLU A 119 0.317 0.512 0.925 0.999 0.999 HIS A 120 0.415 0.134 0.045 0.384 HIS A 121 0.684 0.611 0.413 0.806 HIS A 122 0.655 0.151 0.427 0.299 HIS A 123 0.594 0.476 0.348 0.567 HIS A 124 0.656 0.140 0.230 0.372 HIS A 125 0.632 0.503 0.217 Ranges: 5 from: A 2 to A 36 from: A 40 to A 53 from: A 57 to A 83 from: A 90 to A 99 from: A 102 to A 116 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..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 1 is: 0.677 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 2 is: 0.744 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 3 is: 1.531 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 4 is: 0.650 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 5 is: 0.711 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 6 is: 0.911 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 7 is: 0.703 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 8 is: 0.789 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 9 is: 1.138 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 10 is: 0.841 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 11 is: 0.780 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 12 is: 0.826 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 13 is: 0.513 (*) > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 14 is: 0.819 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 15 is: 1.201 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 16 is: 0.818 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 17 is: 0.759 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 18 is: 0.864 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 19 is: 0.981 > Kabsch RMSD of backbone atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 20 is: 0.550 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..36],[40..53],[57..83],[90..99],[102..116], is: 0.840 > Range of RMSD values to reference struct. is 0.513 to 1.531 > 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..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 1 is: 1.151 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 2 is: 1.201 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 3 is: 1.850 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 4 is: 0.992 (*) > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 5 is: 1.190 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 6 is: 1.389 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 7 is: 1.100 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 8 is: 1.152 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 9 is: 1.487 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 10 is: 1.197 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 11 is: 1.266 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 12 is: 1.317 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 13 is: 1.009 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 14 is: 1.160 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 15 is: 1.627 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 16 is: 1.157 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 17 is: 1.249 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 18 is: 1.267 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 19 is: 1.323 > Kabsch RMSD of heavy atoms in res. A[2..36],A[40..53],A[57..83],A[90..99],A[102..116],for model 20 is: 1.054 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..36],[40..53],[57..83],[90..99],[102..116], is: 1.257 > Range of RMSD values to reference struct. is 0.992 to 1.850 PdbStat> PdbStat> *END* of program detected, BYE! ...