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 `HR5546A_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL PROTEIN 21-OCT-09 2KPW > ReadCoordsPdb(): >> TITLE NMR SOLUTION STRUCTURE OF LAMIN-B1 PROTEIN FROM HOMO > ReadCoordsPdb(): >> TITLE 2 SAPIENS: NORTHEAST STRUCTURAL GENOMICS CONSORTIUM MEGA > ReadCoordsPdb(): >> TITLE 3 TARGET, HR5546A (439-549) > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `HR5546A_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 HR5546A_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 37960 ATOM records read from file > ReadCoordsPdb(): --> 37960 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 0.531 0.283 0.580 0.576 GLY A 2 0.438 0.434 HIS A 3 0.877 0.427 0.255 0.181 HIS A 4 0.809 0.580 0.372 0.155 HIS A 5 0.713 0.549 0.526 0.409 HIS A 6 0.795 0.701 0.426 0.187 HIS A 7 0.668 0.778 0.179 0.269 HIS A 8 0.772 0.740 0.135 0.088 SER A 9 0.819 0.806 0.143 9 HIS A 10 0.809 0.751 0.992 0.873 MET A 11 0.811 0.931 0.989 0.998 0.600 11 THR A 12 0.898 0.347 0.491 GLY A 13 0.061 0.810 ASN A 14 0.927 0.650 0.477 0.145 VAL A 15 0.961 0.949 0.853 15 15 CYS A 16 0.965 0.986 0.479 16 16 ILE A 17 0.984 0.981 0.999 0.837 17 17 GLU A 18 0.981 0.982 0.998 0.988 0.301 18 18 GLU A 19 0.978 0.985 0.996 0.682 0.158 19 19 ILE A 20 0.966 0.980 0.998 0.999 20 20 ASP A 21 0.990 0.986 0.998 0.983 21 21 VAL A 22 0.974 0.979 0.999 22 22 ASP A 23 0.973 0.975 0.994 0.605 23 23 GLY A 24 0.957 0.980 24 24 LYS A 25 0.952 0.966 0.988 0.867 0.795 0.039 25 25 PHE A 26 0.987 0.994 0.999 0.113 26 26 ILE A 27 0.994 0.967 0.999 0.999 27 27 ARG A 28 0.968 0.993 0.990 0.987 0.273 0.736 0.998 28 28 LEU A 29 0.994 0.972 0.998 0.999 29 29 LYS A 30 0.964 0.990 0.995 0.994 0.330 0.507 30 30 ASN A 31 0.985 0.967 0.999 0.958 31 31 THR A 32 0.980 0.827 0.463 32 SER A 33 0.842 0.957 0.369 33 GLU A 34 0.984 0.914 0.998 0.995 0.215 34 34 GLN A 35 0.957 0.988 0.995 0.998 0.602 35 35 ASP A 36 0.993 0.976 0.996 0.458 36 36 GLN A 37 0.966 0.973 0.994 0.998 0.208 37 37 PRO A 38 0.992 0.731 0.932 0.859 MET A 39 0.620 0.763 0.993 0.982 0.397 GLY A 40 0.613 0.469 GLY A 41 0.564 0.905 TRP A 42 0.926 0.975 0.988 0.746 42 42 GLU A 43 0.964 0.990 0.996 0.995 0.353 43 43 MET A 44 0.996 0.992 0.998 0.998 0.919 44 44 ILE A 45 0.985 0.957 0.998 0.623 45 45 ARG A 46 0.939 0.974 0.991 0.967 0.418 0.546 0.998 46 46 LYS A 47 0.961 0.908 0.928 0.995 0.303 0.358 47 47 ILE A 48 0.894 0.289 0.996 0.943 GLY A 49 0.402 0.287 ASP A 50 0.274 0.744 0.313 0.347 THR A 51 0.843 0.970 0.999 51 SER A 52 0.974 0.819 0.998 52 VAL A 53 0.871 0.992 0.999 53 SER A 54 0.980 0.961 0.700 54 54 TYR A 55 0.956 0.988 0.994 0.995 55 55 LYS A 56 0.991 0.985 0.994 0.993 0.167 0.267 56 56 TYR A 57 0.982 0.895 0.997 0.610 57 THR A 58 0.861 0.944 0.996 58 SER A 59 0.974 0.863 0.400 59 ARG A 60 0.889 0.972 0.988 0.986 0.437 0.844 0.998 60 TYR A 61 0.970 0.984 0.996 0.608 61 61 VAL A 62 0.985 0.973 0.513 62 62 LEU A 63 0.972 0.979 0.824 0.401 63 63 LYS A 64 0.994 0.979 0.936 0.996 0.439 0.211 64 64 ALA A 65 0.992 0.987 65 65 GLY A 66 0.982 0.958 66 66 GLN A 67 0.961 0.979 0.907 0.925 0.674 67 67 THR A 68 0.986 0.903 0.998 68 68 VAL A 69 0.908 0.986 0.845 69 69 THR A 70 0.994 0.990 0.998 70 70 ILE A 71 0.992 0.990 0.998 1.000 71 71 TRP A 72 0.989 0.932 0.999 0.990 72 72 ALA A 73 0.956 0.815 73 ALA A 74 0.705 0.941 ASN A 75 0.977 0.903 0.993 0.493 75 75 ALA A 76 0.879 0.936 76 GLY A 77 0.975 0.895 77 VAL A 78 0.933 0.974 0.797 78 78 THR A 79 0.986 0.934 0.361 79 79 ALA A 80 0.908 0.602 SER A 81 0.448 0.937 0.605 PRO A 82 0.994 0.298 0.987 0.972 PRO A 83 0.678 0.495 0.827 0.941 THR A 84 0.484 0.905 0.587 ASP A 85 0.910 0.900 0.995 0.366 85 LEU A 86 0.927 0.975 0.994 0.996 86 86 ILE A 87 0.986 0.990 0.994 0.996 87 87 TRP A 88 0.993 0.969 0.994 0.863 88 88 LYS A 89 0.973 0.951 0.934 0.994 0.118 0.166 89 89 ASN A 90 0.930 0.960 0.996 0.791 90 90 GLN A 91 0.959 0.986 0.992 0.937 0.465 91 91 ASN A 92 0.981 0.752 0.995 0.443 SER A 93 0.773 0.830 0.311 TRP A 94 0.796 0.187 0.996 0.994 GLY A 95 0.400 0.684 THR A 96 0.680 0.608 0.536 GLY A 97 0.503 0.809 GLU A 98 0.888 0.747 0.984 0.994 0.522 ASP A 99 0.761 0.747 0.210 0.479 VAL A 100 0.820 0.953 0.999 100 LYS A 101 0.966 0.974 0.994 0.992 0.364 0.401 101 101 VAL A 102 0.976 0.987 0.594 102 102 ILE A 103 0.988 0.988 0.996 0.999 103 103 LEU A 104 0.988 0.993 0.998 1.000 104 104 LYS A 105 0.989 0.980 0.996 0.999 0.996 0.143 105 105 ASN A 106 0.973 0.915 0.996 0.901 106 106 SER A 107 0.864 0.919 0.224 107 GLN A 108 0.968 0.916 0.995 0.996 0.781 108 108 GLY A 109 0.864 0.929 109 GLU A 110 0.948 0.958 0.994 0.899 0.375 110 110 GLU A 111 0.962 0.989 0.999 0.998 0.604 111 111 VAL A 112 0.970 0.975 0.556 112 112 ALA A 113 0.940 0.975 113 113 GLN A 114 0.966 0.924 0.996 0.997 0.344 114 114 ARG A 115 0.946 0.982 0.961 0.938 0.452 0.663 0.999 115 115 SER A 116 0.962 0.971 0.997 116 116 THR A 117 0.944 0.809 0.914 117 VAL A 118 0.870 0.943 0.519 118 PHE A 119 0.900 0.796 0.476 0.320 LYS A 120 0.909 0.624 0.429 0.663 0.305 0.075 THR A 121 0.637 0.749 0.243 THR A 122 0.798 0.280 Ranges: 9 from: A 15 to A 31 from: A 34 to A 37 from: A 42 to A 47 from: A 54 to A 56 from: A 61 to A 72 from: A 78 to A 79 from: A 86 to A 91 from: A 101 to A 106 from: A 110 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[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 1 is: 0.630 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 2 is: 0.594 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 3 is: 0.587 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 4 is: 0.695 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 5 is: 0.599 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 6 is: 0.770 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 7 is: 1.076 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 8 is: 0.649 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 9 is: 0.569 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 10 is: 0.736 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 11 is: 0.869 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 12 is: 0.566 (*) > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 13 is: 0.587 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 14 is: 0.638 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 15 is: 0.626 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 16 is: 0.632 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 17 is: 0.724 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 18 is: 0.690 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 19 is: 0.673 > Kabsch RMSD of backbone atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 20 is: 0.689 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[15..31],[34..37],[42..47],[54..56],[61..72],[78..79],[86..91],[101..106],[110..116], is: 0.680 > Range of RMSD values to reference struct. is 0.566 to 1.076 > 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[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 1 is: 0.936 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 2 is: 0.936 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 3 is: 0.936 (*) > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 4 is: 1.027 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 5 is: 1.018 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 6 is: 1.076 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 7 is: 1.408 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 8 is: 1.066 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 9 is: 0.977 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 10 is: 1.022 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 11 is: 1.191 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 12 is: 1.069 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 13 is: 0.958 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 14 is: 0.982 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 15 is: 1.002 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 16 is: 1.023 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 17 is: 1.167 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 18 is: 1.071 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 19 is: 1.016 > Kabsch RMSD of heavy atoms in res. A[15..31],A[34..37],A[42..47],A[54..56],A[61..72],A[78..79],A[86..91],A[101..106],A[110..116],for model 20 is: 1.110 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[15..31],[34..37],[42..47],[54..56],[61..72],[78..79],[86..91],[101..106],[110..116], is: 1.050 > Range of RMSD values to reference struct. is 0.936 to 1.408 PdbStat> PdbStat> *END* of program detected, BYE! ...