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_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP.PDB, 20 MODEL/S TEMP.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 122 MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET THR GLY 1 > ReadCoordsPdb(): Counting models in file `HR5546A_R3_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_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 37820 ATOM records read from file > ReadCoordsPdb(): --> 37820 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 0.466 0.861 0.497 0.340 GLY A 2 0.471 0.236 HIS A 3 0.846 0.340 0.332 0.813 HIS A 4 0.802 0.550 0.150 0.318 HIS A 5 0.690 0.593 0.568 0.604 HIS A 6 0.784 0.665 0.586 0.478 HIS A 7 0.662 0.741 0.552 0.596 HIS A 8 0.778 0.753 0.466 0.511 SER A 9 0.828 0.883 0.329 9 HIS A 10 0.810 0.702 0.729 0.819 MET A 11 0.826 0.846 0.427 0.545 0.222 11 THR A 12 0.905 0.345 0.609 GLY A 13 0.052 0.633 ASN A 14 0.892 0.701 0.620 0.751 VAL A 15 0.971 0.996 1.000 15 15 CYS A 16 0.990 0.990 0.525 16 16 ILE A 17 0.989 0.994 1.000 1.000 17 17 GLU A 18 0.990 0.993 0.991 0.538 0.780 18 18 GLU A 19 0.987 0.979 0.490 0.642 0.848 19 19 ILE A 20 0.985 0.993 1.000 0.963 20 20 ASP A 21 0.989 0.991 0.996 0.982 21 21 VAL A 22 0.933 0.962 0.449 22 22 ASP A 23 0.974 0.993 0.998 0.941 23 23 GLY A 24 0.995 0.993 24 24 LYS A 25 0.961 0.969 0.929 0.929 0.998 0.935 25 25 PHE A 26 0.997 0.998 0.999 0.998 26 26 ILE A 27 0.990 0.997 0.999 0.727 27 27 ARG A 28 0.996 0.991 0.817 0.992 0.252 0.761 1.000 28 28 LEU A 29 0.996 0.989 0.988 0.840 29 29 LYS A 30 0.991 0.997 0.999 0.998 0.863 0.999 30 30 ASN A 31 0.993 0.988 0.998 0.928 31 31 THR A 32 0.982 0.821 0.855 32 SER A 33 0.836 0.962 0.662 33 GLU A 34 0.984 0.885 1.000 0.999 0.999 34 GLN A 35 0.938 0.980 0.401 0.501 0.825 35 35 ASP A 36 0.993 0.976 0.617 0.999 36 36 GLN A 37 0.980 0.962 0.650 0.414 0.646 37 37 PRO A 38 0.988 0.646 0.904 0.826 MET A 39 0.579 0.805 0.607 0.137 0.150 GLY A 40 0.574 0.479 GLY A 41 0.590 0.913 TRP A 42 0.914 0.981 0.997 0.764 42 42 GLU A 43 0.982 0.998 1.000 0.999 0.997 43 43 MET A 44 0.995 0.995 0.999 0.755 0.472 44 44 ILE A 45 0.986 0.993 1.000 0.917 45 45 ARG A 46 0.986 0.989 0.702 0.834 0.245 0.674 0.999 46 46 LYS A 47 0.972 0.981 0.607 0.998 0.999 0.930 47 47 ILE A 48 0.930 0.330 0.326 0.999 GLY A 49 0.411 0.344 ASP A 50 0.346 0.760 0.478 0.914 THR A 51 0.886 0.952 0.320 51 SER A 52 0.960 0.825 0.605 52 VAL A 53 0.896 0.965 0.273 53 SER A 54 0.937 0.970 0.536 54 54 TYR A 55 0.976 0.992 0.997 0.992 55 55 LYS A 56 0.992 0.995 0.999 0.933 0.999 1.000 56 56 TYR A 57 0.983 0.944 0.996 0.940 57 57 THR A 58 0.878 0.910 0.264 58 SER A 59 0.972 0.826 0.261 59 ARG A 60 0.906 0.939 0.844 0.580 0.862 0.601 1.000 60 60 TYR A 61 0.947 0.954 0.261 0.887 61 61 VAL A 62 0.979 0.966 0.656 62 62 LEU A 63 0.968 0.982 0.588 0.683 63 63 LYS A 64 0.986 0.976 0.609 0.998 1.000 0.856 64 64 ALA A 65 0.998 0.993 65 65 GLY A 66 0.996 0.992 66 66 GLN A 67 0.966 0.962 0.509 0.295 0.675 67 67 THR A 68 0.967 0.923 0.442 68 68 VAL A 69 0.921 0.983 0.411 69 69 THR A 70 0.993 0.991 0.692 70 70 ILE A 71 0.989 0.995 0.995 0.212 71 71 TRP A 72 0.993 0.990 0.999 0.991 72 72 ALA A 73 0.988 0.850 73 ALA A 74 0.710 0.909 ASN A 75 0.974 0.889 0.495 0.918 75 ALA A 76 0.961 0.969 76 76 GLY A 77 0.987 0.974 77 77 VAL A 78 0.948 0.947 0.408 78 78 THR A 79 0.984 0.954 0.551 79 79 ALA A 80 0.904 0.391 SER A 81 0.416 0.862 0.523 PRO A 82 0.991 0.217 0.931 0.882 PRO A 83 0.828 0.495 0.831 0.865 THR A 84 0.474 0.873 0.501 ASP A 85 0.864 0.948 0.782 0.952 85 LEU A 86 0.956 0.978 0.991 0.889 86 86 ILE A 87 0.979 0.982 0.661 0.426 87 87 TRP A 88 0.982 0.993 0.937 0.959 88 88 LYS A 89 0.987 0.990 0.915 0.999 0.999 0.999 89 89 ASN A 90 0.977 0.943 0.935 0.933 90 90 GLN A 91 0.943 0.971 0.658 0.535 0.758 91 91 ASN A 92 0.967 0.775 0.747 0.959 SER A 93 0.785 0.814 0.379 TRP A 94 0.825 0.228 0.829 0.604 GLY A 95 0.495 0.637 THR A 96 0.748 0.641 0.323 GLY A 97 0.526 0.763 GLU A 98 0.857 0.784 0.847 0.590 0.906 ASP A 99 0.771 0.796 0.707 0.947 VAL A 100 0.854 0.957 0.774 100 LYS A 101 0.952 0.987 0.587 0.999 0.999 0.999 101 101 VAL A 102 0.988 0.992 0.921 102 102 ILE A 103 0.997 0.995 1.000 1.000 103 103 LEU A 104 0.993 0.998 0.925 0.931 104 104 LYS A 105 0.997 0.978 1.000 0.999 1.000 1.000 105 105 ASN A 106 0.980 0.942 0.780 0.989 106 106 SER A 107 0.850 0.933 0.624 107 GLN A 108 0.991 0.951 0.996 0.920 0.977 108 108 GLY A 109 0.896 0.979 109 GLU A 110 0.961 0.982 0.785 0.867 0.867 110 110 GLU A 111 0.982 0.994 0.633 0.998 0.975 111 111 VAL A 112 0.994 0.989 0.848 112 112 ALA A 113 0.992 0.988 113 113 GLN A 114 0.966 0.977 0.320 0.998 0.916 114 114 ARG A 115 0.983 0.966 0.657 0.540 0.227 0.613 1.000 115 115 SER A 116 0.933 0.959 0.797 116 116 THR A 117 0.883 0.871 0.564 117 VAL A 118 0.920 0.954 0.934 118 118 PHE A 119 0.833 0.655 0.404 0.940 LYS A 120 0.863 0.588 0.537 0.998 0.998 0.999 THR A 121 0.663 0.682 0.532 THR A 122 0.726 0.646 Ranges: 9 from: A 15 to A 31 from: A 35 to A 37 from: A 42 to A 47 from: A 54 to A 57 from: A 60 to A 72 from: A 76 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[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 1 is: 0.828 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 2 is: 0.762 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 3 is: 0.649 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 4 is: 0.931 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 5 is: 0.581 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 6 is: 0.748 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 7 is: 0.807 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 8 is: 0.720 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 9 is: 0.521 (*) > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 10 is: 0.981 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 11 is: 0.674 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 12 is: 0.948 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 13 is: 0.584 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 14 is: 1.227 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 15 is: 0.660 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 16 is: 0.602 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 17 is: 0.579 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 18 is: 0.645 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 19 is: 0.925 > Kabsch RMSD of backbone atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 20 is: 0.613 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[15..31],[35..37],[42..47],[54..57],[60..72],[76..79],[86..91],[101..106],[110..116], is: 0.749 > Range of RMSD values to reference struct. is 0.521 to 1.227 > 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[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 1 is: 1.439 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 2 is: 1.216 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 3 is: 1.029 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 4 is: 1.284 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 5 is: 1.008 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 6 is: 1.180 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 7 is: 1.402 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 8 is: 1.273 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 9 is: 0.905 (*) > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 10 is: 1.409 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 11 is: 1.022 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 12 is: 1.278 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 13 is: 0.925 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 14 is: 1.476 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 15 is: 1.212 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 16 is: 1.079 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 17 is: 1.069 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 18 is: 1.173 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 19 is: 1.394 > Kabsch RMSD of heavy atoms in res. A[15..31],A[35..37],A[42..47],A[54..57],A[60..72],A[76..79],A[86..91],A[101..106],A[110..116],for model 20 is: 0.959 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[15..31],[35..37],[42..47],[54..57],[60..72],[76..79],[86..91],[101..106],[110..116], is: 1.187 > Range of RMSD values to reference struct. is 0.905 to 1.476 PdbStat> PdbStat> *END* of program detected, BYE! ...