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 `SSR10_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 129 MET SER ILE SER THR SER ALA GLU VAL TYR TYR GLU GLU 1 > ReadCoordsPdb(): Counting models in file `SSR10_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 SSR10_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 42620 ATOM records read from file > ReadCoordsPdb(): --> 42620 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 0.200 0.743 0.573 0.060 SER A 2 0.842 0.169 0.322 ILE A 3 0.748 0.969 0.766 0.945 SER A 4 0.202 0.606 0.511 THR A 5 0.796 0.994 0.926 SER A 6 0.990 0.989 0.775 6 6 ALA A 7 1.000 1.000 7 7 GLU A 8 0.999 1.000 0.907 0.993 0.688 8 8 VAL A 9 1.000 0.999 1.000 9 9 TYR A 10 1.000 1.000 0.999 0.697 10 10 TYR A 11 1.000 1.000 0.996 0.998 11 11 GLU A 12 1.000 1.000 0.938 0.856 0.926 12 12 GLU A 13 1.000 1.000 1.000 0.998 0.974 13 13 ALA A 14 1.000 1.000 14 14 GLU A 15 1.000 1.000 0.999 0.749 0.962 15 15 GLU A 16 1.000 1.000 0.999 0.702 0.945 16 16 PHE A 17 1.000 1.000 0.993 0.431 17 17 LEU A 18 1.000 1.000 0.936 0.866 18 18 SER A 19 0.999 0.995 0.485 19 19 LYS A 20 0.993 0.991 0.604 0.999 1.000 1.000 20 20 GLY A 21 0.990 0.999 21 21 ASP A 22 0.995 0.995 0.998 0.985 22 22 LEU A 23 0.998 0.998 0.999 0.999 23 23 VAL A 24 1.000 1.000 1.000 24 24 GLN A 25 1.000 1.000 1.000 0.826 0.672 25 25 ALA A 26 1.000 1.000 26 26 CYS A 27 1.000 0.999 0.939 27 27 GLU A 28 1.000 1.000 0.600 0.867 0.956 28 28 LYS A 29 0.998 0.982 0.997 0.941 0.999 0.997 29 29 TYR A 30 0.997 0.981 0.206 0.553 30 30 TYR A 31 1.000 1.000 0.992 0.998 31 31 LYS A 32 1.000 1.000 1.000 0.791 0.812 0.999 32 32 ALA A 33 1.000 0.999 33 33 ALA A 34 1.000 0.999 34 34 GLU A 35 0.999 0.997 0.426 0.996 0.798 35 35 GLU A 36 1.000 1.000 0.934 0.917 0.968 36 36 ALA A 37 1.000 1.000 37 37 ILE A 38 1.000 1.000 1.000 0.844 38 38 LYS A 39 0.999 0.998 0.301 0.998 0.652 0.994 39 39 LEU A 40 1.000 1.000 0.999 1.000 40 40 LEU A 41 1.000 1.000 1.000 1.000 41 41 VAL A 42 0.999 0.999 1.000 42 42 ILE A 43 1.000 1.000 1.000 1.000 43 43 GLU A 44 0.999 1.000 0.999 0.998 0.987 44 44 ASN A 45 0.994 0.940 0.999 0.828 45 45 ASN A 46 0.869 0.982 1.000 0.985 46 LEU A 47 0.997 0.992 0.997 1.000 47 47 LYS A 48 0.994 0.993 0.594 0.999 1.000 1.000 48 48 GLU A 49 0.999 0.999 0.769 0.761 0.996 49 49 ILE A 50 0.996 0.999 0.998 0.621 50 50 THR A 51 0.997 0.995 0.656 51 51 ASN A 52 0.999 1.000 1.000 1.000 52 52 ASN A 53 0.997 0.991 0.999 0.984 53 53 VAL A 54 0.994 0.981 0.999 54 54 LYS A 55 0.991 0.991 0.622 1.000 1.000 0.999 55 55 ASN A 56 0.955 0.980 0.788 0.941 56 56 LYS A 57 0.996 0.468 0.998 0.695 0.998 0.929 GLY A 58 0.410 0.899 ARG A 59 0.953 0.984 0.353 0.601 0.716 0.683 1.000 59 59 TRP A 60 0.987 0.850 0.969 0.966 60 LYS A 61 0.829 0.443 0.475 0.631 0.999 0.998 SER A 62 0.667 0.948 0.127 GLU A 63 0.999 0.999 0.613 1.000 1.000 63 63 ASN A 64 1.000 1.000 0.999 0.986 64 64 LEU A 65 1.000 0.999 0.999 0.999 65 65 PHE A 66 1.000 0.999 0.885 0.939 66 66 LYS A 67 1.000 1.000 0.910 0.934 0.997 0.637 67 67 ALA A 68 1.000 0.999 68 68 SER A 69 1.000 0.999 0.914 69 69 LYS A 70 0.999 1.000 0.885 0.999 1.000 1.000 70 70 LEU A 71 0.990 0.572 0.998 0.999 LEU A 72 0.550 0.983 0.992 0.998 ARG A 73 0.991 0.998 0.938 0.997 0.663 0.923 1.000 73 73 SER A 74 0.999 0.998 1.000 74 74 ASN A 75 0.997 0.999 0.656 0.710 75 75 ASN A 76 0.999 0.997 0.998 0.953 76 76 THR A 77 0.999 0.997 0.852 77 77 GLU A 78 0.998 0.996 1.000 0.998 0.890 78 78 ILE A 79 0.999 1.000 0.999 0.925 79 79 PRO A 80 0.997 0.999 0.970 0.938 80 80 ILE A 81 1.000 1.000 1.000 1.000 81 81 LEU A 82 0.999 0.999 1.000 0.999 82 82 TRP A 83 0.999 0.999 0.999 0.999 83 83 LYS A 84 0.998 0.999 1.000 1.000 1.000 1.000 84 84 SER A 85 0.999 0.999 0.777 85 85 ALA A 86 1.000 1.000 86 86 TRP A 87 0.999 0.999 0.996 0.995 87 87 THR A 88 0.999 0.999 1.000 88 88 LEU A 89 0.999 0.999 0.911 0.939 89 89 HIS A 90 0.998 0.995 0.817 0.661 90 90 VAL A 91 0.999 0.999 1.000 91 91 GLU A 92 0.760 0.780 0.932 0.466 0.872 GLY A 93 0.770 0.469 PHE A 94 0.400 0.750 0.556 0.769 HIS A 95 0.434 0.617 0.422 0.078 GLU A 96 0.515 0.381 0.560 0.794 0.926 LEU A 97 0.988 0.990 0.679 0.717 97 97 SER A 98 0.610 0.736 0.092 LEU A 99 0.404 0.941 0.998 0.999 ASN A 100 0.966 0.989 0.839 0.877 100 100 GLU A 101 1.000 1.000 0.633 0.999 1.000 101 101 LYS A 102 1.000 1.000 0.833 1.000 1.000 1.000 102 102 GLU A 103 1.000 0.999 1.000 0.696 0.977 103 103 VAL A 104 1.000 1.000 1.000 104 104 LYS A 105 1.000 0.999 0.821 1.000 1.000 1.000 105 105 LYS A 106 1.000 0.999 0.874 0.999 0.877 0.999 106 106 LEU A 107 1.000 0.999 0.997 0.865 107 107 LYS A 108 0.999 0.998 0.735 0.952 0.578 0.667 108 108 GLU A 109 0.999 0.999 0.933 0.547 0.928 109 109 ASP A 110 1.000 0.999 1.000 0.999 110 110 VAL A 111 1.000 1.000 1.000 111 111 ARG A 112 1.000 1.000 0.999 0.998 0.554 0.552 1.000 112 112 LYS A 113 1.000 0.999 0.999 0.999 0.689 1.000 113 113 LEU A 114 1.000 1.000 0.643 0.557 114 114 VAL A 115 1.000 1.000 1.000 115 115 ILE A 116 1.000 1.000 1.000 1.000 116 116 PHE A 117 1.000 1.000 0.883 0.915 117 117 ALA A 118 1.000 0.999 118 118 VAL A 119 1.000 1.000 1.000 119 119 ASN A 120 1.000 0.999 0.827 0.924 120 120 SER A 121 1.000 0.999 0.390 121 121 LEU A 122 0.990 0.943 0.931 0.753 122 122 GLU A 123 0.620 0.875 0.998 0.997 0.961 HIS A 124 0.556 0.618 0.390 0.565 HIS A 125 0.562 0.682 0.376 0.359 HIS A 126 0.121 0.106 0.484 0.375 HIS A 127 0.536 0.621 0.499 0.446 HIS A 128 0.437 0.284 0.323 0.629 HIS A 129 0.931 0.609 0.578 Ranges: 5 from: A 6 to A 45 from: A 47 to A 56 from: A 63 to A 70 from: A 73 to A 91 from: A 100 to A 122 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[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 1 is: 0.991 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 2 is: 0.391 (*) > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 3 is: 0.517 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 4 is: 0.704 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 5 is: 0.402 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 6 is: 0.650 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 7 is: 0.498 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 8 is: 0.647 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 9 is: 0.722 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 10 is: 0.431 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 11 is: 0.484 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 12 is: 0.757 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 13 is: 0.746 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 14 is: 0.765 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 15 is: 0.502 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 16 is: 0.568 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 17 is: 0.445 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 18 is: 0.467 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 19 is: 0.471 > Kabsch RMSD of backbone atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 20 is: 0.429 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[6..45],[47..56],[63..70],[73..91],[100..122], is: 0.579 > Range of RMSD values to reference struct. is 0.391 to 0.991 > 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[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 1 is: 1.465 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 2 is: 0.670 (*) > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 3 is: 0.877 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 4 is: 1.004 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 5 is: 0.728 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 6 is: 0.893 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 7 is: 0.881 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 8 is: 0.904 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 9 is: 0.998 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 10 is: 0.772 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 11 is: 0.827 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 12 is: 1.018 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 13 is: 1.090 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 14 is: 1.147 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 15 is: 0.923 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 16 is: 0.909 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 17 is: 0.750 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 18 is: 0.843 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 19 is: 0.812 > Kabsch RMSD of heavy atoms in res. A[6..45],A[47..56],A[63..70],A[73..91],A[100..122],for model 20 is: 0.776 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[6..45],[47..56],[63..70],[73..91],[100..122], is: 0.914 > Range of RMSD values to reference struct. is 0.670 to 1.465 PdbStat> PdbStat> *END* of program detected, BYE! ...