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 `UUR17A_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER LIPID BINDING PROTEIN 22-DEC-09 2KRT > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF A CONSERVED HYPOTHETICAL MEMBRANE > ReadCoordsPdb(): >> TITLE 2 LIPOPROTEIN OBTAINED FROM UREAPLASMA PARVUM: NORTHEAST > ReadCoordsPdb(): >> TITLE 3 STRUCTURAL GENOMICS CONSORTIUM TARGET UUR17A (139-239) > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `UUR17A_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 UUR17A_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 40260 ATOM records read from file > ReadCoordsPdb(): --> 40260 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 0.234 0.502 0.221 0.702 LEU A 2 0.732 0.531 0.689 0.633 SER A 3 0.803 0.658 0.276 GLN A 4 0.775 0.778 0.591 0.744 0.401 ALA A 5 0.783 0.958 ASN A 6 0.989 0.994 0.992 0.718 6 6 GLU A 7 0.996 0.998 0.998 0.993 0.443 7 7 ASP A 8 0.995 0.997 0.589 0.362 8 8 PHE A 9 0.997 0.998 0.994 0.616 9 9 LYS A 10 0.998 1.000 0.996 0.996 0.288 0.633 10 10 LYS A 11 0.998 0.998 0.994 0.776 0.557 0.352 11 11 ILE A 12 0.999 0.999 0.999 1.000 12 12 VAL A 13 0.997 0.997 0.999 13 13 ASN A 14 0.999 0.989 0.999 0.953 14 14 ASN A 15 0.991 0.985 0.862 0.759 15 15 ILE A 16 0.991 0.967 0.999 1.000 16 16 ARG A 17 0.960 0.995 0.956 0.996 0.985 0.858 0.999 17 17 LEU A 18 0.997 0.957 0.999 0.998 18 18 LYS A 19 0.933 0.985 0.697 0.593 0.154 0.346 19 19 ASP A 20 0.978 0.978 0.773 0.543 20 20 THR A 21 0.976 0.996 0.998 21 21 PHE A 22 0.995 0.969 0.997 0.995 22 22 ASP A 23 0.977 0.989 0.417 0.439 23 23 PHE A 24 0.994 0.955 0.998 0.996 24 24 LYS A 25 0.960 0.991 0.992 0.928 0.363 0.318 25 25 LEU A 26 0.990 0.994 0.998 0.999 26 26 ALA A 27 0.995 0.997 27 27 ALA A 28 0.995 0.991 28 28 PHE A 29 0.995 0.993 0.998 0.996 29 29 PRO A 30 0.992 0.955 0.961 0.925 30 30 ASN A 31 0.976 0.846 0.994 0.567 31 GLN A 32 0.949 0.917 0.523 0.349 0.402 32 32 ASN A 33 0.915 0.937 0.684 0.732 33 33 TYR A 34 0.991 0.940 0.991 0.794 34 34 ASP A 35 0.944 0.984 0.224 0.334 35 35 GLN A 36 0.981 0.920 0.710 0.574 0.477 36 36 LEU A 37 0.923 0.979 0.835 0.920 37 37 LEU A 38 0.987 0.994 0.996 0.355 38 38 PRO A 39 0.995 0.991 0.925 0.850 39 39 SER A 40 0.997 0.993 0.339 40 40 GLN A 41 0.994 0.995 0.997 0.773 0.433 41 41 ILE A 42 0.997 0.997 0.999 1.000 42 42 TYR A 43 0.998 0.995 0.993 0.894 43 43 LYS A 44 0.989 0.986 0.998 0.540 0.265 0.308 44 44 ASN A 45 0.977 0.987 0.545 0.209 45 45 TYR A 46 0.998 0.995 0.518 0.509 46 46 TYR A 47 0.988 0.975 0.462 0.442 47 47 GLN A 48 0.961 0.982 0.997 0.550 0.492 48 48 GLY A 49 0.986 0.971 49 49 ILE A 50 0.978 0.994 0.999 0.999 50 50 GLU A 51 0.997 0.978 0.910 0.486 0.349 51 51 ILE A 52 0.986 0.976 1.000 1.000 52 52 GLN A 53 0.984 0.966 0.744 0.312 0.150 53 53 GLN A 54 0.992 0.958 0.613 0.492 0.625 54 54 HIS A 55 0.959 0.866 0.778 0.442 55 LYS A 56 0.896 0.816 0.699 0.950 0.857 0.319 56 TYR A 57 0.646 0.889 0.997 0.992 GLN A 58 0.950 0.838 0.987 0.992 0.581 58 ASN A 59 0.803 0.964 0.682 0.609 59 GLU A 60 0.977 0.984 0.767 0.552 0.385 60 60 LEU A 61 0.991 0.989 0.997 0.803 61 61 ASP A 62 0.990 0.988 0.927 0.620 62 62 ILE A 63 0.986 0.991 0.999 0.999 63 63 LYS A 64 0.990 0.983 0.924 0.576 0.226 0.451 64 64 ILE A 65 0.994 0.989 0.999 1.000 65 65 ILE A 66 0.976 0.984 0.999 1.000 66 66 ASN A 67 0.950 0.982 0.459 0.398 67 67 PHE A 68 0.981 0.991 0.999 0.505 68 68 LEU A 69 0.970 0.985 0.475 0.690 69 69 TYR A 70 0.985 0.975 0.996 0.932 70 70 PRO A 71 0.984 0.387 0.907 0.840 ASP A 72 0.378 0.765 0.644 0.537 GLY A 73 0.701 0.645 ASP A 74 0.904 0.980 0.534 0.786 74 74 PHE A 75 0.995 0.993 0.999 0.800 75 75 GLY A 76 0.997 0.995 76 76 SER A 77 0.998 0.991 0.546 77 77 ALA A 78 0.989 0.993 78 78 ASN A 79 0.995 0.993 0.688 0.424 79 79 LYS A 80 0.985 0.989 0.951 0.992 0.486 0.218 80 80 ASN A 81 0.967 0.960 0.521 0.535 81 81 GLY A 82 0.980 0.962 82 82 THR A 83 0.988 0.993 0.997 83 83 LEU A 84 0.990 0.997 0.643 0.409 84 84 LYS A 85 0.994 0.997 0.978 0.710 0.559 0.198 85 85 LEU A 86 0.995 0.993 0.990 0.422 86 86 SER A 87 0.997 0.997 0.401 87 87 LEU A 88 0.995 0.996 0.998 0.790 88 88 MET A 89 0.994 0.999 0.923 0.944 0.387 89 89 LEU A 90 0.997 0.986 0.998 0.999 90 90 THR A 91 0.979 0.990 0.997 91 91 ASP A 92 0.996 0.959 0.528 0.304 92 92 LYS A 93 0.968 0.957 0.994 0.836 0.619 0.215 93 93 LYS A 94 0.948 0.964 0.804 0.793 0.059 0.144 94 94 ASN A 95 0.970 0.994 0.997 0.360 95 95 ASN A 96 0.997 0.979 0.886 0.740 96 96 GLN A 97 0.975 0.949 0.996 0.998 0.436 97 97 VAL A 98 0.945 0.979 0.999 98 98 TYR A 99 0.976 0.984 0.996 0.992 99 99 TYR A 100 0.976 0.990 0.998 0.966 100 100 LYS A 101 0.981 0.995 0.998 0.988 0.748 0.324 101 101 LEU A 102 0.993 0.992 0.994 0.481 102 102 LEU A 103 0.988 0.959 0.999 0.853 103 103 GLU A 104 0.956 0.993 0.456 0.802 0.303 104 104 VAL A 105 0.989 0.988 0.997 105 105 SER A 106 0.954 0.968 0.065 106 106 GLY A 107 0.967 0.983 107 107 PHE A 108 0.984 0.877 0.996 0.618 108 LYS A 109 0.903 0.838 0.849 0.644 0.853 0.248 109 SER A 110 0.852 0.955 0.998 110 ASN A 111 0.994 0.999 0.997 0.709 111 111 PRO A 112 0.995 0.971 0.944 0.862 112 112 TYR A 113 0.929 0.955 0.994 0.415 113 113 LEU A 114 0.962 0.950 0.998 1.000 114 114 GLU A 115 0.940 0.491 0.423 0.230 0.280 HIS A 116 0.612 0.604 0.305 0.177 HIS A 117 0.843 0.524 0.175 0.321 HIS A 118 0.717 0.602 0.078 0.228 HIS A 119 0.553 0.350 0.266 0.196 HIS A 120 0.638 0.320 0.363 0.120 HIS A 121 0.889 0.323 0.269 Ranges: 5 from: A 6 to A 30 from: A 32 to A 54 from: A 60 to A 70 from: A 74 to A 107 from: A 111 to A 114 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..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 1 is: 0.634 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 2 is: 0.600 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 3 is: 0.753 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 4 is: 0.709 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 5 is: 0.555 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 6 is: 0.700 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 7 is: 0.510 (*) > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 8 is: 0.607 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 9 is: 0.663 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 10 is: 0.837 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 11 is: 0.653 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 12 is: 0.665 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 13 is: 0.663 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 14 is: 0.815 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 15 is: 0.640 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 16 is: 0.750 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 17 is: 0.784 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 18 is: 0.721 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 19 is: 0.761 > Kabsch RMSD of backbone atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 20 is: 0.546 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[6..30],[32..54],[60..70],[74..107],[111..114], is: 0.678 > Range of RMSD values to reference struct. is 0.510 to 0.837 > 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..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 1 is: 1.107 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 2 is: 1.062 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 3 is: 1.195 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 4 is: 1.085 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 5 is: 1.050 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 6 is: 1.305 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 7 is: 1.078 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 8 is: 1.088 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 9 is: 1.189 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 10 is: 1.262 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 11 is: 1.071 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 12 is: 1.069 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 13 is: 1.160 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 14 is: 1.242 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 15 is: 1.131 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 16 is: 1.158 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 17 is: 1.190 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 18 is: 1.058 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 19 is: 1.291 > Kabsch RMSD of heavy atoms in res. A[6..30],A[32..54],A[60..70],A[74..107],A[111..114],for model 20 is: 1.026 (*) > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[6..30],[32..54],[60..70],[74..107],[111..114], is: 1.141 > Range of RMSD values to reference struct. is 1.026 to 1.305 PdbStat> PdbStat> *END* of program detected, BYE! ...