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 `OR8C_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER ANTIVIRAL PROTEIN 29-JUN-09 2KKZ > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE MONOMERIC W187R MUTANT OF > ReadCoordsPdb(): >> TITLE 2 A/UDORN NS1 EFFECTOR DOMAIN. NORTHEAST STRUCTURAL GENOMICS > ReadCoordsPdb(): >> TITLE 3 TARGET OR8C[W187R]. > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `OR8C_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 OR8C_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 42740 ATOM records read from file > ReadCoordsPdb(): --> 42740 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 0.840 0.189 0.340 0.387 PRO A 2 0.992 0.636 0.938 0.853 ALA A 3 0.681 0.866 SER A 4 0.916 0.938 0.325 4 4 ARG A 5 0.934 0.985 0.994 0.998 0.428 0.851 0.998 5 5 TYR A 6 0.975 0.995 0.996 0.151 6 6 ILE A 7 0.998 0.989 0.997 0.999 7 7 THR A 8 0.975 0.980 0.998 8 8 ASP A 9 0.996 0.993 0.525 0.570 9 9 MET A 10 0.991 0.990 0.270 0.909 0.054 10 10 THR A 11 0.990 0.992 0.555 11 11 ILE A 12 0.998 0.998 0.991 0.490 12 12 GLU A 13 0.996 0.986 0.997 0.700 0.274 13 13 GLU A 14 0.982 0.993 0.787 0.619 0.314 14 14 LEU A 15 0.998 0.993 0.944 0.891 15 15 SER A 16 0.988 0.989 0.333 16 16 ARG A 17 0.992 0.993 0.995 0.600 0.799 0.760 0.998 17 17 ASP A 18 0.994 0.980 0.235 0.408 18 18 TRP A 19 0.992 0.985 0.994 0.993 19 19 PHE A 20 0.962 0.986 0.993 0.705 20 20 MET A 21 0.975 0.958 0.636 0.920 0.514 21 21 LEU A 22 0.957 0.988 0.592 0.652 22 22 MET A 23 0.994 0.993 0.997 0.985 0.467 23 23 PRO A 24 0.998 0.980 0.944 0.858 24 24 LYS A 25 0.956 0.989 0.996 0.528 0.788 0.179 25 25 GLN A 26 0.968 0.991 0.986 0.357 0.482 26 26 LYS A 27 0.974 0.962 0.991 0.866 0.450 0.399 27 27 VAL A 28 0.928 0.984 0.997 28 28 GLU A 29 0.987 0.995 0.993 0.994 0.915 29 29 GLY A 30 0.997 0.988 30 30 PRO A 31 0.994 0.991 0.941 0.889 31 31 LEU A 32 0.997 0.942 0.997 0.710 32 32 CYS A 33 0.943 0.984 0.463 33 33 ILE A 34 0.989 0.969 0.999 0.999 34 34 ARG A 35 0.967 0.998 0.780 0.334 0.534 0.638 0.998 35 35 ILE A 36 0.995 0.996 0.998 0.485 36 36 ASP A 37 0.989 0.994 0.914 0.247 37 37 GLN A 38 0.993 0.994 0.999 0.996 0.900 38 38 ALA A 39 0.987 0.984 39 39 ILE A 40 0.996 0.996 0.977 0.621 40 40 MET A 41 0.998 0.995 0.998 0.997 0.997 41 41 ASP A 42 0.996 0.972 0.672 0.633 42 42 LYS A 43 0.980 0.999 0.995 0.997 0.995 0.924 43 43 ASN A 44 0.998 0.998 0.997 0.800 44 44 ILE A 45 0.997 0.988 0.998 0.999 45 45 MET A 46 0.982 0.995 0.991 0.992 0.435 46 46 LEU A 47 0.995 0.987 0.981 0.487 47 47 LYS A 48 0.984 0.988 0.990 0.778 0.138 0.320 48 48 ALA A 49 0.994 0.994 49 49 ASN A 50 0.995 0.995 0.995 0.848 50 50 PHE A 51 0.998 0.999 0.999 0.796 51 51 SER A 52 0.999 0.996 0.249 52 52 VAL A 53 0.994 0.993 0.998 53 53 ILE A 54 0.991 0.998 0.997 0.999 54 54 PHE A 55 0.999 0.929 0.999 0.992 55 55 ASP A 56 0.912 0.982 0.671 0.375 56 56 ARG A 57 0.988 0.995 0.994 0.844 0.380 0.744 0.998 57 57 LEU A 58 0.999 0.993 0.997 0.999 58 58 GLU A 59 0.995 0.997 0.915 0.400 0.306 59 59 THR A 60 0.996 0.997 0.996 60 60 LEU A 61 0.998 0.994 1.000 0.999 61 61 ILE A 62 0.993 0.999 0.985 0.593 62 62 LEU A 63 0.998 0.999 0.999 0.999 63 63 LEU A 64 0.997 0.996 0.999 0.998 64 64 ARG A 65 0.996 0.992 0.393 0.987 0.041 0.593 0.994 65 65 ALA A 66 0.992 0.995 66 66 PHE A 67 0.951 0.965 0.530 0.161 67 67 THR A 68 0.985 0.993 0.996 68 68 GLU A 69 0.995 0.993 0.603 0.144 0.614 69 69 GLU A 70 0.987 0.978 0.760 0.475 0.297 70 70 GLY A 71 0.974 0.982 71 71 ALA A 72 0.985 0.980 72 72 ILE A 73 0.998 0.982 0.998 0.943 73 73 VAL A 74 0.984 0.988 0.999 74 74 GLY A 75 0.989 0.993 75 75 GLU A 76 0.999 0.994 0.997 0.992 0.303 76 76 ILE A 77 0.994 0.992 0.999 0.924 77 77 SER A 78 0.971 0.978 0.051 78 78 PRO A 79 0.997 0.985 0.931 0.832 79 79 LEU A 80 0.995 0.988 0.998 0.998 80 80 PRO A 81 0.996 0.752 0.925 0.834 SER A 82 0.738 0.978 0.488 PHE A 83 0.993 0.966 0.995 0.171 83 83 PRO A 84 0.976 0.736 0.916 0.877 GLY A 85 0.666 0.781 HIS A 86 0.930 0.965 0.909 0.807 86 86 THR A 87 0.978 0.992 0.595 87 87 ILE A 88 0.998 0.998 0.997 0.999 88 88 GLU A 89 0.996 0.993 0.939 0.460 0.320 89 89 ASP A 90 0.993 0.995 0.722 0.354 90 90 VAL A 91 0.999 0.994 0.999 91 91 LYS A 92 0.998 0.995 0.557 0.989 0.177 0.414 92 92 ASN A 93 0.998 0.999 0.996 0.219 93 93 ALA A 94 0.999 0.997 94 94 ILE A 95 0.998 0.998 0.999 1.000 95 95 GLY A 96 0.998 0.996 96 96 VAL A 97 0.998 0.999 0.997 97 97 LEU A 98 0.999 0.998 0.999 0.995 98 98 ILE A 99 0.999 0.998 0.948 0.998 99 99 GLY A 100 0.998 0.995 100 100 GLY A 101 0.991 0.991 101 101 LEU A 102 0.991 0.992 0.994 0.928 102 102 GLU A 103 0.998 0.998 0.927 0.437 0.709 103 103 ARG A 104 0.995 0.992 0.494 0.653 0.100 0.770 0.998 104 104 ASN A 105 0.995 0.990 0.997 0.889 105 105 ASP A 106 0.998 0.975 0.748 0.713 106 106 ASN A 107 0.969 0.946 0.425 0.257 107 107 THR A 108 0.958 0.997 0.999 108 108 VAL A 109 0.987 0.993 0.997 109 109 ARG A 110 0.997 0.993 0.923 0.858 0.358 0.751 0.998 110 110 VAL A 111 0.991 0.996 0.999 111 111 SER A 112 0.997 0.995 0.548 112 112 LYS A 113 0.997 0.994 0.457 0.425 0.333 0.276 113 113 THR A 114 0.997 0.998 0.998 114 114 LEU A 115 0.999 0.997 0.994 0.997 115 115 GLN A 116 0.992 0.989 0.997 0.999 0.957 116 116 ARG A 117 0.979 0.974 0.839 0.577 0.510 0.687 0.994 117 117 PHE A 118 0.982 0.991 0.996 0.987 118 118 ALA A 119 0.990 0.991 119 119 TRP A 120 0.977 0.751 0.996 0.994 GLY A 121 0.625 0.210 SER A 122 0.566 0.687 0.374 SER A 123 0.836 0.437 0.109 ASN A 124 0.483 0.607 0.195 0.052 GLU A 125 0.852 0.720 0.175 0.296 0.217 ASN A 126 0.836 0.593 0.280 0.060 GLY A 127 0.414 0.147 ARG A 128 0.351 0.936 0.503 0.642 0.101 0.736 0.997 PRO A 129 0.987 0.967 0.919 0.841 129 129 PRO A 130 0.995 0.932 0.939 0.847 130 130 LEU A 131 0.960 0.929 0.998 0.999 131 131 THR A 132 0.964 0.885 0.878 132 LEU A 133 0.885 0.896 0.614 0.657 133 GLU A 134 0.904 0.594 0.661 0.264 Ranges: 3 from: A 4 to A 80 from: A 86 to A 119 from: A 129 to A 131 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[4..80],A[86..119],A[129..131],for model 1 is: 3.924 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 2 is: 3.335 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 3 is: 3.753 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 4 is: 2.123 (*) > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 5 is: 2.942 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 6 is: 5.346 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 7 is: 4.309 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 8 is: 2.909 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 9 is: 2.569 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 10 is: 5.091 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 11 is: 2.827 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 12 is: 5.091 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 13 is: 2.790 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 14 is: 3.555 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 15 is: 3.577 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 16 is: 2.953 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 17 is: 2.373 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 18 is: 2.330 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 19 is: 3.112 > Kabsch RMSD of backbone atoms in res. A[4..80],A[86..119],A[129..131],for model 20 is: 3.570 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..80],[86..119],[129..131], is: 3.424 > Range of RMSD values to reference struct. is 2.123 to 5.346 > 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[4..80],A[86..119],A[129..131],for model 1 is: 3.890 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 2 is: 3.290 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 3 is: 3.743 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 4 is: 2.179 (*) > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 5 is: 2.935 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 6 is: 5.253 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 7 is: 4.287 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 8 is: 2.919 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 9 is: 2.631 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 10 is: 4.976 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 11 is: 2.870 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 12 is: 5.021 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 13 is: 2.847 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 14 is: 3.460 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 15 is: 3.599 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 16 is: 2.886 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 17 is: 2.504 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 18 is: 2.477 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 19 is: 3.150 > Kabsch RMSD of heavy atoms in res. A[4..80],A[86..119],A[129..131],for model 20 is: 3.548 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..80],[86..119],[129..131], is: 3.423 > Range of RMSD values to reference struct. is 2.179 to 5.253 PdbStat> PdbStat> *END* of program detected, BYE! ...