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 `HR4527E_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER TRANSCRIPTION REGULATOR 03-SEP-10 2L33 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF DRBM 2 DOMAIN OF INTERLEUKIN ENHANCER- > ReadCoordsPdb(): >> TITLE 2 BINDING FACTOR 3 FROM HOMO SAPIENS, NORTHEAST STRUCTURAL GENOMICS > ReadCoordsPdb(): >> TITLE 3 CONSORTIUM TARGET HR4527E > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `HR4527E_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 HR4527E_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 28720 ATOM records read from file > ReadCoordsPdb(): --> 28720 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 0.537 0.369 0.319 0.617 GLY A 2 0.234 0.364 HIS A 3 0.515 0.355 0.187 0.146 HIS A 4 0.704 0.496 0.390 0.279 HIS A 5 0.850 0.536 0.478 0.210 HIS A 6 0.683 0.603 0.427 0.462 HIS A 7 0.679 0.331 0.398 0.379 HIS A 8 0.594 0.380 0.296 0.195 SER A 9 0.536 0.307 0.296 HIS A 10 0.726 0.749 0.223 0.665 MET A 11 0.813 0.861 0.077 0.572 0.337 11 LEU A 12 0.971 0.829 0.940 0.772 12 THR A 13 0.782 0.485 0.570 LYS A 14 0.714 0.321 0.572 0.416 0.568 0.264 HIS A 15 0.633 0.275 0.861 0.361 GLY A 16 0.253 0.871 LYS A 17 0.956 0.702 0.990 0.697 0.427 0.193 ASN A 18 0.786 0.991 0.813 0.437 PRO A 19 0.997 0.998 0.998 0.999 19 19 VAL A 20 0.999 0.998 0.999 20 20 MET A 21 0.997 0.995 0.999 0.998 0.999 21 21 GLU A 22 0.993 0.997 0.998 0.799 0.605 22 22 LEU A 23 0.999 0.998 0.999 1.000 23 23 ASN A 24 0.995 0.995 0.832 0.755 24 24 GLU A 25 0.994 0.990 0.997 0.877 0.771 25 25 LYS A 26 0.996 0.995 0.992 0.997 0.751 0.479 26 26 ARG A 27 0.994 0.936 0.992 0.998 0.916 0.858 0.999 27 27 ARG A 28 0.936 0.969 0.626 0.658 0.654 0.875 0.998 28 28 GLY A 29 0.978 0.979 29 29 LEU A 30 0.986 0.997 0.998 1.000 30 30 LYS A 31 0.974 0.986 0.993 0.980 0.289 0.178 31 31 TYR A 32 0.979 0.993 0.998 0.797 32 32 GLU A 33 0.990 1.000 0.998 0.990 0.701 33 33 LEU A 34 0.998 0.990 0.999 0.999 34 34 ILE A 35 0.988 0.995 1.000 1.000 35 35 SER A 36 0.980 0.990 0.999 36 36 GLU A 37 0.977 0.922 0.389 0.646 0.322 37 37 THR A 38 0.973 0.958 0.147 38 38 GLY A 39 0.782 0.512 GLY A 40 0.272 0.329 SER A 41 0.529 0.762 0.475 HIS A 42 0.554 0.311 0.607 0.104 ASP A 43 0.444 0.807 0.134 0.371 LYS A 44 0.887 0.930 0.925 0.486 0.394 0.365 44 ARG A 45 0.955 0.981 0.991 0.727 0.055 0.734 0.999 45 45 PHE A 46 0.988 0.982 0.998 0.802 46 46 VAL A 47 0.992 0.998 0.999 47 47 MET A 48 0.997 0.996 0.999 1.000 1.000 48 48 GLU A 49 0.992 0.995 1.000 0.998 0.318 49 49 VAL A 50 0.991 0.997 1.000 50 50 GLU A 51 0.995 0.995 0.997 0.828 0.673 51 51 VAL A 52 0.991 0.991 1.000 52 52 ASP A 53 0.998 0.984 0.705 0.575 53 53 GLY A 54 0.985 0.978 54 54 GLN A 55 0.977 0.994 0.999 0.998 1.000 55 55 LYS A 56 0.994 0.995 0.996 0.998 0.997 0.849 56 56 PHE A 57 0.993 0.992 1.000 0.800 57 57 GLN A 58 0.995 0.996 0.999 0.999 1.000 58 58 GLY A 59 0.995 0.996 59 59 ALA A 60 0.999 0.993 60 60 GLY A 61 0.994 0.949 61 61 SER A 62 0.920 0.949 0.401 62 62 ASN A 63 0.969 0.990 0.998 0.338 63 63 LYS A 64 0.997 0.990 0.887 0.997 0.548 0.338 64 64 LYS A 65 0.996 0.996 0.996 0.439 0.245 0.561 65 65 VAL A 66 0.998 0.998 0.998 66 66 ALA A 67 1.000 0.998 67 67 LYS A 68 1.000 0.999 0.999 0.999 1.000 0.998 68 68 ALA A 69 1.000 0.999 69 69 TYR A 70 0.999 0.997 0.997 0.897 70 70 ALA A 71 0.999 0.999 71 71 ALA A 72 0.999 0.999 72 72 LEU A 73 0.999 0.997 0.997 1.000 73 73 ALA A 74 0.999 0.997 74 74 ALA A 75 0.997 0.998 75 75 LEU A 76 0.998 0.991 0.999 0.999 76 76 GLU A 77 0.993 0.989 0.996 0.929 0.520 77 77 LYS A 78 0.996 0.995 0.998 0.998 0.998 0.557 78 78 LEU A 79 0.992 0.981 0.999 1.000 79 79 PHE A 80 0.995 0.991 0.995 0.999 80 80 PRO A 81 0.986 0.990 0.968 0.947 81 81 ASP A 82 0.994 0.779 0.894 0.900 THR A 83 0.936 0.969 0.998 83 83 PRO A 84 0.993 0.812 0.923 0.847 84 LEU A 85 0.813 0.909 0.594 0.940 85 ALA A 86 0.802 0.803 86 LEU A 87 0.892 0.920 0.998 0.728 87 ASP A 88 0.697 0.451 0.249 0.315 ALA A 89 0.670 0.573 ASN A 90 0.725 0.549 0.325 0.422 LYS A 91 0.816 0.116 0.429 0.251 0.246 Ranges: 2 from: A 19 to A 38 from: A 45 to A 81 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[19..38],A[45..81],for model 1 is: 0.278 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 2 is: 0.397 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 3 is: 0.338 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 4 is: 0.324 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 5 is: 0.384 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 6 is: 0.257 (*) > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 7 is: 0.357 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 8 is: 0.332 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 9 is: 0.449 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 10 is: 0.400 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 11 is: 0.328 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 12 is: 0.356 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 13 is: 0.302 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 14 is: 0.352 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 15 is: 0.325 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 16 is: 0.405 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 17 is: 0.423 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 18 is: 0.376 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 19 is: 0.358 > Kabsch RMSD of backbone atoms in res. A[19..38],A[45..81],for model 20 is: 0.339 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[19..38],[45..81], is: 0.354 > Range of RMSD values to reference struct. is 0.257 to 0.449 > 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[19..38],A[45..81],for model 1 is: 0.823 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 2 is: 0.777 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 3 is: 0.660 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 4 is: 0.820 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 5 is: 0.726 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 6 is: 0.614 (*) > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 7 is: 0.789 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 8 is: 0.813 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 9 is: 0.747 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 10 is: 0.913 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 11 is: 0.832 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 12 is: 0.792 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 13 is: 0.628 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 14 is: 0.861 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 15 is: 0.838 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 16 is: 0.834 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 17 is: 0.855 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 18 is: 0.772 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 19 is: 0.699 > Kabsch RMSD of heavy atoms in res. A[19..38],A[45..81],for model 20 is: 0.808 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[19..38],[45..81], is: 0.780 > Range of RMSD values to reference struct. is 0.614 to 0.913 PdbStat> PdbStat> *END* of program detected, BYE! ...