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 `HR4435B_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER DNA BINDING PROTEIN 02-AUG-10 2L1P > ReadCoordsPdb(): >> TITLE NMR SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA-BINDING PROTEIN > ReadCoordsPdb(): >> TITLE 2 SATB1 FROM HOMO SAPIENS: NORTHEAST STRUCTURAL GENOMICS TARGET > ReadCoordsPdb(): >> TITLE 3 HR4435B(179-250) > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `HR4435B_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 HR4435B_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 26820 ATOM records read from file > ReadCoordsPdb(): --> 26820 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 0.571 0.495 0.510 0.403 GLY A 2 0.317 0.256 HIS A 3 0.615 0.330 0.524 0.259 HIS A 4 0.635 0.640 0.264 0.095 HIS A 5 0.825 0.435 0.289 0.380 HIS A 6 0.313 0.567 0.290 0.079 HIS A 7 0.626 0.491 0.250 0.121 HIS A 8 0.568 0.610 0.342 0.380 SER A 9 0.551 0.520 0.243 HIS A 10 0.538 0.764 0.707 0.261 MET A 11 0.986 0.964 0.418 0.707 0.424 11 11 LEU A 12 0.984 0.999 0.831 0.630 12 12 PRO A 13 0.981 0.957 0.921 0.865 13 13 PRO A 14 0.985 0.703 0.937 0.882 GLU A 15 0.630 0.620 0.550 0.775 0.366 GLN A 16 0.470 0.586 0.497 0.725 0.406 TRP A 17 0.771 0.898 0.991 0.968 SER A 18 0.920 0.969 0.143 18 18 HIS A 19 0.990 0.986 0.405 0.333 19 19 THR A 20 0.974 0.975 0.863 20 20 THR A 21 0.996 0.990 0.854 21 21 VAL A 22 0.996 0.987 0.999 22 22 ARG A 23 0.996 0.993 0.992 0.782 0.525 0.716 0.999 23 23 ASN A 24 0.989 0.975 0.724 0.459 24 24 ALA A 25 0.971 0.983 25 25 LEU A 26 0.983 0.966 0.725 0.993 26 26 LYS A 27 0.983 0.941 0.169 0.348 0.660 0.356 27 27 ASP A 28 0.964 0.979 0.656 0.434 28 28 LEU A 29 0.989 0.992 0.937 0.486 29 29 LEU A 30 0.981 0.944 0.999 0.999 30 30 LYS A 31 0.986 0.969 0.484 0.501 0.220 0.412 31 31 ASP A 32 0.972 0.914 0.656 0.446 32 32 MET A 33 0.920 0.946 0.411 0.322 0.468 33 33 ASN A 34 0.972 0.968 0.861 0.311 34 34 GLN A 35 0.992 0.978 0.853 0.792 0.473 35 35 SER A 36 0.997 0.974 0.447 36 36 SER A 37 0.978 0.988 0.593 37 37 LEU A 38 0.993 0.988 0.994 0.327 38 38 ALA A 39 0.997 0.980 39 39 LYS A 40 0.984 0.960 0.552 0.685 0.403 0.411 40 40 GLU A 41 0.980 0.936 0.627 0.599 0.472 41 41 CYS A 42 0.984 0.989 0.477 42 42 PRO A 43 0.992 0.910 0.941 0.884 43 43 LEU A 44 0.966 0.934 0.997 0.867 44 44 SER A 45 0.972 0.957 0.444 45 45 GLN A 46 0.997 0.989 0.994 0.727 0.807 46 46 SER A 47 0.996 0.991 0.569 47 47 MET A 48 0.992 0.941 0.956 0.668 0.577 48 48 ILE A 49 0.943 0.986 0.996 0.932 49 49 SER A 50 0.991 0.992 0.533 50 50 SER A 51 0.987 0.981 0.570 51 51 ILE A 52 0.975 0.987 0.998 0.999 52 52 VAL A 53 0.990 0.982 0.651 53 53 ASN A 54 0.963 0.899 0.562 0.209 54 SER A 55 0.310 0.599 0.373 THR A 56 0.834 0.877 0.644 56 TYR A 57 0.935 0.793 0.597 0.512 TYR A 58 0.796 0.452 0.379 0.286 ALA A 59 0.471 0.422 ASN A 60 0.561 0.689 0.687 0.397 VAL A 61 0.861 0.913 0.333 61 SER A 62 0.972 0.948 0.469 62 62 ALA A 63 0.978 0.969 63 63 ALA A 64 0.997 0.974 64 64 LYS A 65 0.990 0.978 0.351 0.179 0.440 0.130 65 65 CYS A 66 0.967 0.986 0.533 66 66 GLN A 67 0.990 0.974 0.857 0.646 0.429 67 67 GLU A 68 0.997 0.976 0.810 0.140 0.244 68 68 PHE A 69 0.997 0.995 0.998 0.995 69 69 GLY A 70 0.999 0.993 70 70 ARG A 71 0.994 0.993 0.909 0.571 0.273 0.744 0.999 71 71 TRP A 72 0.996 0.993 0.997 0.998 72 72 TYR A 73 0.997 0.989 0.987 0.980 73 73 LYS A 74 0.997 0.989 0.721 0.884 0.419 0.710 74 74 HIS A 75 0.976 0.992 0.565 0.796 75 75 PHE A 76 0.991 0.990 0.998 0.997 76 76 LYS A 77 0.970 0.967 0.623 0.887 0.234 0.521 77 77 LYS A 78 0.340 0.577 0.640 0.442 0.351 0.145 THR A 79 0.450 0.537 0.262 LYS A 80 0.267 0.607 0.483 0.649 0.228 0.556 ASP A 81 0.699 0.168 0.462 0.450 MET A 82 0.519 0.207 0.474 0.531 0.337 MET A 83 0.528 0.329 0.591 0.575 Ranges: 3 from: A 11 to A 13 from: A 18 to A 53 from: A 62 to A 77 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[11..13],A[18..53],A[62..77],for model 1 is: 0.678 (*) > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 2 is: 0.968 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 3 is: 0.982 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 4 is: 0.948 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 5 is: 1.003 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 6 is: 0.907 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 7 is: 0.940 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 8 is: 0.965 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 9 is: 0.852 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 10 is: 1.468 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 11 is: 0.937 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 12 is: 0.728 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 13 is: 1.010 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 14 is: 1.057 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 15 is: 0.929 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 16 is: 0.852 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 17 is: 0.765 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 18 is: 0.920 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 19 is: 0.814 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[62..77],for model 20 is: 0.792 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[11..13],[18..53],[62..77], is: 0.926 > Range of RMSD values to reference struct. is 0.678 to 1.468 > 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[11..13],A[18..53],A[62..77],for model 1 is: 1.400 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 2 is: 1.372 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 3 is: 1.425 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 4 is: 1.427 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 5 is: 1.521 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 6 is: 1.420 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 7 is: 1.261 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 8 is: 1.243 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 9 is: 1.307 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 10 is: 1.961 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 11 is: 1.444 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 12 is: 1.263 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 13 is: 1.467 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 14 is: 1.515 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 15 is: 1.446 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 16 is: 1.420 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 17 is: 1.407 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 18 is: 1.344 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 19 is: 1.202 (*) > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[62..77],for model 20 is: 1.320 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[11..13],[18..53],[62..77], is: 1.408 > Range of RMSD values to reference struct. is 1.202 to 1.961 PdbStat> PdbStat> *END* of program detected, BYE! ...