Running PDBSTAT from Linux Ayuda is on: /farm/software/PdbStat/PdbStat-5.9 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2013 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.9-exp mar may 14 00:20:00 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 ...) 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 `ZR18_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 19-JUN-03 1PQX > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF STAPHYLOCOCCUS AUREUS PROTEIN > ReadCoordsPdb(): >> TITLE 2 SAV1430. NORTHEAST STRUCUTRAL GENOMICS CONSORTIUM TARGET > ReadCoordsPdb(): >> TITLE 3 ZR18. > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): Counting models in file `ZR18_NMR_em_bcr3.pdb'; Model: > ReadCoordsPdb(): After scanning there is(are) 10 model(s) > ReadCoordsPdb(): what model do you want [(1 to 10) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file ZR18_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (10) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 14440 ATOM records read from file > ReadCoordsPdb(): --> 14440 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 0.843 0.897 0.714 0.623 LYS A 2 0.971 0.691 0.376 0.667 0.381 0.352 ILE A 3 0.666 0.983 0.995 0.985 ILE A 4 0.999 0.949 0.945 0.581 4 4 SER A 5 0.897 0.974 0.221 5 ILE A 6 0.963 0.701 0.974 0.446 SER A 7 0.156 0.722 0.367 GLU A 8 0.767 0.124 0.560 0.530 0.708 THR A 9 0.963 0.396 0.178 PRO A 10 0.984 0.948 1.000 0.983 10 10 ASN A 11 0.928 0.436 0.234 0.513 HIS A 12 0.416 0.122 0.306 0.244 ASN A 13 0.130 0.974 0.651 0.545 THR A 14 0.998 0.988 0.987 14 14 MET A 15 0.989 0.986 0.512 0.885 0.117 15 15 LYS A 16 0.998 0.961 0.514 0.796 0.333 0.019 16 16 ILE A 17 0.952 0.994 0.991 0.996 17 17 THR A 18 1.000 0.991 0.987 18 18 LEU A 19 0.995 0.765 0.994 0.993 SER A 20 0.807 0.980 0.359 20 GLU A 21 0.400 0.817 0.813 0.380 0.483 SER A 22 0.891 0.566 0.399 ARG A 23 0.295 0.275 0.522 0.573 0.415 0.364 0.747 GLU A 24 0.783 0.394 0.712 0.457 0.629 GLY A 25 0.774 0.109 MET A 26 0.599 0.211 0.626 0.429 0.580 THR A 27 0.155 0.912 0.369 SER A 28 1.000 0.980 0.983 28 28 ASP A 29 0.998 0.982 0.977 0.966 29 29 THR A 30 0.966 0.976 0.238 30 30 TYR A 31 0.983 0.992 0.992 0.979 31 31 THR A 32 0.997 0.945 0.869 32 32 LYS A 33 0.863 0.742 0.509 0.885 0.359 0.539 VAL A 34 0.778 0.815 0.982 ASP A 35 0.415 0.480 0.521 0.584 ASP A 36 0.552 0.608 0.797 0.664 SER A 37 0.134 0.825 0.458 GLN A 38 0.970 0.979 0.718 0.562 0.102 38 38 PRO A 39 0.991 0.997 1.000 0.991 39 39 ALA A 40 1.000 0.999 40 40 PHE A 41 1.000 0.997 0.998 0.997 41 41 ILE A 42 0.994 0.999 0.998 0.999 42 42 ASN A 43 1.000 0.999 0.998 0.976 43 43 ASP A 44 1.000 0.996 0.521 0.695 44 44 ILE A 45 0.996 0.997 0.993 0.990 45 45 LEU A 46 0.990 1.000 0.995 0.990 46 46 LYS A 47 1.000 0.999 0.949 0.784 0.899 0.624 47 47 VAL A 48 1.000 0.994 0.992 48 48 GLU A 49 0.999 0.969 0.662 0.497 0.614 49 49 GLY A 50 0.946 0.950 50 50 VAL A 51 1.000 0.413 0.907 LYS A 52 0.432 0.972 0.981 0.931 0.225 0.221 SER A 53 0.996 0.997 0.434 53 53 ILE A 54 0.999 0.997 0.996 0.998 54 54 PHE A 55 0.998 0.998 0.985 0.985 55 55 HIS A 56 0.999 0.997 0.970 0.740 56 56 VAL A 57 1.000 0.987 0.990 57 57 MET A 58 0.994 0.944 0.631 0.713 0.425 58 58 ASP A 59 0.945 0.979 0.987 0.600 59 59 PHE A 60 0.971 0.993 0.994 0.599 60 60 ILE A 61 0.993 0.997 0.991 0.906 61 61 SER A 62 0.997 0.974 0.458 62 62 VAL A 63 0.976 0.997 0.998 63 63 ASP A 64 0.996 0.989 0.626 0.681 64 64 LYS A 65 0.989 0.984 0.993 0.984 0.821 0.209 65 65 GLU A 66 0.953 0.853 0.935 0.576 0.578 66 ASN A 67 0.967 0.982 0.327 0.338 67 67 ASP A 68 0.780 0.989 0.176 0.453 ALA A 69 0.416 0.934 ASN A 70 0.972 0.915 0.616 0.402 70 70 TRP A 71 0.985 0.997 0.997 0.999 71 71 GLU A 72 0.999 1.000 0.148 0.401 0.447 72 72 THR A 73 1.000 1.000 0.701 73 73 VAL A 74 0.997 1.000 0.999 74 74 LEU A 75 1.000 0.999 0.920 0.459 75 75 PRO A 76 0.999 1.000 1.000 1.000 76 76 LYS A 77 1.000 0.997 0.975 0.685 0.887 0.431 77 77 VAL A 78 0.995 0.995 0.995 78 78 GLU A 79 1.000 0.998 0.749 0.871 0.621 79 79 ALA A 80 1.000 1.000 80 80 VAL A 81 0.999 0.998 1.000 81 81 PHE A 82 1.000 0.890 0.999 0.426 82 GLU A 83 0.857 0.488 0.835 0.542 0.547 LEU A 84 0.236 0.630 0.673 0.540 GLU A 85 0.510 0.726 0.448 0.189 0.399 HIS A 86 0.923 0.431 0.441 0.323 HIS A 87 0.648 0.144 0.288 0.647 HIS A 88 0.639 0.577 0.239 0.437 HIS A 89 0.867 0.297 0.572 0.278 HIS A 90 0.564 0.306 0.212 0.531 HIS A 91 0.188 0.513 0.456 Ranges: 5 from: A 14 to A 18 from: A 28 to A 32 from: A 38 to A 50 from: A 53 to A 65 from: A 70 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[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 1 is: 0.284 > Kabsch RMSD of backbone atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 2 is: 0.407 > Kabsch RMSD of backbone atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 3 is: 0.527 > Kabsch RMSD of backbone atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 4 is: 0.369 > Kabsch RMSD of backbone atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 5 is: 0.269 > Kabsch RMSD of backbone atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 6 is: 0.304 > Kabsch RMSD of backbone atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 7 is: 0.304 > Kabsch RMSD of backbone atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 8 is: 0.334 > Kabsch RMSD of backbone atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 9 is: 0.408 > Kabsch RMSD of backbone atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 10 is: 0.264 (*) > > Kabsch RMSD statistics for 10 structures: > Mean RMSD using as refer. str. `average' for res.[14..18],[28..32],[38..50],[53..65],[70..81], is: 0.347 > Range of RMSD values to reference struct. is 0.264 to 0.527 > 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[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 1 is: 0.639 > Kabsch RMSD of heavy atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 2 is: 0.772 > Kabsch RMSD of heavy atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 3 is: 0.857 > Kabsch RMSD of heavy atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 4 is: 0.730 > Kabsch RMSD of heavy atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 5 is: 0.600 (*) > Kabsch RMSD of heavy atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 6 is: 0.760 > Kabsch RMSD of heavy atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 7 is: 0.712 > Kabsch RMSD of heavy atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 8 is: 0.660 > Kabsch RMSD of heavy atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 9 is: 0.794 > Kabsch RMSD of heavy atoms in res. A[14..18],A[28..32],A[38..50],A[53..65],A[70..81],for model 10 is: 0.676 > > Kabsch RMSD statistics for 10 structures: > Mean RMSD using as refer. str. `average' for res.[14..18],[28..32],[38..50],[53..65],[70..81], is: 0.720 > Range of RMSD values to reference struct. is 0.600 to 0.857 PdbStat> PdbStat> *END* of program detected, BYE! ...