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_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP.PDB, 20 MODEL/S TEMP.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 83 MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET LEU PRO 1 > ReadCoordsPdb(): Counting models in file `HR4435B_R3_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_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 26640 ATOM records read from file > ReadCoordsPdb(): --> 26640 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 0.552 0.740 0.488 0.300 GLY A 2 0.321 0.286 HIS A 3 0.590 0.364 0.541 0.361 HIS A 4 0.656 0.594 0.545 0.652 HIS A 5 0.801 0.380 0.597 0.508 HIS A 6 0.300 0.516 0.582 0.898 HIS A 7 0.657 0.417 0.399 0.378 HIS A 8 0.565 0.552 0.410 0.387 SER A 9 0.559 0.556 0.344 HIS A 10 0.582 0.766 0.999 0.683 MET A 11 0.975 0.936 0.612 0.564 0.257 11 11 LEU A 12 0.973 0.997 0.595 0.615 12 12 PRO A 13 0.992 0.970 0.977 0.966 13 13 PRO A 14 0.989 0.743 0.915 0.861 GLU A 15 0.632 0.564 0.747 0.531 0.854 GLN A 16 0.505 0.589 0.594 0.406 0.691 TRP A 17 0.780 0.875 0.995 0.749 SER A 18 0.918 0.986 0.726 18 18 HIS A 19 0.984 0.966 0.334 0.155 19 19 THR A 20 0.958 0.983 0.549 20 20 THR A 21 0.992 0.994 0.849 21 21 VAL A 22 0.997 0.989 0.841 22 22 ARG A 23 0.991 0.989 0.743 0.899 0.469 0.687 0.999 23 23 ASN A 24 0.999 0.997 1.000 1.000 24 24 ALA A 25 0.997 0.996 25 25 LEU A 26 0.987 0.987 0.871 0.869 26 26 LYS A 27 0.997 0.986 0.674 0.999 0.999 0.927 27 27 ASP A 28 0.981 0.998 0.998 0.954 28 28 LEU A 29 0.997 0.995 0.996 0.914 29 29 LEU A 30 0.977 0.966 0.888 0.866 30 30 LYS A 31 0.987 0.982 0.702 0.999 0.999 0.943 31 31 ASP A 32 0.979 0.955 0.776 0.943 32 32 MET A 33 0.913 0.985 0.726 0.680 0.270 33 33 ASN A 34 0.987 0.966 0.363 0.877 34 34 GLN A 35 0.995 0.990 0.529 0.897 0.864 35 35 SER A 36 0.989 0.985 0.381 36 36 SER A 37 0.981 0.992 0.450 37 37 LEU A 38 0.995 0.995 0.667 0.652 38 38 ALA A 39 0.997 0.994 39 39 LYS A 40 0.974 0.981 0.595 0.999 1.000 1.000 40 40 GLU A 41 0.960 0.979 0.937 0.470 0.875 41 41 CYS A 42 0.974 0.977 0.447 42 42 PRO A 43 0.988 0.916 0.897 0.812 43 43 LEU A 44 0.937 0.984 0.751 0.632 44 44 SER A 45 0.993 0.977 0.688 45 45 GLN A 46 0.995 0.992 0.589 0.995 0.948 46 46 SER A 47 0.994 0.993 0.917 47 47 MET A 48 0.977 0.983 0.823 0.594 0.376 48 48 ILE A 49 0.980 0.992 0.999 0.914 49 49 SER A 50 0.990 0.981 0.241 50 50 SER A 51 0.978 0.982 0.457 51 51 ILE A 52 0.971 0.982 0.918 0.924 52 52 VAL A 53 0.983 0.990 0.941 53 53 ASN A 54 0.976 0.890 0.996 0.944 54 SER A 55 0.278 0.553 0.545 THR A 56 0.815 0.873 0.549 56 TYR A 57 0.970 0.737 0.850 0.992 TYR A 58 0.751 0.396 0.350 0.980 ALA A 59 0.471 0.293 ASN A 60 0.487 0.660 0.398 0.823 VAL A 61 0.930 0.971 0.702 61 61 SER A 62 0.982 0.959 0.631 62 62 ALA A 63 0.995 0.997 63 63 ALA A 64 0.998 0.997 64 64 LYS A 65 0.991 0.982 0.995 0.473 0.992 0.786 65 65 CYS A 66 0.973 0.993 0.935 66 66 GLN A 67 0.997 0.994 0.762 0.865 0.888 67 67 GLU A 68 0.998 0.991 0.879 0.559 0.888 68 68 PHE A 69 0.997 0.999 0.996 0.964 69 69 GLY A 70 0.998 0.997 70 70 ARG A 71 0.996 0.994 0.675 0.999 0.637 0.723 1.000 71 71 TRP A 72 0.992 0.991 0.831 0.988 72 72 TYR A 73 0.998 0.995 0.937 0.995 73 73 LYS A 74 0.996 0.989 0.737 0.898 0.883 0.929 74 74 HIS A 75 0.980 0.989 0.931 0.240 75 75 PHE A 76 0.998 0.994 0.794 0.835 76 76 LYS A 77 0.973 0.963 0.626 0.624 0.937 0.874 77 77 LYS A 78 0.348 0.590 0.733 0.999 0.999 0.917 THR A 79 0.447 0.549 0.454 LYS A 80 0.296 0.585 0.568 0.859 0.998 0.999 ASP A 81 0.723 0.436 0.586 0.940 MET A 82 0.574 0.317 0.648 0.576 0.420 MET A 83 0.543 0.476 0.359 0.500 Ranges: 3 from: A 11 to A 13 from: A 18 to A 53 from: A 61 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[61..77],for model 1 is: 0.788 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 2 is: 1.239 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 3 is: 0.670 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 4 is: 1.017 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 5 is: 1.169 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 6 is: 0.617 (*) > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 7 is: 1.055 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 8 is: 1.121 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 9 is: 1.402 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 10 is: 1.285 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 11 is: 0.974 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 12 is: 1.765 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 13 is: 1.259 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 14 is: 0.761 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 15 is: 1.122 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 16 is: 1.206 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 17 is: 0.872 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 18 is: 1.314 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 19 is: 0.978 > Kabsch RMSD of backbone atoms in res. A[11..13],A[18..53],A[61..77],for model 20 is: 1.198 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[11..13],[18..53],[61..77], is: 1.091 > Range of RMSD values to reference struct. is 0.617 to 1.765 > 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[61..77],for model 1 is: 1.302 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 2 is: 1.528 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 3 is: 1.057 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 4 is: 1.541 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 5 is: 1.621 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 6 is: 0.887 (*) > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 7 is: 1.316 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 8 is: 1.502 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 9 is: 1.830 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 10 is: 1.803 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 11 is: 1.430 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 12 is: 2.389 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 13 is: 1.551 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 14 is: 1.219 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 15 is: 1.377 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 16 is: 1.743 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 17 is: 1.253 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 18 is: 1.703 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 19 is: 1.494 > Kabsch RMSD of heavy atoms in res. A[11..13],A[18..53],A[61..77],for model 20 is: 1.742 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[11..13],[18..53],[61..77], is: 1.514 > Range of RMSD values to reference struct. is 0.887 to 2.389 PdbStat> PdbStat> *END* of program detected, BYE! ...