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 `HR4694F_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 86 HIS MET PRO LYS SER PRO GLN LYS PRO ILE VAL ARG VAL 1 > ReadCoordsPdb(): Counting models in file `HR4694F_R3Cons_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 HR4694F_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 27960 ATOM records read from file > ReadCoordsPdb(): --> 27960 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 ----------------------------------------------------------------------------------- HIS A 1 0.362 0.547 0.412 MET A 2 0.288 0.952 0.576 0.212 0.216 PRO A 3 0.989 0.905 0.920 0.864 3 3 LYS A 4 0.921 0.593 0.647 0.862 0.998 0.999 SER A 5 0.563 0.882 0.391 PRO A 6 0.978 0.751 0.883 0.812 GLN A 7 0.780 0.558 0.540 0.452 0.728 LYS A 8 0.979 0.987 0.652 0.928 0.999 1.000 8 8 PRO A 9 0.998 0.992 1.000 1.000 9 9 ILE A 10 0.999 1.000 1.000 0.839 10 10 VAL A 11 1.000 1.000 1.000 11 11 ARG A 12 0.999 0.998 0.997 0.992 0.613 0.778 1.000 12 12 VAL A 13 0.999 0.999 1.000 13 13 PHE A 14 0.998 0.998 1.000 0.999 14 14 LEU A 15 0.998 1.000 1.000 1.000 15 15 PRO A 16 0.997 0.999 0.939 0.873 16 16 ASN A 17 0.999 0.995 0.715 0.901 17 17 LYS A 18 1.000 0.999 1.000 1.000 1.000 1.000 18 18 GLN A 19 0.998 0.999 1.000 1.000 1.000 19 19 ARG A 20 0.999 0.996 0.482 0.997 0.996 0.724 1.000 20 20 THR A 21 0.999 0.989 1.000 21 21 VAL A 22 0.998 0.999 1.000 22 22 VAL A 23 0.999 0.998 1.000 23 23 PRO A 24 0.996 0.999 0.944 0.891 24 24 ALA A 25 0.999 0.995 25 25 ARG A 26 0.995 0.997 1.000 0.999 1.000 0.944 1.000 26 26 CYS A 27 1.000 1.000 1.000 27 27 GLY A 28 0.999 0.999 28 28 VAL A 29 0.999 0.999 1.000 29 29 THR A 30 1.000 1.000 1.000 30 30 VAL A 31 1.000 1.000 1.000 31 31 ARG A 32 0.999 0.996 0.998 0.877 0.994 0.654 1.000 32 32 ASP A 33 0.998 0.997 0.940 0.923 33 33 SER A 34 0.998 0.996 0.150 34 34 LEU A 35 0.998 0.996 1.000 0.999 35 35 LYS A 36 0.996 0.995 0.741 0.998 0.999 0.997 36 36 LYS A 37 0.996 0.999 0.875 0.999 1.000 1.000 37 37 ALA A 38 1.000 0.999 38 38 LEU A 39 0.996 0.998 1.000 0.999 39 39 MET A 40 0.999 0.999 1.000 1.000 1.000 40 40 MET A 41 0.999 0.998 0.999 0.999 0.207 41 41 ARG A 42 0.993 0.996 0.999 0.815 0.432 0.642 1.000 42 42 GLY A 43 0.998 0.997 43 43 LEU A 44 0.997 0.999 1.000 1.000 44 44 ILE A 45 0.997 0.997 0.999 1.000 45 45 PRO A 46 0.996 0.997 0.915 0.829 46 46 GLU A 47 0.998 0.999 0.999 0.845 0.965 47 47 CYS A 48 0.991 0.984 0.548 48 48 CYS A 49 0.995 0.990 0.938 49 49 ALA A 50 0.997 0.998 50 50 VAL A 51 0.997 1.000 1.000 51 51 TYR A 52 1.000 1.000 1.000 0.700 52 52 ARG A 53 0.999 0.994 0.749 0.998 0.448 0.442 1.000 53 53 ILE A 54 0.998 0.996 1.000 1.000 54 54 GLN A 55 0.996 0.998 1.000 0.937 0.917 55 55 ASP A 56 1.000 1.000 0.947 0.972 56 56 GLY A 57 0.999 0.999 57 57 GLU A 58 0.998 0.998 0.859 1.000 1.000 58 58 LYS A 59 0.999 0.997 1.000 0.999 1.000 0.999 59 59 LYS A 60 0.998 0.995 0.683 0.744 0.999 0.998 60 60 PRO A 61 0.994 0.999 0.922 0.846 61 61 ILE A 62 0.999 1.000 1.000 0.925 62 62 GLY A 63 0.998 0.999 63 63 TRP A 64 0.999 0.999 0.999 1.000 64 64 ASP A 65 1.000 0.997 0.429 0.983 65 65 THR A 66 0.999 0.999 1.000 66 66 ASP A 67 1.000 1.000 0.999 0.982 67 67 ILE A 68 1.000 1.000 1.000 1.000 68 68 SER A 69 1.000 1.000 1.000 69 69 TRP A 70 1.000 1.000 1.000 1.000 70 70 LEU A 71 1.000 0.999 1.000 1.000 71 71 THR A 72 1.000 1.000 1.000 72 72 GLY A 73 1.000 0.999 73 73 GLU A 74 0.998 0.999 0.999 0.750 0.879 74 74 GLU A 75 0.997 0.999 0.923 0.947 0.979 75 75 LEU A 76 1.000 0.999 1.000 1.000 76 76 HIS A 77 1.000 1.000 1.000 1.000 77 77 VAL A 78 1.000 0.999 1.000 78 78 GLU A 79 0.995 0.999 0.570 1.000 0.999 79 79 VAL A 80 0.998 0.998 1.000 80 80 LEU A 81 0.995 0.980 1.000 1.000 81 81 GLU A 82 0.933 0.958 0.697 1.000 0.999 82 82 ASN A 83 0.964 0.829 0.668 0.880 83 VAL A 84 0.779 0.932 0.858 PRO A 85 0.993 0.906 0.964 0.939 85 85 LEU A 86 0.888 0.527 0.575 Ranges: 1 from: A 8 to A 82 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[8..82],for model 1 is: 0.338 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 2 is: 0.455 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 3 is: 0.503 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 4 is: 0.443 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 5 is: 0.731 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 6 is: 0.421 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 7 is: 0.646 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 8 is: 0.422 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 9 is: 0.362 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 10 is: 0.483 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 11 is: 0.451 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 12 is: 0.405 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 13 is: 0.423 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 14 is: 0.468 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 15 is: 0.435 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 16 is: 0.380 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 17 is: 0.261 (*) > Kabsch RMSD of backbone atoms in res. A[8..82],for model 18 is: 0.475 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 19 is: 0.317 > Kabsch RMSD of backbone atoms in res. A[8..82],for model 20 is: 0.399 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[8..82], is: 0.441 > Range of RMSD values to reference struct. is 0.261 to 0.731 > 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[8..82],for model 1 is: 0.611 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 2 is: 0.764 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 3 is: 0.779 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 4 is: 0.705 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 5 is: 1.016 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 6 is: 0.635 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 7 is: 0.945 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 8 is: 0.689 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 9 is: 0.689 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 10 is: 0.839 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 11 is: 0.800 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 12 is: 0.805 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 13 is: 0.743 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 14 is: 0.813 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 15 is: 0.782 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 16 is: 0.699 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 17 is: 0.587 (*) > Kabsch RMSD of heavy atoms in res. A[8..82],for model 18 is: 0.799 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 19 is: 0.630 > Kabsch RMSD of heavy atoms in res. A[8..82],for model 20 is: 0.743 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[8..82], is: 0.754 > Range of RMSD values to reference struct. is 0.587 to 1.016 PdbStat> PdbStat> *END* of program detected, BYE! ...