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_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 11 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 10 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 91 MET LYS ILE ILE SER ILE SER GLU THR PRO ASN HIS ASN > ReadCoordsPdb(): Counting models in file `ZR18_R3Cons_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_R3Cons_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 0.917 0.870 0.731 0.357 LYS A 2 0.949 0.734 0.275 0.727 0.998 0.745 ILE A 3 0.671 0.987 0.999 0.839 ILE A 4 0.996 0.998 0.999 0.840 4 4 SER A 5 0.996 0.993 1.000 5 5 ILE A 6 0.985 0.737 0.704 0.471 SER A 7 0.354 0.833 0.656 GLU A 8 0.817 0.196 0.655 0.999 0.960 THR A 9 0.952 0.471 0.447 PRO A 10 0.988 0.995 0.900 0.819 10 10 ASN A 11 0.938 0.472 0.413 0.902 HIS A 12 0.382 0.146 0.449 0.534 ASN A 13 0.107 0.940 0.846 0.485 THR A 14 0.985 0.998 0.998 14 14 MET A 15 0.988 0.994 0.680 0.747 0.382 15 15 LYS A 16 0.998 0.979 0.750 0.993 0.764 0.866 16 16 ILE A 17 0.989 0.997 1.000 1.000 17 17 THR A 18 0.996 0.999 1.000 18 18 LEU A 19 0.997 0.758 1.000 1.000 SER A 20 0.808 0.988 0.990 20 GLU A 21 0.436 0.822 0.579 0.426 0.875 SER A 22 0.868 0.682 0.368 ARG A 23 0.330 0.201 0.420 0.999 0.868 0.998 1.000 GLU A 24 0.814 0.370 0.748 0.854 0.962 GLY A 25 0.675 0.064 MET A 26 0.612 0.307 0.996 0.512 0.283 THR A 27 0.172 0.910 0.709 SER A 28 0.957 0.907 0.567 28 28 ASP A 29 0.968 0.986 0.749 0.878 29 29 THR A 30 0.992 1.000 1.000 30 30 TYR A 31 1.000 0.995 1.000 0.399 31 31 THR A 32 0.996 0.942 1.000 32 32 LYS A 33 0.801 0.674 0.459 0.999 0.999 0.863 VAL A 34 0.760 0.811 0.845 ASP A 35 0.420 0.342 0.557 0.926 ASP A 36 0.506 0.487 0.728 0.951 SER A 37 0.175 0.770 0.279 GLN A 38 0.966 0.982 0.840 0.739 0.682 38 38 PRO A 39 1.000 0.998 1.000 1.000 39 39 ALA A 40 0.999 0.998 40 40 PHE A 41 0.998 0.995 0.997 0.680 41 41 ILE A 42 0.998 0.999 0.999 1.000 42 42 ASN A 43 1.000 0.998 0.993 0.754 43 43 ASP A 44 1.000 0.999 1.000 1.000 44 44 ILE A 45 0.999 0.999 1.000 0.841 45 45 LEU A 46 0.999 1.000 1.000 0.999 46 46 LYS A 47 1.000 0.999 1.000 1.000 1.000 1.000 47 47 VAL A 48 0.997 0.999 0.999 48 48 GLU A 49 0.999 0.999 1.000 1.000 1.000 49 49 GLY A 50 0.999 0.995 50 50 VAL A 51 0.990 0.435 0.998 LYS A 52 0.431 0.982 1.000 0.999 1.000 0.996 SER A 53 0.994 0.985 0.580 53 53 ILE A 54 0.999 0.996 1.000 0.999 54 54 PHE A 55 0.995 0.998 0.999 0.982 55 55 HIS A 56 0.993 0.990 0.998 0.918 56 56 VAL A 57 0.989 0.993 0.995 57 57 MET A 58 0.992 0.969 0.611 0.709 0.222 58 58 ASP A 59 0.964 0.998 1.000 0.997 59 59 PHE A 60 1.000 0.998 1.000 1.000 60 60 ILE A 61 0.995 0.999 1.000 1.000 61 61 SER A 62 0.999 0.998 1.000 62 62 VAL A 63 0.997 0.996 1.000 63 63 ASP A 64 0.989 0.983 0.700 0.766 64 64 LYS A 65 0.971 0.995 0.996 0.894 0.999 0.462 65 65 GLU A 66 0.994 0.962 0.999 0.673 0.955 66 66 ASN A 67 0.993 0.997 1.000 0.999 67 67 ASP A 68 0.880 1.000 0.879 0.934 68 ALA A 69 0.589 0.854 ASN A 70 0.947 0.926 0.673 0.762 70 70 TRP A 71 0.997 0.996 0.995 0.993 71 71 GLU A 72 0.999 0.999 0.618 1.000 1.000 72 72 THR A 73 0.999 1.000 1.000 73 73 VAL A 74 1.000 1.000 1.000 74 74 LEU A 75 1.000 1.000 0.637 0.644 75 75 PRO A 76 0.999 1.000 1.000 1.000 76 76 LYS A 77 0.999 1.000 1.000 0.611 0.992 1.000 77 77 VAL A 78 0.999 0.998 1.000 78 78 GLU A 79 0.999 0.998 0.600 0.999 1.000 79 79 ALA A 80 0.999 1.000 80 80 VAL A 81 0.997 0.999 1.000 81 81 PHE A 82 0.989 0.888 0.978 0.182 82 GLU A 83 0.887 0.466 0.595 0.383 0.890 LEU A 84 0.392 0.618 0.997 1.000 GLU A 85 0.440 0.605 0.577 1.000 0.962 HIS A 86 0.989 0.389 0.758 0.287 HIS A 87 0.661 0.206 0.081 0.379 HIS A 88 0.689 0.622 0.572 0.876 HIS A 89 0.946 0.254 0.277 0.321 HIS A 90 0.661 0.271 0.228 0.624 HIS A 91 0.240 0.641 0.496 Ranges: 6 from: A 4 to A 5 from: A 14 to A 18 from: A 28 to A 32 from: A 38 to A 50 from: A 53 to A 67 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[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 1 is: 0.513 > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 2 is: 0.536 > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 3 is: 0.648 > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 4 is: 0.481 > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 5 is: 0.573 > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 6 is: 0.689 > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 7 is: 0.709 > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 8 is: 0.452 (*) > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 9 is: 0.541 > Kabsch RMSD of backbone atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 10 is: 0.458 > > Kabsch RMSD statistics for 10 structures: > Mean RMSD using as refer. str. `average' for res.[4..5],[14..18],[28..32],[38..50],[53..67],[70..81], is: 0.560 > Range of RMSD values to reference struct. is 0.452 to 0.709 > 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[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 1 is: 0.760 > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 2 is: 0.715 > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 3 is: 0.867 > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 4 is: 0.656 (*) > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 5 is: 0.795 > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 6 is: 0.894 > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 7 is: 1.002 > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 8 is: 0.689 > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 9 is: 0.806 > Kabsch RMSD of heavy atoms in res. A[4..5],A[14..18],A[28..32],A[38..50],A[53..67],A[70..81],for model 10 is: 0.737 > > Kabsch RMSD statistics for 10 structures: > Mean RMSD using as refer. str. `average' for res.[4..5],[14..18],[28..32],[38..50],[53..67],[70..81], is: 0.792 > Range of RMSD values to reference struct. is 0.656 to 1.002 PdbStat> PdbStat> *END* of program detected, BYE! ...