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 `HR3102A_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 86 MET GLY HIS HIS HIS HIS HIS HIS SER HIS PRO ASN GLU 1 > ReadCoordsPdb(): Counting models in file `HR3102A_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 HR3102A_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 27280 ATOM records read from file > ReadCoordsPdb(): --> 27280 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 0.339 0.865 0.506 0.325 GLY A 2 0.227 0.505 HIS A 3 0.768 0.478 0.453 0.750 HIS A 4 0.804 0.745 0.552 0.430 HIS A 5 0.850 0.542 0.479 0.629 HIS A 6 0.651 0.462 0.401 0.363 HIS A 7 0.796 0.653 0.423 0.572 HIS A 8 0.807 0.492 0.585 0.787 SER A 9 0.780 0.276 0.581 HIS A 10 0.282 0.804 0.789 0.581 PRO A 11 0.987 0.985 0.901 0.821 11 11 ASN A 12 0.987 0.986 0.590 0.872 12 12 GLU A 13 0.998 0.993 0.929 0.999 0.982 13 13 GLU A 14 0.994 0.998 0.999 0.733 0.971 14 14 ALA A 15 1.000 0.993 15 15 ARG A 16 0.999 0.992 0.078 0.984 0.247 0.316 1.000 16 16 LEU A 17 0.998 0.999 0.999 1.000 17 17 ASP A 18 0.999 0.997 1.000 1.000 18 18 ILE A 19 0.999 1.000 1.000 0.918 19 19 LEU A 20 0.998 0.998 0.811 0.812 20 20 LYS A 21 0.999 0.998 1.000 1.000 0.998 0.999 21 21 ILE A 22 0.998 1.000 1.000 1.000 22 22 HIS A 23 0.995 0.994 0.937 0.918 23 23 SER A 24 0.991 0.993 0.999 24 24 ARG A 25 0.959 0.969 0.426 0.999 0.784 0.737 1.000 25 25 LYS A 26 0.975 0.972 0.999 0.930 1.000 0.999 26 26 MET A 27 0.928 0.984 0.458 0.926 0.199 27 27 ASN A 28 0.986 0.949 0.813 0.919 28 28 LEU A 29 0.979 0.995 0.954 0.507 29 29 THR A 30 0.989 0.969 0.302 30 30 ARG A 31 0.978 0.378 0.701 0.999 0.790 0.996 1.000 GLY A 32 0.320 0.936 ILE A 33 0.915 0.982 0.585 0.999 33 33 ASN A 34 0.951 0.994 0.932 0.981 34 34 LEU A 35 0.994 0.996 0.999 1.000 35 35 ARG A 36 0.995 0.998 0.938 0.931 0.602 0.689 1.000 36 36 LYS A 37 0.998 0.997 0.935 0.930 0.998 0.764 37 37 ILE A 38 0.999 1.000 0.999 0.672 38 38 ALA A 39 1.000 0.998 39 39 GLU A 40 0.996 0.998 1.000 1.000 1.000 40 40 LEU A 41 0.997 0.994 1.000 1.000 41 41 MET A 42 0.981 0.980 0.868 0.998 0.886 42 42 PRO A 43 0.995 0.462 0.949 0.911 GLY A 44 0.421 0.839 ALA A 45 0.814 0.992 45 SER A 46 0.951 0.987 0.924 46 46 GLY A 47 0.999 0.994 47 47 ALA A 48 0.999 0.995 48 48 GLU A 49 0.998 0.999 0.998 0.697 0.747 49 49 VAL A 50 0.999 0.999 1.000 50 50 LYS A 51 0.996 0.995 0.759 1.000 1.000 1.000 51 51 GLY A 52 0.999 0.999 52 52 VAL A 53 1.000 1.000 1.000 53 53 CYS A 54 1.000 1.000 0.999 54 54 THR A 55 1.000 1.000 1.000 55 55 GLU A 56 0.999 0.998 0.999 0.997 0.959 56 56 ALA A 57 0.999 0.999 57 57 GLY A 58 1.000 0.999 58 58 MET A 59 1.000 0.998 0.933 0.839 0.831 59 59 TYR A 60 0.999 0.997 0.938 0.837 60 60 ALA A 61 0.992 0.999 61 61 LEU A 62 1.000 0.997 1.000 1.000 62 62 ARG A 63 0.987 0.986 0.506 0.759 0.928 0.650 1.000 63 63 GLU A 64 0.998 0.996 0.996 0.537 0.872 64 64 ARG A 65 1.000 0.998 1.000 0.999 1.000 1.000 1.000 65 65 ARG A 66 0.985 0.981 0.999 0.997 0.623 0.693 1.000 66 66 VAL A 67 0.991 0.998 1.000 67 67 HIS A 68 0.980 0.968 0.998 0.983 68 68 VAL A 69 0.995 0.997 1.000 69 69 THR A 70 0.996 0.999 0.923 70 70 GLN A 71 0.997 0.993 0.581 0.998 0.801 71 71 GLU A 72 0.996 0.996 0.605 0.999 0.940 72 72 ASP A 73 0.995 0.999 0.999 0.683 73 73 PHE A 74 0.999 0.999 0.997 0.995 74 74 GLU A 75 0.998 0.998 0.670 0.999 1.000 75 75 MET A 76 0.999 0.999 1.000 0.933 1.000 76 76 ALA A 77 1.000 0.999 77 77 VAL A 78 1.000 0.999 1.000 78 78 ALA A 79 0.999 0.991 79 79 LYS A 80 0.989 0.989 0.929 0.859 0.999 0.999 80 80 VAL A 81 0.977 0.986 0.999 81 81 MET A 82 0.986 0.945 0.752 0.686 0.743 82 82 GLN A 83 0.999 0.991 0.999 0.578 0.816 83 83 LYS A 84 0.833 0.701 0.550 0.464 0.996 0.936 ASP A 85 0.549 0.373 0.451 0.911 SER A 86 0.701 1.000 Ranges: 3 from: A 11 to A 30 from: A 33 to A 42 from: A 46 to A 83 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..30],A[33..42],A[46..83],for model 1 is: 0.608 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 2 is: 0.741 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 3 is: 0.394 (*) > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 4 is: 0.545 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 5 is: 0.698 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 6 is: 0.616 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 7 is: 0.545 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 8 is: 0.432 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 9 is: 0.726 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 10 is: 0.534 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 11 is: 0.647 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 12 is: 0.503 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 13 is: 0.570 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 14 is: 0.623 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 15 is: 0.704 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 16 is: 0.554 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 17 is: 0.813 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 18 is: 0.444 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 19 is: 0.518 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 20 is: 0.715 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[11..30],[33..42],[46..83], is: 0.597 > Range of RMSD values to reference struct. is 0.394 to 0.813 > 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..30],A[33..42],A[46..83],for model 1 is: 0.976 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 2 is: 1.202 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 3 is: 0.823 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 4 is: 0.970 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 5 is: 1.207 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 6 is: 0.983 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 7 is: 0.917 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 8 is: 0.770 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 9 is: 1.038 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 10 is: 0.964 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 11 is: 1.146 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 12 is: 0.939 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 13 is: 0.951 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 14 is: 0.922 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 15 is: 1.105 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 16 is: 0.879 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 17 is: 1.237 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 18 is: 0.760 (*) > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 19 is: 0.886 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 20 is: 1.157 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[11..30],[33..42],[46..83], is: 0.992 > Range of RMSD values to reference struct. is 0.760 to 1.237 PdbStat> PdbStat> *END* of program detected, BYE! ...