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_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER PROTEIN BINDING 18-DEC-09 2KRK > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF 26S PROTEASE REGULATORY SUBUNIT 8 > ReadCoordsPdb(): >> TITLE 2 FROM H.SAPIENS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM > ReadCoordsPdb(): >> TITLE 3 TARGET TARGET HR3102A > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `HR3102A_NMR_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_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 27460 ATOM records read from file > ReadCoordsPdb(): --> 27460 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 0.334 0.123 0.335 0.649 GLY A 2 0.290 0.440 HIS A 3 0.783 0.471 0.569 0.219 HIS A 4 0.827 0.712 0.590 0.144 HIS A 5 0.893 0.539 0.293 0.187 HIS A 6 0.670 0.406 0.164 0.192 HIS A 7 0.809 0.668 0.237 0.054 HIS A 8 0.844 0.533 0.283 0.198 SER A 9 0.770 0.274 0.438 HIS A 10 0.263 0.870 0.140 0.489 PRO A 11 0.983 0.955 0.943 0.896 11 11 ASN A 12 0.989 0.985 0.352 0.656 12 12 GLU A 13 0.998 0.996 0.998 0.906 0.325 13 13 GLU A 14 0.996 0.993 0.662 0.278 0.435 14 14 ALA A 15 0.996 0.999 15 15 ARG A 16 0.998 0.999 0.997 0.995 0.387 0.710 0.999 16 16 LEU A 17 0.997 0.997 0.995 0.999 17 17 ASP A 18 0.999 0.995 0.885 0.696 18 18 ILE A 19 0.998 0.999 0.999 0.999 19 19 LEU A 20 0.997 0.998 0.998 0.855 20 20 LYS A 21 0.999 0.991 0.997 0.992 0.782 0.550 21 21 ILE A 22 0.989 0.995 0.999 1.000 22 22 HIS A 23 0.993 0.983 0.998 0.977 23 23 SER A 24 0.983 0.982 0.845 24 24 ARG A 25 0.991 0.979 0.692 0.838 0.411 0.887 0.999 25 25 LYS A 26 0.983 0.974 0.927 0.405 0.352 0.310 26 26 MET A 27 0.951 0.969 0.999 0.993 0.674 27 27 ASN A 28 0.979 0.951 0.739 0.850 28 28 LEU A 29 0.952 0.978 0.998 0.999 29 29 THR A 30 0.989 0.954 0.998 30 30 ARG A 31 0.980 0.402 0.791 0.127 0.269 0.785 0.999 GLY A 32 0.333 0.933 ILE A 33 0.934 0.974 0.998 1.000 33 33 ASN A 34 0.956 0.993 0.998 0.899 34 34 LEU A 35 0.987 0.995 0.999 1.000 35 35 ARG A 36 0.997 0.997 0.985 0.857 0.645 0.835 0.999 36 36 LYS A 37 0.999 0.998 0.992 0.959 0.701 0.681 37 37 ILE A 38 0.998 0.998 0.999 1.000 38 38 ALA A 39 0.998 0.998 39 39 GLU A 40 0.996 0.993 0.996 0.824 0.177 40 40 LEU A 41 0.997 0.984 0.999 0.999 41 41 MET A 42 0.991 0.987 0.932 0.727 0.378 42 42 PRO A 43 0.990 0.433 0.977 0.954 GLY A 44 0.396 0.743 ALA A 45 0.799 0.945 SER A 46 0.910 0.980 0.368 46 46 GLY A 47 0.997 0.992 47 47 ALA A 48 0.998 0.998 48 48 GLU A 49 0.994 0.995 0.878 0.266 0.173 49 49 VAL A 50 0.999 0.998 0.998 50 50 LYS A 51 0.999 0.997 0.985 0.678 0.312 0.587 51 51 GLY A 52 0.999 0.997 52 52 VAL A 53 0.999 0.998 1.000 53 53 CYS A 54 0.999 0.997 0.312 54 54 THR A 55 0.998 0.999 0.999 55 55 GLU A 56 0.998 0.995 0.992 0.996 0.626 56 56 ALA A 57 0.999 0.999 57 57 GLY A 58 0.999 0.997 58 58 MET A 59 0.998 0.997 0.998 0.942 0.919 59 59 TYR A 60 0.998 0.994 0.987 0.925 60 60 ALA A 61 0.993 0.996 61 61 LEU A 62 0.998 0.994 0.999 1.000 62 62 ARG A 63 0.998 0.995 0.991 0.991 0.204 0.800 0.998 63 63 GLU A 64 0.997 0.995 0.998 0.993 0.858 64 64 ARG A 65 0.999 0.993 0.988 0.408 0.560 0.761 0.998 65 65 ARG A 66 0.982 0.963 0.992 0.999 0.645 0.821 0.998 66 66 VAL A 67 0.984 0.990 0.999 67 67 HIS A 68 0.974 0.975 0.573 0.445 68 68 VAL A 69 0.978 0.993 1.000 69 69 THR A 70 0.994 0.991 0.999 70 70 GLN A 71 0.997 0.998 0.994 0.750 0.724 71 71 GLU A 72 0.998 0.997 0.764 0.857 0.570 72 72 ASP A 73 0.997 0.998 0.998 0.522 73 73 PHE A 74 0.999 0.999 0.998 0.603 74 74 GLU A 75 0.999 0.999 0.999 0.998 0.609 75 75 MET A 76 0.999 0.997 0.999 0.866 0.799 76 76 ALA A 77 0.998 0.997 77 77 VAL A 78 0.999 0.999 0.999 78 78 ALA A 79 0.999 0.994 79 79 LYS A 80 0.993 0.985 0.997 0.617 0.060 0.525 80 80 VAL A 81 0.987 0.995 0.999 81 81 MET A 82 0.992 0.985 0.999 0.711 0.626 82 82 GLN A 83 0.995 0.944 0.998 0.995 0.458 83 83 LYS A 84 0.903 0.740 0.355 0.112 0.396 0.269 ASP A 85 0.479 0.365 0.223 0.435 SER A 86 0.728 0.126 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: 0.479 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 2 is: 0.500 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 3 is: 0.539 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 4 is: 0.431 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 5 is: 0.574 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 6 is: 0.489 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 7 is: 0.500 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 8 is: 0.590 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 9 is: 0.435 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 10 is: 0.562 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 11 is: 0.476 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 12 is: 0.459 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 13 is: 0.406 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 14 is: 0.450 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 15 is: 0.664 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 16 is: 0.453 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 17 is: 0.398 (*) > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 18 is: 0.486 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 19 is: 0.528 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 20 is: 0.548 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[11..30],[33..42],[46..83], is: 0.498 > Range of RMSD values to reference struct. is 0.398 to 0.664 > 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: 0.963 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 2 is: 0.910 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 3 is: 1.074 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 4 is: 0.811 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 5 is: 0.953 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 6 is: 0.839 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 7 is: 0.957 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 8 is: 1.024 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 9 is: 0.850 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 10 is: 0.993 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 11 is: 0.927 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 12 is: 0.891 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 13 is: 0.840 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 14 is: 0.754 (*) > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 15 is: 1.037 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 16 is: 0.821 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 17 is: 0.859 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 18 is: 0.950 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 19 is: 0.919 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 20 is: 0.905 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[11..30],[33..42],[46..83], is: 0.914 > Range of RMSD values to reference struct. is 0.754 to 1.074 PdbStat> PdbStat> *END* of program detected, BYE! ...