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 `CCR55_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS 05-JUN-07 2JQN > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF CC0527 FROM CAULOBACTER > ReadCoordsPdb(): >> TITLE 2 CRESCENTUS. NORTHEAST STRUCTURAL GENOMICS TARGET CCR55 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): >> COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN; 1 > ReadCoordsPdb(): Counting models in file `CCR55_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 CCR55_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 35480 ATOM records read from file > ReadCoordsPdb(): --> 35480 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 0.228 0.507 0.620 0.703 THR A 2 0.558 0.617 0.356 LEU A 3 0.945 0.968 0.859 0.661 3 3 ILE A 4 0.986 0.995 0.893 0.942 4 4 TYR A 5 0.991 0.968 0.993 0.623 5 5 LYS A 6 0.954 0.991 0.993 0.869 0.578 0.127 6 6 ILE A 7 0.997 0.994 0.955 0.688 7 7 LEU A 8 0.984 0.995 0.908 0.915 8 8 SER A 9 0.996 0.998 0.275 9 9 ARG A 10 0.999 0.990 0.914 0.613 0.827 0.762 0.999 10 10 ALA A 11 0.997 0.986 11 11 GLU A 12 0.987 0.994 0.622 0.510 0.372 12 12 TRP A 13 0.998 0.989 0.998 0.995 13 13 ASP A 14 0.999 0.990 0.767 0.433 14 14 ALA A 15 0.998 0.992 15 15 ALA A 16 0.997 0.993 16 16 LYS A 17 0.997 0.994 0.536 0.988 0.269 0.360 17 17 ALA A 18 0.995 0.992 18 18 GLN A 19 0.983 0.981 0.627 0.712 0.396 19 19 GLY A 20 0.991 0.981 20 20 ARG A 21 0.972 0.962 0.142 0.991 0.470 0.600 0.998 21 21 PHE A 22 0.946 0.917 0.908 0.908 22 22 GLU A 23 0.741 0.164 0.507 0.509 0.314 GLY A 24 0.373 0.536 SER A 25 0.762 0.986 0.195 ALA A 26 0.998 0.988 26 26 VAL A 27 0.994 0.990 0.721 27 27 ASP A 28 0.996 0.992 0.683 0.402 28 28 LEU A 29 0.996 0.994 0.772 0.100 29 29 ALA A 30 0.995 0.988 30 30 ASP A 31 0.991 0.988 0.391 0.451 31 31 GLY A 32 0.892 0.802 32 PHE A 33 0.674 0.939 0.592 0.194 ILE A 34 0.987 0.900 0.999 0.999 34 34 HIS A 35 0.843 0.958 0.571 0.313 35 LEU A 36 0.946 0.495 0.996 0.678 SER A 37 0.453 0.936 0.569 ALA A 38 0.952 0.869 38 GLY A 39 0.658 0.903 GLU A 40 0.995 0.981 0.293 0.492 0.405 40 40 GLN A 41 0.994 0.989 0.665 0.820 0.060 41 41 ALA A 42 0.997 0.997 42 42 GLN A 43 0.998 0.995 0.980 0.446 0.361 43 43 GLU A 44 0.998 0.991 0.598 0.452 0.573 44 44 THR A 45 0.996 0.998 0.999 45 45 ALA A 46 0.999 0.991 46 46 ALA A 47 0.986 0.990 47 47 LYS A 48 0.990 0.988 0.808 0.586 0.916 0.201 48 48 TRP A 49 0.972 0.969 0.998 0.922 49 49 PHE A 50 0.961 0.818 0.996 0.894 50 ARG A 51 0.864 0.271 0.275 0.647 0.388 0.709 0.999 GLY A 52 0.513 0.812 GLN A 53 0.836 0.719 0.922 0.655 0.532 ALA A 54 0.767 0.421 ASN A 55 0.285 0.895 0.681 0.198 LEU A 56 0.966 0.937 0.892 0.883 56 56 VAL A 57 0.953 0.984 0.999 57 57 LEU A 58 0.983 0.990 0.991 0.728 58 58 LEU A 59 0.992 0.983 0.999 1.000 59 59 ALA A 60 0.978 0.986 60 60 VAL A 61 0.988 0.991 0.999 61 61 GLU A 62 0.994 0.941 0.485 0.607 0.204 62 62 ALA A 63 0.901 0.693 GLU A 64 0.376 0.151 0.716 0.091 0.425 PRO A 65 0.984 0.529 0.915 0.842 LEU A 66 0.573 0.734 0.254 0.616 GLY A 67 0.170 0.411 GLU A 68 0.687 0.930 0.107 0.616 0.290 ASP A 69 0.972 0.915 0.662 0.328 69 69 LEU A 70 0.950 0.936 0.931 0.938 70 70 LYS A 71 0.945 0.978 0.807 0.766 0.281 0.368 71 71 TRP A 72 0.996 0.964 0.995 0.993 72 72 GLU A 73 0.908 0.964 0.643 0.493 0.369 73 73 ALA A 74 0.918 0.825 74 SER A 75 0.826 0.312 0.134 ARG A 76 0.317 0.226 0.495 0.626 0.088 0.639 0.999 GLY A 77 0.342 0.477 GLY A 78 0.408 0.345 ALA A 79 0.419 0.881 ARG A 80 0.947 0.960 0.844 0.815 0.154 0.794 0.999 80 80 PHE A 81 0.962 0.986 0.996 0.414 81 81 PRO A 82 0.997 0.980 0.955 0.897 82 82 HIS A 83 0.981 0.972 0.995 0.834 83 83 LEU A 84 0.983 0.981 0.862 0.668 84 84 TYR A 85 0.976 0.932 0.935 0.264 85 85 ARG A 86 0.933 0.990 0.400 0.570 0.087 0.722 0.997 86 86 PRO A 87 0.992 0.975 0.934 0.861 87 87 LEU A 88 0.981 0.971 0.933 0.681 88 88 LEU A 89 0.986 0.987 0.988 0.734 89 89 VAL A 90 0.930 0.963 0.634 90 90 SER A 91 0.920 0.979 0.135 91 91 GLU A 92 0.899 0.975 0.721 0.456 0.360 92 VAL A 93 0.994 0.969 0.996 93 93 THR A 94 0.987 0.989 0.803 94 94 ARG A 95 0.971 0.993 0.411 0.621 0.145 0.529 0.999 95 95 GLU A 96 0.959 0.885 0.790 0.832 0.291 96 ALA A 97 0.831 0.922 97 ASP A 98 0.989 0.956 0.159 0.358 98 98 LEU A 99 0.790 0.919 0.095 0.392 ASP A 100 0.948 0.657 0.265 0.278 LEU A 101 0.614 0.919 0.741 0.845 ASP A 102 0.893 0.979 0.413 0.405 102 ALA A 103 0.524 0.766 ASP A 104 0.861 0.968 0.501 0.459 104 GLY A 105 0.788 0.897 VAL A 106 0.714 0.776 0.983 PRO A 107 0.970 0.754 0.911 0.848 GLN A 108 0.889 0.867 0.561 0.332 0.510 108 LEU A 109 0.969 0.969 0.650 0.996 109 109 GLY A 110 0.997 0.986 110 110 ASP A 111 0.982 0.988 0.340 0.282 111 111 HIS A 112 0.984 0.986 0.632 0.438 112 112 LEU A 113 0.976 0.729 0.998 0.998 ALA A 114 0.397 0.317 LEU A 115 0.506 0.379 0.534 0.409 GLU A 116 0.611 0.415 0.468 0.289 Ranges: 8 from: A 3 to A 22 from: A 26 to A 31 from: A 40 to A 49 from: A 56 to A 62 from: A 69 to A 73 from: A 80 to A 91 from: A 93 to A 95 from: A 109 to A 112 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[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 1 is: 1.058 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 2 is: 0.639 (*) > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 3 is: 0.808 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 4 is: 0.864 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 5 is: 0.775 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 6 is: 0.795 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 7 is: 0.683 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 8 is: 1.110 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 9 is: 0.908 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 10 is: 0.645 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 11 is: 0.872 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 12 is: 1.091 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 13 is: 0.660 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 14 is: 0.863 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 15 is: 0.890 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 16 is: 1.260 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 17 is: 0.703 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 18 is: 0.887 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 19 is: 1.015 > Kabsch RMSD of backbone atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 20 is: 0.820 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[3..22],[26..31],[40..49],[56..62],[69..73],[80..91],[93..95],[109..112], is: 0.867 > Range of RMSD values to reference struct. is 0.639 to 1.260 > 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[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 1 is: 1.361 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 2 is: 1.000 (*) > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 3 is: 1.178 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 4 is: 1.227 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 5 is: 1.189 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 6 is: 1.189 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 7 is: 1.087 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 8 is: 1.450 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 9 is: 1.260 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 10 is: 1.099 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 11 is: 1.389 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 12 is: 1.471 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 13 is: 1.200 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 14 is: 1.309 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 15 is: 1.260 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 16 is: 1.625 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 17 is: 1.207 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 18 is: 1.397 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 19 is: 1.478 > Kabsch RMSD of heavy atoms in res. A[3..22],A[26..31],A[40..49],A[56..62],A[69..73],A[80..91],A[93..95],A[109..112],for model 20 is: 1.333 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[3..22],[26..31],[40..49],[56..62],[69..73],[80..91],[93..95],[109..112], is: 1.285 > Range of RMSD values to reference struct. is 1.000 to 1.625 PdbStat> PdbStat> *END* of program detected, BYE! ...