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 `STR70_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 142 MET ALA ASN ASP THR PRO PHE SER ALA LEU TRP GLN ARG 1 > ReadCoordsPdb(): Counting models in file `STR70_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 STR70_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 44980 ATOM records read from file > ReadCoordsPdb(): --> 44980 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 0.245 0.618 0.292 0.421 ALA A 2 0.352 0.297 ASN A 3 0.550 0.272 0.504 0.774 ASP A 4 0.352 0.397 0.652 0.946 THR A 5 0.296 0.834 0.601 PRO A 6 0.980 0.137 0.904 0.830 PHE A 7 0.423 0.247 0.918 0.641 SER A 8 0.490 0.413 0.460 ALA A 9 0.999 0.999 9 9 LEU A 10 0.999 1.000 0.865 0.866 10 10 TRP A 11 0.998 1.000 0.998 0.988 11 11 GLN A 12 0.999 0.999 0.999 1.000 0.952 12 12 ARG A 13 1.000 1.000 0.803 0.930 1.000 0.999 1.000 13 13 LEU A 14 1.000 1.000 0.988 0.823 14 14 LEU A 15 1.000 1.000 0.991 0.847 15 15 THR A 16 1.000 1.000 1.000 16 16 ARG A 17 0.995 0.880 0.879 0.637 0.566 0.686 1.000 17 GLY A 18 0.870 0.609 TRP A 19 0.611 0.991 0.999 0.972 GLN A 20 0.983 0.996 0.789 0.765 0.807 20 20 PRO A 21 0.998 0.996 0.986 0.971 21 21 VAL A 22 0.998 0.998 1.000 22 22 GLU A 23 0.994 0.999 0.952 0.870 0.886 23 23 ALA A 24 0.998 0.994 24 24 SER A 25 0.997 0.984 0.922 25 25 THR A 26 0.953 0.987 0.770 26 26 VAL A 27 1.000 1.000 0.999 27 27 ASP A 28 1.000 1.000 0.862 0.967 28 28 ASP A 29 1.000 1.000 0.903 0.926 29 29 TRP A 30 1.000 1.000 1.000 1.000 30 30 ILE A 31 1.000 0.999 1.000 1.000 31 31 LYS A 32 1.000 0.999 0.595 0.950 0.934 0.999 32 32 ARG A 33 1.000 1.000 0.999 0.592 0.993 0.995 1.000 33 33 VAL A 34 0.999 1.000 1.000 34 34 GLY A 35 1.000 0.996 35 35 ASP A 36 0.997 0.998 0.999 0.963 36 36 GLY A 37 0.996 0.998 37 37 VAL A 38 1.000 0.999 1.000 38 38 ILE A 39 0.999 1.000 0.999 0.931 39 39 LEU A 40 0.998 0.996 0.999 0.999 40 40 LEU A 41 0.995 0.990 0.993 0.934 41 41 SER A 42 0.973 0.366 0.929 SER A 43 0.369 0.382 0.358 ASP A 44 0.361 0.733 0.749 0.991 PRO A 45 0.985 0.349 0.925 0.888 ARG A 46 0.611 0.303 0.320 0.783 0.503 0.705 1.000 ARG A 47 0.633 0.090 0.518 0.730 0.861 0.785 1.000 THR A 48 0.184 0.688 0.687 PRO A 49 0.993 0.176 0.979 0.968 GLU A 50 0.178 0.187 0.758 0.752 0.963 VAL A 51 0.354 0.374 0.581 SER A 52 0.385 0.216 0.226 ASP A 53 0.658 0.318 0.509 0.785 ASN A 54 0.228 0.886 0.685 0.877 PRO A 55 0.983 0.608 0.910 0.852 VAL A 56 0.811 0.265 0.516 MET A 57 0.304 0.981 0.841 0.569 0.344 ILE A 58 1.000 0.997 0.758 0.622 58 58 ALA A 59 0.999 1.000 59 59 GLU A 60 1.000 1.000 1.000 0.622 0.995 60 60 LEU A 61 1.000 1.000 0.823 0.810 61 61 LEU A 62 0.999 0.998 0.972 0.299 62 62 ARG A 63 0.997 0.991 0.999 0.996 0.669 0.839 1.000 63 63 GLU A 64 0.998 0.998 0.999 0.999 1.000 64 64 PHE A 65 1.000 0.998 0.999 0.895 65 65 PRO A 66 0.999 0.853 0.999 1.000 66 GLN A 67 0.869 0.994 0.695 0.271 0.694 67 PHE A 68 0.965 0.895 0.879 0.997 68 ASP A 69 0.904 0.988 0.999 0.999 69 69 TRP A 70 0.998 0.999 0.998 0.989 70 70 GLN A 71 0.991 0.996 0.925 0.771 0.252 71 71 VAL A 72 0.996 0.999 1.000 72 72 ALA A 73 0.998 0.995 73 73 VAL A 74 1.000 0.992 0.674 74 74 ALA A 75 0.948 0.716 ASP A 76 0.688 0.504 0.570 0.740 LEU A 77 0.628 0.992 0.820 0.866 GLU A 78 1.000 1.000 0.999 0.804 0.939 78 78 GLN A 79 1.000 0.999 0.997 0.583 0.966 79 79 SER A 80 0.999 0.999 0.479 80 80 GLU A 81 1.000 1.000 1.000 0.932 0.999 81 81 ALA A 82 1.000 1.000 82 82 ILE A 83 1.000 1.000 1.000 1.000 83 83 GLY A 84 1.000 1.000 84 84 ASP A 85 1.000 1.000 0.999 0.999 85 85 ARG A 86 0.999 0.999 0.998 0.667 0.866 0.711 1.000 86 86 PHE A 87 0.996 0.997 0.999 0.504 87 87 ASN A 88 0.998 0.995 0.999 0.998 88 88 VAL A 89 0.961 0.348 0.776 ARG A 90 0.048 0.255 0.562 0.744 0.510 0.775 1.000 ARG A 91 0.469 0.415 0.488 0.927 0.711 0.714 1.000 PHE A 92 0.513 0.966 0.075 0.824 PRO A 93 0.996 0.879 0.934 0.860 93 ALA A 94 0.911 0.996 94 94 THR A 95 0.993 0.999 1.000 95 95 LEU A 96 1.000 1.000 0.997 0.999 96 96 VAL A 97 1.000 0.999 1.000 97 97 PHE A 98 0.999 0.999 0.998 0.998 98 98 THR A 99 0.999 0.998 0.999 99 99 ASP A 100 0.998 0.999 0.996 0.946 100 100 GLY A 101 0.997 0.995 101 101 LYS A 102 0.996 0.998 0.914 0.860 0.944 0.998 102 102 LEU A 103 0.998 0.998 1.000 0.999 103 103 ARG A 104 0.992 0.998 0.947 0.841 0.189 0.623 1.000 104 104 GLY A 105 0.989 0.994 105 105 ALA A 106 0.949 0.997 106 106 LEU A 107 0.938 0.744 0.908 0.904 SER A 108 0.683 0.728 0.205 GLY A 109 0.485 0.521 ILE A 110 0.889 0.280 0.498 0.767 HIS A 111 0.570 0.387 0.519 0.290 PRO A 112 0.979 0.352 0.879 0.813 TRP A 113 0.403 0.561 0.959 0.960 ALA A 114 0.458 0.971 GLU A 115 0.983 0.983 0.842 0.527 0.906 115 115 LEU A 116 1.000 0.999 0.995 0.922 116 116 LEU A 117 1.000 1.000 0.713 0.698 117 117 THR A 118 0.999 1.000 1.000 118 118 LEU A 119 1.000 1.000 0.730 0.751 119 119 MET A 120 0.999 0.999 0.447 0.075 0.232 120 120 ARG A 121 0.994 0.999 0.636 0.918 0.922 0.588 1.000 121 121 SER A 122 1.000 1.000 1.000 122 122 ILE A 123 0.999 1.000 1.000 1.000 123 123 VAL A 124 0.981 0.963 0.922 124 124 ASP A 125 0.984 0.971 0.635 0.823 125 125 THR A 126 0.357 0.946 0.857 PRO A 127 0.997 0.207 0.981 0.969 ALA A 128 0.510 0.187 ALA A 129 0.582 0.226 GLN A 130 0.409 0.414 0.501 0.510 0.780 GLU A 131 0.398 0.621 0.473 0.932 0.946 THR A 132 0.540 0.246 0.445 VAL A 133 0.749 0.588 0.708 GLN A 134 0.389 0.616 0.648 0.268 0.804 LEU A 135 0.698 0.547 0.851 0.787 GLU A 136 0.668 0.606 0.649 0.750 0.964 HIS A 137 0.616 0.476 0.446 0.712 HIS A 138 0.545 0.547 0.481 0.442 HIS A 139 0.653 0.609 0.485 0.240 HIS A 140 0.716 0.619 0.423 0.602 HIS A 141 0.830 0.270 0.382 0.449 HIS A 142 0.926 0.625 0.378 Ranges: 7 from: A 9 to A 16 from: A 20 to A 41 from: A 58 to A 65 from: A 69 to A 74 from: A 78 to A 88 from: A 94 to A 106 from: A 115 to A 125 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[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 1 is: 0.507 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 2 is: 0.478 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 3 is: 0.423 (*) > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 4 is: 0.688 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 5 is: 0.554 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 6 is: 0.705 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 7 is: 0.896 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 8 is: 0.919 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 9 is: 0.812 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 10 is: 1.060 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 11 is: 0.686 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 12 is: 0.919 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 13 is: 0.575 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 14 is: 0.763 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 15 is: 0.901 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 16 is: 0.444 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 17 is: 0.489 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 18 is: 0.493 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 19 is: 1.082 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 20 is: 0.838 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..16],[20..41],[58..65],[69..74],[78..88],[94..106],[115..125], is: 0.712 > Range of RMSD values to reference struct. is 0.423 to 1.082 > 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[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 1 is: 0.836 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 2 is: 0.746 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 3 is: 0.708 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 4 is: 1.028 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 5 is: 0.825 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 6 is: 1.027 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 7 is: 1.202 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 8 is: 1.180 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 9 is: 1.139 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 10 is: 1.363 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 11 is: 0.997 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 12 is: 1.122 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 13 is: 0.885 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 14 is: 1.155 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 15 is: 1.128 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 16 is: 0.704 (*) > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 17 is: 0.848 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 18 is: 0.867 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 19 is: 1.420 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..65],A[69..74],A[78..88],A[94..106],A[115..125],for model 20 is: 1.152 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..16],[20..41],[58..65],[69..74],[78..88],[94..106],[115..125], is: 1.017 > Range of RMSD values to reference struct. is 0.704 to 1.420 PdbStat> PdbStat> *END* of program detected, BYE! ...