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_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER ISOMERASE 16-JAN-08 2JZT > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF Q8ZP25_SALTY FROM SALMONELLA > ReadCoordsPdb(): >> TITLE 2 TYPHIMURIUM. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM > ReadCoordsPdb(): >> TITLE 3 TARGET STR70 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `STR70_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 STR70_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 45120 ATOM records read from file > ReadCoordsPdb(): --> 45120 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 0.323 0.576 0.285 ALA A 2 0.397 0.375 ASN A 3 0.442 0.343 0.195 0.311 ASP A 4 0.394 0.389 0.556 0.442 THR A 5 0.077 0.869 0.495 PRO A 6 0.978 0.293 0.940 0.899 PHE A 7 0.347 0.171 0.349 0.276 SER A 8 0.376 0.472 0.246 ALA A 9 0.994 0.990 9 9 LEU A 10 0.996 0.988 0.532 0.517 10 10 TRP A 11 0.985 0.998 0.998 0.988 11 11 GLN A 12 0.997 0.995 0.935 0.996 0.496 12 12 ARG A 13 0.997 0.997 0.378 0.346 0.405 0.845 0.999 13 13 LEU A 14 0.998 0.996 0.982 0.412 14 14 LEU A 15 0.997 0.994 0.998 1.000 15 15 THR A 16 0.998 0.997 0.866 16 16 ARG A 17 0.996 0.865 0.822 0.949 0.370 0.690 0.998 17 GLY A 18 0.857 0.602 TRP A 19 0.598 0.988 0.998 0.968 GLN A 20 0.990 0.993 0.905 0.868 0.284 20 20 PRO A 21 0.998 0.990 0.962 0.907 21 21 VAL A 22 0.986 0.989 0.999 22 22 GLU A 23 0.986 0.990 0.954 0.973 0.246 23 23 ALA A 24 0.991 0.981 24 24 SER A 25 0.987 0.926 0.293 25 25 THR A 26 0.909 0.977 0.385 26 26 VAL A 27 0.999 0.994 0.998 27 27 ASP A 28 0.996 0.984 0.511 0.513 28 28 ASP A 29 0.997 0.998 0.996 0.609 29 29 TRP A 30 0.998 0.999 0.997 0.999 30 30 ILE A 31 1.000 0.998 0.999 0.999 31 31 LYS A 32 0.996 0.994 0.669 0.355 0.535 0.430 32 32 ARG A 33 0.997 0.999 0.968 0.642 0.816 0.587 0.998 33 33 VAL A 34 0.995 0.998 0.999 34 34 GLY A 35 0.996 0.989 35 35 ASP A 36 0.994 0.981 0.844 0.839 36 36 GLY A 37 0.972 0.996 37 37 VAL A 38 0.999 0.997 0.999 38 38 ILE A 39 0.997 0.997 0.997 0.952 39 39 LEU A 40 0.993 0.995 0.995 0.925 40 40 LEU A 41 0.991 0.980 0.994 0.999 41 41 SER A 42 0.975 0.346 0.731 SER A 43 0.421 0.352 0.456 ASP A 44 0.361 0.724 0.572 0.387 PRO A 45 0.983 0.366 0.962 0.914 ARG A 46 0.590 0.215 0.363 0.740 0.501 0.753 0.999 ARG A 47 0.598 0.101 0.393 0.451 0.468 0.817 0.997 THR A 48 0.119 0.692 0.422 PRO A 49 0.985 0.161 0.961 0.911 GLU A 50 0.217 0.183 0.455 0.460 0.210 VAL A 51 0.328 0.328 0.201 SER A 52 0.372 0.198 0.260 ASP A 53 0.631 0.298 0.119 0.276 ASN A 54 0.287 0.880 0.657 0.394 PRO A 55 0.982 0.692 0.935 0.877 VAL A 56 0.833 0.275 0.286 MET A 57 0.278 0.971 0.503 0.658 0.263 ILE A 58 0.991 0.994 0.909 0.812 58 58 ALA A 59 0.995 0.990 59 59 GLU A 60 0.997 0.999 0.653 0.488 0.229 60 60 LEU A 61 0.995 0.997 0.961 0.776 61 61 LEU A 62 0.996 0.988 0.648 0.047 62 62 ARG A 63 0.996 0.984 0.456 0.926 0.467 0.757 0.998 63 63 GLU A 64 0.997 0.991 0.629 0.370 0.371 64 64 PHE A 65 0.996 0.987 0.994 0.989 65 65 PRO A 66 0.998 0.949 0.971 0.938 66 66 GLN A 67 0.939 0.985 0.843 0.425 0.326 67 67 PHE A 68 0.964 0.890 0.937 0.807 68 ASP A 69 0.885 0.988 0.991 0.832 69 TRP A 70 0.991 0.995 0.995 0.980 70 70 GLN A 71 0.981 0.980 0.976 0.491 0.310 71 71 VAL A 72 0.991 0.994 1.000 72 72 ALA A 73 0.994 0.994 73 73 VAL A 74 0.995 0.978 0.943 74 74 ALA A 75 0.944 0.702 ASP A 76 0.701 0.516 0.446 0.811 LEU A 77 0.633 0.964 0.691 0.669 GLU A 78 0.991 0.991 0.693 0.351 0.484 78 78 GLN A 79 0.995 0.992 0.813 0.313 0.370 79 79 SER A 80 0.996 0.994 0.688 80 80 GLU A 81 0.997 0.997 0.989 0.475 0.348 81 81 ALA A 82 0.996 0.996 82 82 ILE A 83 0.999 0.996 0.999 0.999 83 83 GLY A 84 0.999 0.995 84 84 ASP A 85 0.995 0.996 0.994 0.423 85 85 ARG A 86 0.998 0.998 0.990 0.634 0.920 0.857 0.998 86 86 PHE A 87 0.991 0.996 0.998 0.981 87 87 ASN A 88 0.997 0.978 0.993 0.749 88 88 VAL A 89 0.948 0.317 0.620 ARG A 90 0.034 0.259 0.320 0.389 0.282 0.660 0.997 ARG A 91 0.457 0.371 0.570 0.588 0.195 0.765 0.999 PHE A 92 0.469 0.961 0.514 0.698 PRO A 93 0.994 0.876 0.957 0.873 93 ALA A 94 0.903 0.983 94 94 THR A 95 0.983 0.997 0.999 95 95 LEU A 96 1.000 1.000 0.999 0.999 96 96 VAL A 97 0.999 0.996 1.000 97 97 PHE A 98 0.996 0.996 0.999 0.900 98 98 THR A 99 0.995 0.990 0.839 99 99 ASP A 100 0.998 0.998 0.410 0.542 100 100 GLY A 101 0.988 0.983 101 101 LYS A 102 0.983 0.986 0.707 0.642 0.679 0.101 102 102 LEU A 103 0.995 0.989 0.999 0.999 103 103 ARG A 104 0.987 0.992 0.934 0.831 0.073 0.772 0.997 104 104 GLY A 105 0.977 0.990 105 105 ALA A 106 0.973 0.985 106 106 LEU A 107 0.962 0.766 0.889 0.851 SER A 108 0.738 0.738 0.534 GLY A 109 0.481 0.641 ILE A 110 0.886 0.275 0.353 0.616 HIS A 111 0.613 0.402 0.673 0.370 PRO A 112 0.988 0.327 0.936 0.857 TRP A 113 0.401 0.542 0.972 0.972 ALA A 114 0.449 0.949 GLU A 115 0.982 0.992 0.639 0.482 0.234 115 115 LEU A 116 0.998 0.998 0.957 0.995 116 116 LEU A 117 0.998 0.993 0.985 0.504 117 117 THR A 118 0.986 0.997 0.997 118 118 LEU A 119 0.997 0.999 0.825 0.921 119 119 MET A 120 0.996 0.994 0.476 0.484 0.789 120 120 ARG A 121 0.997 0.998 0.830 0.847 0.985 0.729 0.999 121 121 SER A 122 0.996 0.999 0.665 122 122 ILE A 123 0.990 0.998 0.998 0.650 123 123 VAL A 124 0.990 0.972 0.999 124 124 ASP A 125 0.989 0.957 0.993 0.890 125 125 THR A 126 0.290 0.917 0.384 PRO A 127 0.992 0.170 0.946 0.877 ALA A 128 0.501 0.191 ALA A 129 0.579 0.258 GLN A 130 0.391 0.334 0.295 0.441 0.124 GLU A 131 0.378 0.640 0.550 0.474 0.276 THR A 132 0.525 0.318 0.306 VAL A 133 0.702 0.544 0.275 GLN A 134 0.366 0.588 0.298 0.449 0.429 LEU A 135 0.656 0.631 0.420 0.250 GLU A 136 0.689 0.582 0.378 0.498 0.355 HIS A 137 0.591 0.457 0.547 0.271 HIS A 138 0.563 0.566 0.481 0.283 HIS A 139 0.660 0.634 0.349 0.324 HIS A 140 0.742 0.590 0.429 0.303 HIS A 141 0.837 0.272 0.554 0.282 HIS A 142 0.850 0.325 0.267 Ranges: 7 from: A 9 to A 16 from: A 20 to A 41 from: A 58 to A 67 from: A 70 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..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 1 is: 0.886 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 2 is: 0.590 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 3 is: 0.658 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 4 is: 0.827 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 5 is: 0.710 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 6 is: 0.684 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 7 is: 0.423 (*) > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 8 is: 0.581 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 9 is: 0.714 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 10 is: 0.734 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 11 is: 0.919 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 12 is: 0.630 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 13 is: 0.720 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 14 is: 0.750 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 15 is: 0.841 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 16 is: 0.920 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 17 is: 0.778 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 18 is: 0.701 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 19 is: 0.788 > Kabsch RMSD of backbone atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 20 is: 0.722 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..16],[20..41],[58..67],[70..74],[78..88],[94..106],[115..125], is: 0.729 > Range of RMSD values to reference struct. is 0.423 to 0.920 > 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..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 1 is: 1.212 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 2 is: 1.045 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 3 is: 1.149 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 4 is: 1.216 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 5 is: 1.082 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 6 is: 1.011 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 7 is: 1.000 (*) > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 8 is: 1.032 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 9 is: 1.142 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 10 is: 1.241 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 11 is: 1.257 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 12 is: 1.059 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 13 is: 1.150 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 14 is: 1.116 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 15 is: 1.122 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 16 is: 1.330 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 17 is: 1.206 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 18 is: 1.096 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 19 is: 1.161 > Kabsch RMSD of heavy atoms in res. A[9..16],A[20..41],A[58..67],A[70..74],A[78..88],A[94..106],A[115..125],for model 20 is: 1.179 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[9..16],[20..41],[58..67],[70..74],[78..88],[94..106],[115..125], is: 1.140 > Range of RMSD values to reference struct. is 1.000 to 1.330 PdbStat> PdbStat> *END* of program detected, BYE! ...