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 `RPR324_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 101 MET THR SER THR PHE ASP ARG VAL ALA THR ILE ILE ALA 1 > ReadCoordsPdb(): Counting models in file `RPR324_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 RPR324_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 31500 ATOM records read from file > ReadCoordsPdb(): --> 31500 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 0.231 0.738 0.527 0.343 THR A 2 0.929 0.974 0.851 2 2 SER A 3 0.975 0.986 0.889 3 3 THR A 4 1.000 0.999 1.000 4 4 PHE A 5 1.000 0.999 0.999 0.999 5 5 ASP A 6 1.000 1.000 0.940 0.931 6 6 ARG A 7 1.000 1.000 0.999 0.929 0.056 0.319 1.000 7 7 VAL A 8 0.999 1.000 1.000 8 8 ALA A 9 1.000 1.000 9 9 THR A 10 0.997 0.994 0.724 10 10 ILE A 11 1.000 0.999 1.000 1.000 11 11 ILE A 12 1.000 1.000 1.000 1.000 12 12 ALA A 13 1.000 1.000 13 13 GLU A 14 1.000 1.000 1.000 1.000 1.000 14 14 THR A 15 1.000 1.000 1.000 15 15 CYS A 16 1.000 0.999 1.000 16 16 ASP A 17 1.000 0.989 0.644 0.854 17 17 ILE A 18 0.988 0.998 1.000 0.919 18 18 PRO A 19 0.996 0.997 0.919 0.836 19 19 ARG A 20 0.999 0.999 0.637 0.282 0.472 0.104 1.000 20 20 GLU A 21 0.999 1.000 1.000 1.000 1.000 21 21 THR A 22 1.000 1.000 1.000 22 22 ILE A 23 0.996 0.998 1.000 1.000 23 23 THR A 24 0.999 1.000 1.000 24 24 PRO A 25 0.998 0.999 0.919 0.818 25 25 GLU A 26 1.000 1.000 0.998 0.748 0.967 26 26 SER A 27 0.999 0.996 0.999 27 27 HIS A 28 0.997 0.999 1.000 0.998 28 28 ALA A 29 1.000 1.000 29 29 ILE A 30 1.000 0.999 1.000 1.000 30 30 ASP A 31 0.997 0.997 0.999 0.981 31 31 ASP A 32 0.996 0.998 0.998 0.952 32 32 LEU A 33 0.998 0.995 1.000 1.000 33 33 GLY A 34 0.996 0.999 34 34 ILE A 35 0.997 0.999 1.000 1.000 35 35 ASP A 36 0.999 0.996 0.787 0.999 36 36 SER A 37 0.999 0.998 0.530 37 37 LEU A 38 0.998 0.999 0.999 1.000 38 38 ASP A 39 1.000 1.000 1.000 1.000 39 39 PHE A 40 0.999 0.999 0.999 0.802 40 40 LEU A 41 0.999 0.999 0.933 0.992 41 41 ASP A 42 1.000 1.000 1.000 1.000 42 42 ILE A 43 1.000 0.999 1.000 1.000 43 43 ALA A 44 0.999 1.000 44 44 PHE A 45 0.999 0.999 0.991 0.788 45 45 ALA A 46 1.000 1.000 46 46 ILE A 47 1.000 1.000 1.000 1.000 47 47 ASP A 48 1.000 1.000 1.000 1.000 48 48 LYS A 49 1.000 0.999 1.000 1.000 1.000 1.000 49 49 ALA A 50 1.000 0.999 50 50 PHE A 51 0.997 1.000 0.999 0.999 51 51 GLY A 52 1.000 1.000 52 52 ILE A 53 1.000 1.000 1.000 1.000 53 53 LYS A 54 0.999 0.999 1.000 1.000 1.000 1.000 54 54 LEU A 55 0.999 0.999 1.000 0.995 55 55 PRO A 56 0.999 0.999 1.000 1.000 56 56 LEU A 57 0.999 1.000 0.999 1.000 57 57 GLU A 58 0.999 1.000 1.000 1.000 1.000 58 58 LYS A 59 0.999 1.000 1.000 0.999 0.999 0.436 59 59 TRP A 60 1.000 1.000 0.999 0.997 60 60 THR A 61 1.000 1.000 1.000 61 61 GLN A 62 1.000 1.000 0.999 1.000 0.998 62 62 GLU A 63 1.000 0.999 1.000 1.000 1.000 63 63 VAL A 64 1.000 1.000 1.000 64 64 ASN A 65 1.000 1.000 1.000 1.000 65 65 ASP A 66 1.000 1.000 0.998 0.966 66 66 GLY A 67 1.000 0.999 67 67 LYS A 68 0.995 0.997 0.999 1.000 1.000 1.000 68 68 ALA A 69 0.998 1.000 69 69 THR A 70 0.999 1.000 0.999 70 70 THR A 71 0.999 1.000 1.000 71 71 GLU A 72 0.999 0.999 1.000 1.000 1.000 72 72 GLN A 73 0.996 0.994 0.575 0.991 0.662 73 73 TYR A 74 0.997 0.948 0.999 0.997 74 74 PHE A 75 0.954 0.999 1.000 0.999 75 75 VAL A 76 0.999 0.999 1.000 76 76 LEU A 77 0.999 0.999 1.000 1.000 77 77 LYS A 78 1.000 1.000 0.999 0.997 0.999 0.928 78 78 ASN A 79 1.000 1.000 1.000 0.999 79 79 LEU A 80 1.000 0.999 0.999 1.000 80 80 ALA A 81 1.000 1.000 81 81 ALA A 82 1.000 0.999 82 82 ARG A 83 1.000 1.000 0.823 0.766 0.465 0.847 1.000 83 83 ILE A 84 1.000 1.000 1.000 1.000 84 84 ASP A 85 1.000 1.000 0.817 0.834 85 85 GLU A 86 1.000 1.000 0.820 0.999 0.999 86 86 LEU A 87 1.000 1.000 1.000 1.000 87 87 VAL A 88 1.000 1.000 1.000 88 88 ALA A 89 1.000 1.000 89 89 ALA A 90 1.000 1.000 90 90 LYS A 91 1.000 1.000 0.999 0.997 0.993 0.579 91 91 GLY A 92 1.000 1.000 92 92 ALA A 93 1.000 1.000 93 93 LEU A 94 0.998 0.995 1.000 1.000 94 94 GLU A 95 0.803 0.392 0.581 0.998 0.980 HIS A 96 0.789 0.724 0.376 0.517 HIS A 97 0.488 0.524 0.564 0.541 HIS A 98 0.577 0.538 0.348 0.377 HIS A 99 0.886 0.656 0.409 0.655 HIS A 100 0.685 0.505 0.631 0.731 HIS A 101 0.716 0.604 0.498 Ranges: 1 from: A 2 to A 94 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[2..94],for model 1 is: 0.360 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 2 is: 0.377 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 3 is: 0.349 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 4 is: 0.465 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 5 is: 0.280 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 6 is: 0.408 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 7 is: 0.268 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 8 is: 0.463 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 9 is: 0.226 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 10 is: 0.312 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 11 is: 0.249 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 12 is: 0.369 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 13 is: 0.434 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 14 is: 0.268 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 15 is: 0.238 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 16 is: 0.202 (*) > Kabsch RMSD of backbone atoms in res. A[2..94],for model 17 is: 0.214 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 18 is: 0.343 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 19 is: 0.219 > Kabsch RMSD of backbone atoms in res. A[2..94],for model 20 is: 0.253 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..94], is: 0.315 > Range of RMSD values to reference struct. is 0.202 to 0.465 > 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[2..94],for model 1 is: 0.514 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 2 is: 0.546 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 3 is: 0.491 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 4 is: 0.634 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 5 is: 0.571 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 6 is: 0.607 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 7 is: 0.432 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 8 is: 0.758 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 9 is: 0.406 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 10 is: 0.555 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 11 is: 0.505 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 12 is: 0.554 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 13 is: 0.556 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 14 is: 0.417 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 15 is: 0.399 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 16 is: 0.389 (*) > Kabsch RMSD of heavy atoms in res. A[2..94],for model 17 is: 0.411 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 18 is: 0.486 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 19 is: 0.484 > Kabsch RMSD of heavy atoms in res. A[2..94],for model 20 is: 0.460 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..94], is: 0.509 > Range of RMSD values to reference struct. is 0.389 to 0.758 PdbStat> PdbStat> *END* of program detected, BYE! ...