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 `SRR115C_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 99 GLU ASP PRO GLU ASP PRO PHE THR ARG TYR ALA LEU ALA 1 > ReadCoordsPdb(): Counting models in file `SRR115C_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 SRR115C_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 31160 ATOM records read from file > ReadCoordsPdb(): --> 31160 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 ----------------------------------------------------------------------------------- GLU A 1 0.449 0.930 0.792 0.935 ASP A 2 0.960 0.950 0.528 0.983 2 2 PRO A 3 0.986 0.987 0.902 0.818 3 3 GLU A 4 0.978 0.986 0.999 0.713 0.932 4 4 ASP A 5 0.995 0.995 0.934 0.623 5 5 PRO A 6 0.999 0.997 1.000 1.000 6 6 PHE A 7 1.000 1.000 1.000 1.000 7 7 THR A 8 0.999 1.000 1.000 8 8 ARG A 9 1.000 0.999 0.988 0.970 0.794 0.847 0.996 9 9 TYR A 10 0.999 1.000 0.998 0.998 10 10 ALA A 11 1.000 1.000 11 11 LEU A 12 1.000 1.000 1.000 1.000 12 12 ALA A 13 1.000 1.000 13 13 GLN A 14 1.000 1.000 1.000 1.000 0.822 14 14 GLU A 15 1.000 1.000 1.000 1.000 1.000 15 15 HIS A 16 1.000 1.000 1.000 0.999 16 16 LEU A 17 1.000 1.000 1.000 1.000 17 17 LYS A 18 1.000 1.000 1.000 1.000 0.999 1.000 18 18 HIS A 19 0.999 0.998 1.000 1.000 19 19 ASP A 20 0.998 0.983 0.999 0.987 20 20 ASN A 21 0.995 0.998 0.999 0.905 21 21 ALA A 22 1.000 1.000 22 22 SER A 23 1.000 1.000 1.000 23 23 ARG A 24 1.000 1.000 1.000 1.000 1.000 1.000 1.000 24 24 ALA A 25 1.000 1.000 25 25 LEU A 26 1.000 1.000 1.000 1.000 26 26 ALA A 27 1.000 1.000 27 27 LEU A 28 1.000 0.999 1.000 1.000 28 28 PHE A 29 0.999 1.000 0.999 0.300 29 29 GLU A 30 1.000 0.999 1.000 1.000 1.000 30 30 GLU A 31 1.000 1.000 0.895 0.934 0.791 31 31 LEU A 32 1.000 1.000 0.999 1.000 32 32 VAL A 33 1.000 1.000 1.000 33 33 GLU A 34 1.000 1.000 1.000 1.000 0.980 34 34 THR A 35 1.000 1.000 1.000 35 35 ASP A 36 1.000 0.997 1.000 0.999 36 36 PRO A 37 0.998 0.997 0.970 0.938 37 37 ASP A 38 0.990 0.988 0.998 0.958 38 38 TYR A 39 0.994 0.998 0.994 0.797 39 39 VAL A 40 0.998 1.000 1.000 40 40 GLY A 41 1.000 0.999 41 41 THR A 42 1.000 1.000 1.000 42 42 TYR A 43 1.000 1.000 0.998 0.204 43 43 TYR A 44 1.000 1.000 1.000 0.998 44 44 HIS A 45 1.000 1.000 0.999 0.474 45 45 LEU A 46 1.000 1.000 1.000 1.000 46 46 GLY A 47 1.000 1.000 47 47 LYS A 48 1.000 1.000 0.997 0.989 0.756 0.272 48 48 LEU A 49 1.000 1.000 1.000 1.000 49 49 TYR A 50 1.000 1.000 1.000 1.000 50 50 GLU A 51 1.000 1.000 0.999 0.997 0.888 51 51 ARG A 52 1.000 1.000 1.000 1.000 1.000 0.882 1.000 52 52 LEU A 53 0.999 0.999 1.000 1.000 53 53 ASP A 54 1.000 0.998 1.000 1.000 54 54 ARG A 55 0.996 0.980 1.000 0.997 0.999 0.998 0.999 55 55 THR A 56 0.999 0.999 1.000 56 56 ASP A 57 1.000 1.000 0.939 0.955 57 57 ASP A 58 1.000 1.000 1.000 1.000 58 58 ALA A 59 1.000 1.000 59 59 ILE A 60 1.000 1.000 1.000 1.000 60 60 ASP A 61 1.000 1.000 1.000 1.000 61 61 THR A 62 1.000 1.000 1.000 62 62 TYR A 63 1.000 1.000 1.000 0.300 63 63 ALA A 64 1.000 1.000 64 64 GLN A 65 1.000 1.000 1.000 1.000 1.000 65 65 GLY A 66 1.000 1.000 66 66 ILE A 67 1.000 1.000 1.000 1.000 67 67 GLU A 68 1.000 1.000 1.000 1.000 0.940 68 68 VAL A 69 1.000 1.000 1.000 69 69 ALA A 70 1.000 1.000 70 70 ARG A 71 1.000 1.000 1.000 0.999 0.935 0.948 0.999 71 71 GLU A 72 1.000 1.000 1.000 1.000 1.000 72 72 GLU A 73 1.000 1.000 1.000 0.992 0.948 73 73 GLY A 74 1.000 1.000 74 74 THR A 75 0.997 0.999 1.000 75 75 GLN A 76 1.000 1.000 0.999 0.875 0.987 76 76 LYS A 77 1.000 1.000 1.000 1.000 0.997 0.685 77 77 ASP A 78 1.000 1.000 0.999 0.979 78 78 LEU A 79 1.000 1.000 1.000 1.000 79 79 SER A 80 1.000 1.000 0.800 80 80 GLU A 81 1.000 1.000 0.998 0.577 0.926 81 81 LEU A 82 1.000 1.000 1.000 1.000 82 82 GLN A 83 1.000 1.000 1.000 0.997 0.868 83 83 ASP A 84 1.000 1.000 0.838 0.901 84 84 ALA A 85 1.000 1.000 85 85 LYS A 86 1.000 1.000 0.999 0.999 0.999 0.862 86 86 LEU A 87 1.000 1.000 1.000 1.000 87 87 LYS A 88 1.000 0.999 1.000 0.999 0.764 0.935 88 88 ALA A 89 1.000 0.999 89 89 GLU A 90 0.999 0.999 1.000 1.000 0.974 90 90 GLY A 91 0.990 0.981 91 91 LEU A 92 0.983 0.985 0.999 1.000 92 92 GLU A 93 0.929 0.628 0.840 0.568 0.921 HIS A 94 0.560 0.442 0.172 0.473 HIS A 95 0.619 0.659 0.511 0.387 HIS A 96 0.876 0.570 0.403 0.057 HIS A 97 0.532 0.456 0.552 0.323 HIS A 98 0.602 0.363 0.259 0.476 HIS A 99 0.737 0.655 0.718 Ranges: 1 from: A 2 to A 92 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..92],for model 1 is: 0.474 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 2 is: 0.276 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 3 is: 0.277 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 4 is: 0.399 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 5 is: 0.260 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 6 is: 0.301 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 7 is: 0.311 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 8 is: 0.491 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 9 is: 0.228 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 10 is: 0.177 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 11 is: 0.307 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 12 is: 0.219 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 13 is: 0.238 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 14 is: 0.172 (*) > Kabsch RMSD of backbone atoms in res. A[2..92],for model 15 is: 0.358 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 16 is: 0.287 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 17 is: 0.429 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 18 is: 0.342 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 19 is: 0.307 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 20 is: 0.248 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..92], is: 0.305 > Range of RMSD values to reference struct. is 0.172 to 0.491 > 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..92],for model 1 is: 0.659 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 2 is: 0.482 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 3 is: 0.455 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 4 is: 0.510 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 5 is: 0.423 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 6 is: 0.576 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 7 is: 0.523 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 8 is: 0.605 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 9 is: 0.437 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 10 is: 0.356 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 11 is: 0.461 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 12 is: 0.472 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 13 is: 0.383 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 14 is: 0.330 (*) > Kabsch RMSD of heavy atoms in res. A[2..92],for model 15 is: 0.455 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 16 is: 0.406 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 17 is: 0.602 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 18 is: 0.558 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 19 is: 0.484 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 20 is: 0.459 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..92], is: 0.482 > Range of RMSD values to reference struct. is 0.330 to 0.659 PdbStat> PdbStat> *END* of program detected, BYE! ...