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_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP.PDB, 20 MODEL/S TEMP.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_R3_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_R3_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 0.454 0.803 0.791 0.960 ASP A 2 0.936 0.977 0.623 0.964 2 2 PRO A 3 0.989 0.994 0.935 0.881 3 3 GLU A 4 0.982 0.986 0.999 0.604 0.908 4 4 ASP A 5 0.989 0.992 0.878 0.663 5 5 PRO A 6 0.999 0.998 1.000 1.000 6 6 PHE A 7 0.994 0.992 0.932 0.995 7 7 THR A 8 0.993 0.998 1.000 8 8 ARG A 9 0.999 0.993 0.471 0.987 0.428 0.909 1.000 9 9 TYR A 10 0.999 0.999 0.997 0.999 10 10 ALA A 11 1.000 1.000 11 11 LEU A 12 0.999 0.998 0.646 0.655 12 12 ALA A 13 1.000 1.000 13 13 GLN A 14 1.000 1.000 0.774 0.516 0.716 14 14 GLU A 15 0.999 0.996 0.872 0.847 0.968 15 15 HIS A 16 0.997 0.998 0.999 0.911 16 16 LEU A 17 0.998 0.997 0.653 0.696 17 17 LYS A 18 0.998 0.998 1.000 1.000 0.998 0.999 18 18 HIS A 19 0.999 0.985 1.000 0.920 19 19 ASP A 20 0.999 0.975 0.999 0.984 20 20 ASN A 21 0.994 0.998 1.000 0.988 21 21 ALA A 22 0.998 0.997 22 22 SER A 23 0.998 0.992 0.446 23 23 ARG A 24 0.996 1.000 1.000 1.000 1.000 0.942 1.000 24 24 ALA A 25 1.000 0.998 25 25 LEU A 26 0.999 0.999 0.936 0.878 26 26 ALA A 27 0.999 0.999 27 27 LEU A 28 0.999 0.998 1.000 1.000 28 28 PHE A 29 0.998 0.996 0.999 0.453 29 29 GLU A 30 0.999 0.997 0.766 0.852 0.969 30 30 GLU A 31 0.998 0.998 0.622 0.776 0.916 31 31 LEU A 32 0.998 0.999 0.978 0.360 32 32 VAL A 33 1.000 1.000 1.000 33 33 GLU A 34 0.999 0.998 1.000 1.000 1.000 34 34 THR A 35 0.982 0.978 0.517 35 35 ASP A 36 0.993 0.996 1.000 0.999 36 36 PRO A 37 0.998 0.997 0.983 0.968 37 37 ASP A 38 0.989 0.972 0.998 0.971 38 38 TYR A 39 0.984 0.991 0.996 0.916 39 39 VAL A 40 0.995 0.994 0.473 40 40 GLY A 41 0.999 0.996 41 41 THR A 42 0.998 0.999 1.000 42 42 TYR A 43 0.999 0.999 0.999 0.201 43 43 TYR A 44 0.999 0.999 0.999 0.997 44 44 HIS A 45 0.999 1.000 0.999 0.997 45 45 LEU A 46 0.999 0.999 1.000 1.000 46 46 GLY A 47 0.999 0.995 47 47 LYS A 48 0.999 0.998 0.999 0.867 0.932 0.999 48 48 LEU A 49 0.998 0.998 0.586 0.556 49 49 TYR A 50 0.999 0.996 0.997 0.568 50 50 GLU A 51 0.998 0.995 0.603 0.949 0.791 51 51 ARG A 52 0.996 0.998 0.999 0.949 0.885 0.997 1.000 52 52 LEU A 53 0.990 0.985 1.000 0.999 53 53 ASP A 54 0.998 0.994 1.000 1.000 54 54 ARG A 55 0.992 0.965 1.000 0.618 0.606 0.997 1.000 55 55 THR A 56 0.995 0.987 0.600 56 56 ASP A 57 0.998 0.999 0.859 0.964 57 57 ASP A 58 0.999 0.999 1.000 1.000 58 58 ALA A 59 1.000 0.999 59 59 ILE A 60 0.999 1.000 1.000 1.000 60 60 ASP A 61 0.999 0.999 0.940 0.965 61 61 THR A 62 1.000 0.999 1.000 62 62 TYR A 63 0.999 0.998 0.999 0.210 63 63 ALA A 64 0.999 0.999 64 64 GLN A 65 1.000 0.999 0.827 0.532 0.874 65 65 GLY A 66 0.999 0.999 66 66 ILE A 67 1.000 1.000 1.000 1.000 67 67 GLU A 68 0.997 0.995 0.667 0.243 0.877 68 68 VAL A 69 0.977 0.987 0.762 69 69 ALA A 70 0.999 0.999 70 70 ARG A 71 0.995 0.985 0.692 0.993 0.847 0.579 1.000 71 71 GLU A 72 0.994 0.996 0.994 0.931 0.989 72 72 GLU A 73 0.988 0.998 0.923 0.920 0.959 73 73 GLY A 74 0.999 0.996 74 74 THR A 75 0.997 0.998 1.000 75 75 GLN A 76 0.999 1.000 1.000 1.000 1.000 76 76 LYS A 77 0.999 0.995 0.875 1.000 0.998 0.658 77 77 ASP A 78 0.996 0.997 0.998 0.971 78 78 LEU A 79 0.998 0.998 0.999 1.000 79 79 SER A 80 0.998 0.994 0.295 80 80 GLU A 81 0.999 0.997 0.700 0.210 0.904 81 81 LEU A 82 0.999 0.999 0.996 0.927 82 82 GLN A 83 0.999 0.997 0.626 0.999 0.995 83 83 ASP A 84 0.999 0.998 1.000 1.000 84 84 ALA A 85 1.000 0.999 85 85 LYS A 86 1.000 0.997 0.867 0.999 0.875 0.683 86 86 LEU A 87 0.998 1.000 1.000 1.000 87 87 LYS A 88 0.999 0.999 1.000 1.000 1.000 1.000 88 88 ALA A 89 1.000 1.000 89 89 GLU A 90 0.998 0.998 1.000 0.999 0.948 90 90 GLY A 91 0.983 0.973 91 91 LEU A 92 0.982 0.978 0.930 0.932 92 92 GLU A 93 0.909 0.574 0.544 0.483 0.902 HIS A 94 0.573 0.430 0.260 0.371 HIS A 95 0.595 0.696 0.478 0.287 HIS A 96 0.862 0.545 0.306 0.253 HIS A 97 0.519 0.398 0.462 0.408 HIS A 98 0.588 0.402 0.280 0.441 HIS A 99 0.765 0.615 0.556 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: 0.489 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 2 is: 0.556 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 3 is: 0.400 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 4 is: 0.671 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 5 is: 0.552 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 6 is: 0.512 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 7 is: 0.470 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 8 is: 0.808 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 9 is: 0.321 (*) > Kabsch RMSD of backbone atoms in res. A[2..92],for model 10 is: 0.494 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 11 is: 0.954 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 12 is: 0.343 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 13 is: 0.373 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 14 is: 0.604 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 15 is: 0.809 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 16 is: 0.542 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 17 is: 0.649 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 18 is: 0.498 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 19 is: 0.445 > Kabsch RMSD of backbone atoms in res. A[2..92],for model 20 is: 0.597 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..92], is: 0.554 > Range of RMSD values to reference struct. is 0.321 to 0.954 > 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: 0.798 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 2 is: 0.861 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 3 is: 0.707 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 4 is: 0.893 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 5 is: 0.837 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 6 is: 0.900 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 7 is: 0.740 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 8 is: 1.014 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 9 is: 0.538 (*) > Kabsch RMSD of heavy atoms in res. A[2..92],for model 10 is: 0.757 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 11 is: 1.197 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 12 is: 0.629 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 13 is: 0.639 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 14 is: 0.901 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 15 is: 1.103 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 16 is: 0.828 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 17 is: 1.033 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 18 is: 0.745 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 19 is: 0.693 > Kabsch RMSD of heavy atoms in res. A[2..92],for model 20 is: 1.010 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..92], is: 0.841 > Range of RMSD values to reference struct. is 0.538 to 1.197 PdbStat> PdbStat> *END* of program detected, BYE! ...