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 `PFR193A_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 108 MET GLU PHE PRO ASP LEU THR VAL GLU ILE LYS GLY PRO 1 > ReadCoordsPdb(): Counting models in file `PFR193A_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 PFR193A_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 33780 ATOM records read from file > ReadCoordsPdb(): --> 33780 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 0.963 0.860 0.770 0.751 GLU A 2 0.988 0.969 0.616 0.938 0.959 2 2 PHE A 3 0.991 0.992 0.998 0.845 3 3 PRO A 4 0.996 0.996 0.955 0.913 4 4 ASP A 5 0.997 0.997 0.999 0.992 5 5 LEU A 6 0.996 0.941 0.999 0.998 6 6 THR A 7 0.911 0.973 0.035 7 7 VAL A 8 0.968 0.996 0.480 8 8 GLU A 9 0.996 0.978 0.215 0.998 0.974 9 9 ILE A 10 0.987 0.997 1.000 1.000 10 10 LYS A 11 0.997 0.999 1.000 1.000 1.000 1.000 11 11 GLY A 12 0.999 0.999 12 12 PRO A 13 0.995 0.990 0.927 0.864 13 13 ASP A 14 0.992 0.971 0.433 0.923 14 14 VAL A 15 0.997 0.996 1.000 15 15 VAL A 16 0.998 0.994 0.849 16 16 GLY A 17 0.997 0.998 17 17 VAL A 18 0.999 0.999 1.000 18 18 ASN A 19 0.999 0.989 0.865 0.941 19 19 LYS A 20 0.997 0.968 0.998 0.865 1.000 0.998 20 20 LEU A 21 0.984 0.969 0.587 0.564 21 21 ALA A 22 0.980 0.974 22 22 GLU A 23 0.984 0.999 1.000 1.000 1.000 23 23 TYR A 24 1.000 0.998 0.999 0.999 24 24 GLU A 25 0.991 0.982 0.780 0.998 0.941 25 25 VAL A 26 0.986 0.996 1.000 26 26 HIS A 27 0.996 0.999 0.923 0.890 27 27 VAL A 28 0.997 0.993 0.613 28 28 LYS A 29 0.987 0.977 0.450 0.981 0.812 0.995 29 29 ASN A 30 0.982 0.998 0.998 0.982 30 30 LEU A 31 0.998 0.997 1.000 1.000 31 31 GLY A 32 0.998 0.998 32 32 GLY A 33 0.996 0.989 33 33 ILE A 34 0.952 0.991 0.604 0.435 34 34 GLY A 35 0.997 0.990 35 35 VAL A 36 0.999 0.998 1.000 36 36 PRO A 37 1.000 0.999 1.000 1.000 37 37 SER A 38 0.983 0.937 0.923 38 38 THR A 39 0.970 0.991 1.000 39 39 LYS A 40 0.983 0.977 1.000 0.998 0.999 0.930 40 40 VAL A 41 0.988 0.997 1.000 41 41 ARG A 42 0.995 0.982 0.999 0.994 0.998 0.871 1.000 42 42 VAL A 43 0.993 0.998 1.000 43 43 TYR A 44 0.997 0.980 0.999 0.799 44 44 ILE A 45 0.989 0.997 1.000 1.000 45 45 ASN A 46 0.999 1.000 0.957 0.985 46 46 GLY A 47 0.998 0.997 47 47 THR A 48 0.995 0.999 1.000 48 48 LEU A 49 1.000 0.999 1.000 0.999 49 49 TYR A 50 0.997 0.997 0.995 0.999 50 50 LYS A 51 0.998 0.992 0.998 0.589 1.000 0.935 51 51 ASN A 52 0.968 0.990 1.000 0.840 52 52 TRP A 53 0.986 0.984 0.740 0.418 53 53 THR A 54 0.990 0.995 1.000 54 54 VAL A 55 0.996 0.985 0.710 55 55 SER A 56 0.993 0.997 0.782 56 56 LEU A 57 0.998 0.991 0.999 1.000 57 57 GLY A 58 0.998 0.998 58 58 PRO A 59 0.999 0.999 0.984 0.969 59 59 LYS A 60 0.999 0.999 0.998 0.592 1.000 0.999 60 60 GLU A 61 0.992 0.990 0.670 0.921 0.975 61 61 GLU A 62 0.988 0.990 0.868 0.998 0.997 62 62 LYS A 63 0.985 0.991 0.931 0.501 0.996 0.923 63 63 VAL A 64 0.992 0.994 0.926 64 64 LEU A 65 0.991 0.965 0.674 0.759 65 65 THR A 66 0.986 0.987 0.646 66 66 PHE A 67 0.996 0.992 0.999 1.000 67 67 SER A 68 0.989 0.965 0.494 68 68 TRP A 69 0.931 0.996 0.998 0.969 69 69 THR A 70 0.997 0.972 0.861 70 70 PRO A 71 0.996 0.993 0.940 0.888 71 71 THR A 72 0.981 0.956 1.000 72 72 GLN A 73 0.971 0.983 0.420 0.869 0.864 73 73 GLU A 74 0.990 0.992 0.930 0.999 0.948 74 74 GLY A 75 0.996 0.997 75 75 MET A 76 0.997 0.998 0.999 1.000 1.000 76 76 TYR A 77 0.999 0.984 1.000 0.900 77 77 ARG A 78 0.993 0.999 0.636 0.998 0.613 0.996 1.000 78 78 ILE A 79 0.997 0.998 1.000 1.000 79 79 ASN A 80 0.996 0.995 0.999 0.998 80 80 ALA A 81 0.997 0.994 81 81 THR A 82 0.990 0.987 0.704 82 82 VAL A 83 0.984 0.997 1.000 83 83 ASP A 84 0.996 0.994 0.999 0.987 84 84 GLU A 85 0.995 0.994 0.800 0.931 0.874 85 85 GLU A 86 0.992 0.986 0.999 0.921 0.890 86 86 ASN A 87 0.998 0.995 0.802 0.932 87 87 THR A 88 0.980 0.998 1.000 88 88 VAL A 89 0.988 0.961 0.616 89 89 VAL A 90 0.987 0.996 1.000 90 90 GLU A 91 0.971 0.983 0.997 0.487 0.605 91 91 LEU A 92 0.980 0.988 0.932 0.933 92 92 ASN A 93 0.972 0.935 0.616 0.890 93 93 GLU A 94 0.944 0.961 0.915 0.877 0.984 94 94 ASN A 95 0.957 0.934 0.998 0.922 95 95 ASN A 96 0.966 0.960 0.801 0.949 96 96 ASN A 97 0.983 0.971 0.233 0.549 97 97 VAL A 98 0.998 0.993 1.000 98 98 ALA A 99 0.990 0.997 99 99 THR A 100 0.997 0.998 1.000 100 100 PHE A 101 0.995 0.999 0.998 0.845 101 101 ASP A 102 0.999 0.984 0.731 0.969 102 102 VAL A 103 0.988 0.998 1.000 103 103 SER A 104 0.996 0.994 1.000 104 104 VAL A 105 0.994 0.999 1.000 105 105 VAL A 106 1.000 0.999 1.000 106 106 LEU A 107 0.996 0.994 1.000 1.000 107 107 GLU A 108 0.787 0.590 1.000 1.000 Ranges: 1 from: A 2 to A 107 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..107],for model 1 is: 0.481 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 2 is: 0.531 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 3 is: 0.455 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 4 is: 0.493 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 5 is: 0.370 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 6 is: 0.361 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 7 is: 0.416 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 8 is: 0.366 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 9 is: 0.265 (*) > Kabsch RMSD of backbone atoms in res. A[2..107],for model 10 is: 0.401 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 11 is: 0.616 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 12 is: 0.408 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 13 is: 0.405 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 14 is: 0.386 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 15 is: 0.439 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 16 is: 0.427 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 17 is: 0.449 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 18 is: 0.453 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 19 is: 0.354 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 20 is: 0.359 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..107], is: 0.422 > Range of RMSD values to reference struct. is 0.265 to 0.616 > 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..107],for model 1 is: 0.730 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 2 is: 0.865 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 3 is: 0.679 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 4 is: 0.765 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 5 is: 0.619 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 6 is: 0.651 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 7 is: 0.850 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 8 is: 0.616 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 9 is: 0.560 (*) > Kabsch RMSD of heavy atoms in res. A[2..107],for model 10 is: 0.674 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 11 is: 0.829 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 12 is: 0.804 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 13 is: 0.813 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 14 is: 0.670 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 15 is: 0.844 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 16 is: 0.695 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 17 is: 0.649 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 18 is: 0.677 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 19 is: 0.636 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 20 is: 0.769 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..107], is: 0.720 > Range of RMSD values to reference struct. is 0.560 to 0.865 PdbStat> PdbStat> *END* of program detected, BYE! ...