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_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 108 MET GLU PHE PRO ASP LEU THR VAL GLU ILE LYS GLY PRO 1 > ReadCoordsPdb(): Counting models in file `PFR193A_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 PFR193A_R3Cons_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 0.308 0.861 0.525 0.341 GLU A 2 0.979 0.993 0.807 0.777 0.907 2 2 PHE A 3 0.997 0.985 0.998 0.699 3 3 PRO A 4 0.998 0.998 0.963 0.927 4 4 ASP A 5 0.997 0.996 1.000 0.995 5 5 LEU A 6 0.997 0.998 0.998 1.000 6 6 THR A 7 1.000 0.999 0.999 7 7 VAL A 8 1.000 1.000 1.000 8 8 GLU A 9 1.000 1.000 0.998 0.998 0.885 9 9 ILE A 10 0.999 0.999 1.000 1.000 10 10 LYS A 11 1.000 0.999 0.768 0.998 1.000 1.000 11 11 GLY A 12 0.998 0.999 12 12 PRO A 13 1.000 0.991 1.000 1.000 13 13 ASP A 14 0.988 0.978 0.507 0.927 14 14 VAL A 15 0.998 1.000 1.000 15 15 VAL A 16 1.000 1.000 1.000 16 16 GLY A 17 1.000 0.999 17 17 VAL A 18 0.999 1.000 1.000 18 18 ASN A 19 1.000 0.999 0.999 0.975 19 19 LYS A 20 0.996 0.991 0.999 1.000 0.999 0.999 20 20 LEU A 21 0.996 1.000 1.000 1.000 21 21 ALA A 22 1.000 1.000 22 22 GLU A 23 0.998 0.999 0.999 0.999 0.705 23 23 TYR A 24 1.000 1.000 1.000 1.000 24 24 GLU A 25 1.000 1.000 1.000 1.000 0.979 25 25 VAL A 26 1.000 1.000 1.000 26 26 HIS A 27 0.999 0.999 0.999 0.999 27 27 VAL A 28 1.000 1.000 1.000 28 28 LYS A 29 1.000 1.000 0.998 0.997 0.983 0.325 29 29 ASN A 30 1.000 0.999 0.995 0.953 30 30 LEU A 31 0.999 0.998 0.999 1.000 31 31 GLY A 32 0.999 0.999 32 32 GLY A 33 1.000 1.000 33 33 ILE A 34 1.000 1.000 0.999 1.000 34 34 GLY A 35 0.999 0.999 35 35 VAL A 36 1.000 1.000 1.000 36 36 PRO A 37 1.000 1.000 1.000 1.000 37 37 SER A 38 1.000 1.000 1.000 38 38 THR A 39 1.000 0.999 1.000 39 39 LYS A 40 1.000 1.000 1.000 0.997 0.998 0.999 40 40 VAL A 41 1.000 1.000 1.000 41 41 ARG A 42 1.000 1.000 0.999 0.959 0.860 0.784 1.000 42 42 VAL A 43 1.000 1.000 1.000 43 43 TYR A 44 1.000 1.000 0.997 0.799 44 44 ILE A 45 1.000 1.000 1.000 1.000 45 45 ASN A 46 1.000 1.000 0.950 0.984 46 46 GLY A 47 1.000 0.999 47 47 THR A 48 1.000 1.000 1.000 48 48 LEU A 49 1.000 1.000 1.000 1.000 49 49 TYR A 50 1.000 1.000 0.998 0.999 50 50 LYS A 51 1.000 1.000 1.000 0.998 1.000 1.000 51 51 ASN A 52 0.999 1.000 1.000 1.000 52 52 TRP A 53 1.000 1.000 0.997 0.999 53 53 THR A 54 0.999 1.000 1.000 54 54 VAL A 55 1.000 1.000 1.000 55 55 SER A 56 1.000 1.000 0.706 56 56 LEU A 57 1.000 1.000 1.000 1.000 57 57 GLY A 58 1.000 0.999 58 58 PRO A 59 0.999 0.999 0.986 0.972 59 59 LYS A 60 0.999 0.999 1.000 1.000 1.000 1.000 60 60 GLU A 61 1.000 1.000 0.998 0.724 0.839 61 61 GLU A 62 1.000 1.000 1.000 1.000 0.923 62 62 LYS A 63 1.000 1.000 0.999 0.787 0.701 0.899 63 63 VAL A 64 1.000 1.000 1.000 64 64 LEU A 65 1.000 1.000 0.999 1.000 65 65 THR A 66 1.000 1.000 1.000 66 66 PHE A 67 1.000 1.000 1.000 1.000 67 67 SER A 68 1.000 0.999 1.000 68 68 TRP A 69 0.998 1.000 0.999 0.984 69 69 THR A 70 1.000 0.999 1.000 70 70 PRO A 71 1.000 0.957 1.000 1.000 71 71 THR A 72 0.965 0.996 1.000 72 72 GLN A 73 0.996 0.999 0.560 0.999 0.949 73 73 GLU A 74 0.997 1.000 0.991 0.478 0.909 74 74 GLY A 75 0.999 1.000 75 75 MET A 76 1.000 1.000 1.000 1.000 1.000 76 76 TYR A 77 1.000 0.999 1.000 0.899 77 77 ARG A 78 1.000 1.000 0.996 0.996 0.521 0.976 1.000 78 78 ILE A 79 1.000 1.000 1.000 1.000 79 79 ASN A 80 1.000 1.000 0.997 0.952 80 80 ALA A 81 1.000 1.000 81 81 THR A 82 1.000 1.000 1.000 82 82 VAL A 83 0.999 1.000 1.000 83 83 ASP A 84 0.998 0.996 0.999 0.982 84 84 GLU A 85 1.000 1.000 0.715 0.832 0.900 85 85 GLU A 86 1.000 0.999 0.999 0.770 0.872 86 86 ASN A 87 0.999 0.997 0.753 0.902 87 87 THR A 88 0.987 0.998 0.999 88 88 VAL A 89 0.990 0.999 0.588 89 89 VAL A 90 1.000 0.999 1.000 90 90 GLU A 91 0.993 0.997 0.998 0.702 0.594 91 91 LEU A 92 0.999 1.000 0.999 1.000 92 92 ASN A 93 0.990 0.976 0.755 0.850 93 93 GLU A 94 0.990 0.995 0.998 0.738 0.982 94 94 ASN A 95 0.998 0.995 1.000 0.986 95 95 ASN A 96 0.999 0.991 0.468 0.930 96 96 ASN A 97 0.981 0.996 0.997 0.850 97 97 VAL A 98 1.000 1.000 1.000 98 98 ALA A 99 1.000 1.000 99 99 THR A 100 1.000 1.000 1.000 100 100 PHE A 101 1.000 1.000 1.000 0.899 101 101 ASP A 102 1.000 1.000 0.770 0.935 102 102 VAL A 103 1.000 1.000 1.000 103 103 SER A 104 1.000 1.000 1.000 104 104 VAL A 105 1.000 1.000 1.000 105 105 VAL A 106 1.000 0.995 1.000 106 106 LEU A 107 0.992 0.937 0.999 1.000 107 107 GLU A 108 0.747 0.772 0.999 0.706 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: 0.219 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 2 is: 0.239 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 3 is: 0.382 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 4 is: 0.207 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 5 is: 0.218 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 6 is: 0.313 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 7 is: 0.467 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 8 is: 0.213 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 9 is: 0.255 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 10 is: 0.281 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 11 is: 0.202 (*) > Kabsch RMSD of backbone atoms in res. A[2..107],for model 12 is: 0.375 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 13 is: 0.212 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 14 is: 0.268 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 15 is: 0.266 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 16 is: 0.262 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 17 is: 0.229 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 18 is: 0.210 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 19 is: 0.237 > Kabsch RMSD of backbone atoms in res. A[2..107],for model 20 is: 0.231 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..107], is: 0.264 > Range of RMSD values to reference struct. is 0.202 to 0.467 > 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: 0.424 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 2 is: 0.554 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 3 is: 0.533 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 4 is: 0.462 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 5 is: 0.402 (*) > Kabsch RMSD of heavy atoms in res. A[2..107],for model 6 is: 0.548 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 7 is: 0.627 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 8 is: 0.410 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 9 is: 0.458 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 10 is: 0.538 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 11 is: 0.436 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 12 is: 0.526 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 13 is: 0.418 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 14 is: 0.437 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 15 is: 0.527 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 16 is: 0.488 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 17 is: 0.453 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 18 is: 0.434 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 19 is: 0.480 > Kabsch RMSD of heavy atoms in res. A[2..107],for model 20 is: 0.442 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[2..107], is: 0.480 > Range of RMSD values to reference struct. is 0.402 to 0.627 PdbStat> PdbStat> *END* of program detected, BYE! ...