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 `SR384_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 19 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 18 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 48 MET ILE SER ASN ALA LYS ILE ALA ARG ILE ASN GLU LEU 1 > ReadCoordsPdb(): Counting models in file `SR384_R3Cons_em_bcr3.pdb'; Model: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 > ReadCoordsPdb(): After scanning there is(are) 18 model(s) > ReadCoordsPdb(): what model do you want [(1 to 18) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file SR384_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (18) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 14166 ATOM records read from file > ReadCoordsPdb(): --> 14166 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 0.770 0.839 0.449 0.211 ILE A 2 0.838 0.998 0.995 0.887 2 SER A 3 0.965 0.994 0.937 3 3 ASN A 4 1.000 0.999 1.000 1.000 4 4 ALA A 5 1.000 1.000 5 5 LYS A 6 1.000 1.000 1.000 1.000 0.998 0.919 6 6 ILE A 7 1.000 1.000 1.000 1.000 7 7 ALA A 8 1.000 1.000 8 8 ARG A 9 1.000 1.000 1.000 1.000 1.000 0.996 1.000 9 9 ILE A 10 1.000 1.000 1.000 1.000 10 10 ASN A 11 1.000 1.000 1.000 1.000 11 11 GLU A 12 1.000 1.000 0.998 0.995 0.938 12 12 LEU A 13 1.000 1.000 1.000 1.000 13 13 ALA A 14 1.000 1.000 14 14 ALA A 15 1.000 1.000 15 15 LYS A 16 1.000 0.999 1.000 0.998 1.000 0.994 16 16 ALA A 17 1.000 0.999 17 17 LYS A 18 1.000 1.000 1.000 0.998 0.765 1.000 18 18 ALA A 19 1.000 1.000 19 19 GLY A 20 1.000 1.000 20 20 VAL A 21 1.000 0.987 1.000 21 21 ILE A 22 0.986 1.000 1.000 1.000 22 22 THR A 23 0.999 0.999 0.999 23 23 GLU A 24 1.000 1.000 1.000 0.669 0.934 24 24 GLU A 25 0.999 0.999 0.737 1.000 1.000 25 25 GLU A 26 1.000 1.000 0.999 0.998 0.940 26 26 LYS A 27 1.000 0.999 1.000 1.000 1.000 1.000 27 27 ALA A 28 1.000 1.000 28 28 GLU A 29 1.000 0.999 1.000 0.999 0.876 29 29 GLN A 30 1.000 1.000 1.000 1.000 0.477 30 30 GLN A 31 1.000 1.000 1.000 1.000 1.000 31 31 LYS A 32 0.999 0.999 0.860 1.000 1.000 1.000 32 32 LEU A 33 1.000 1.000 1.000 1.000 33 33 ARG A 34 1.000 1.000 1.000 0.994 0.628 0.778 1.000 34 34 GLN A 35 0.999 0.999 1.000 1.000 1.000 35 35 GLU A 36 0.999 0.999 0.999 0.982 0.751 36 36 TYR A 37 0.999 0.999 1.000 0.999 37 37 LEU A 38 0.995 0.992 1.000 1.000 38 38 LYS A 39 0.721 0.892 0.997 1.000 0.922 1.000 GLY A 40 0.991 0.970 40 40 PHE A 41 0.961 0.535 0.784 0.905 ARG A 42 0.490 0.308 0.910 0.994 0.775 0.937 1.000 SER A 43 0.524 0.479 0.445 SER A 44 0.619 0.516 0.312 MET A 45 0.741 0.525 0.779 0.478 0.458 LYS A 46 0.730 0.620 0.622 0.925 0.999 0.999 LEU A 47 0.679 0.712 0.606 0.777 GLU A 48 0.877 0.583 0.999 1.000 Ranges: 1 from: A 3 to A 38 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[3..38],for model 1 is: 0.121 > Kabsch RMSD of backbone atoms in res. A[3..38],for model 2 is: 0.242 > Kabsch RMSD of backbone atoms in res. A[3..38],for model 3 is: 0.118 > Kabsch RMSD of backbone atoms in res. A[3..38],for model 4 is: 0.138 > Kabsch RMSD of backbone atoms in res. A[3..38],for model 5 is: 0.185 > Kabsch RMSD of backbone atoms in res. A[3..38],for model 6 is: 0.225 > Kabsch RMSD of backbone atoms in res. A[3..38],for model 7 is: 0.136 > Kabsch RMSD of backbone atoms in res. A[3..38],for model 8 is: 0.123 > Kabsch RMSD of backbone atoms in res. A[3..38],for model 9 is: 0.153 > Kabsch RMSD of backbone atoms in res. A[3..38],for model 10 is: 0.272 > Kabsch RMSD of backbone atoms in res. A[3..38],for model 11 is: 0.094 > Kabsch RMSD of backbone atoms in res. A[3..38],for model 12 is: 0.068 (*) > Kabsch RMSD of backbone atoms in res. A[3..38],for model 13 is: 0.100 > Kabsch RMSD of backbone atoms in res. A[3..38],for model 14 is: 0.147 > Kabsch RMSD of backbone atoms in res. A[3..38],for model 15 is: 0.200 > Kabsch RMSD of backbone atoms in res. A[3..38],for model 16 is: 0.105 > Kabsch RMSD of backbone atoms in res. A[3..38],for model 17 is: 0.092 > Kabsch RMSD of backbone atoms in res. A[3..38],for model 18 is: 0.226 > > Kabsch RMSD statistics for 18 structures: > Mean RMSD using as refer. str. `average' for res.[3..38], is: 0.152 > Range of RMSD values to reference struct. is 0.068 to 0.272 > 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[3..38],for model 1 is: 0.476 > Kabsch RMSD of heavy atoms in res. A[3..38],for model 2 is: 0.546 > Kabsch RMSD of heavy atoms in res. A[3..38],for model 3 is: 0.264 > Kabsch RMSD of heavy atoms in res. A[3..38],for model 4 is: 0.309 > Kabsch RMSD of heavy atoms in res. A[3..38],for model 5 is: 0.409 > Kabsch RMSD of heavy atoms in res. A[3..38],for model 6 is: 0.377 > Kabsch RMSD of heavy atoms in res. A[3..38],for model 7 is: 0.536 > Kabsch RMSD of heavy atoms in res. A[3..38],for model 8 is: 0.396 > Kabsch RMSD of heavy atoms in res. A[3..38],for model 9 is: 0.346 > Kabsch RMSD of heavy atoms in res. A[3..38],for model 10 is: 0.722 > Kabsch RMSD of heavy atoms in res. A[3..38],for model 11 is: 0.241 > Kabsch RMSD of heavy atoms in res. A[3..38],for model 12 is: 0.473 > Kabsch RMSD of heavy atoms in res. A[3..38],for model 13 is: 0.238 (*) > Kabsch RMSD of heavy atoms in res. A[3..38],for model 14 is: 0.349 > Kabsch RMSD of heavy atoms in res. A[3..38],for model 15 is: 0.503 > Kabsch RMSD of heavy atoms in res. A[3..38],for model 16 is: 0.304 > Kabsch RMSD of heavy atoms in res. A[3..38],for model 17 is: 0.339 > Kabsch RMSD of heavy atoms in res. A[3..38],for model 18 is: 0.340 > > Kabsch RMSD statistics for 18 structures: > Mean RMSD using as refer. str. `average' for res.[3..38], is: 0.398 > Range of RMSD values to reference struct. is 0.238 to 0.722 PdbStat> PdbStat> *END* of program detected, BYE! ...