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 `temp_bcm_111.pdb' opened for reading > ReadCoordsPdb(): >> HEADER TRANSFERASE 14-JUL-10 3NY5 > ReadCoordsPdb(): >> TITLE CRYSTAL STRUCTURE OF THE RBD DOMAIN OF SERINE/THREONINE-PROTEIN KINASE > ReadCoordsPdb(): >> TITLE 2 B-RAF FROM HOMO SAPIENS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM > ReadCoordsPdb(): >> TITLE 3 TARGET HR4694F > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): After scanning there is(are) 1 model(s) > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2574 ATOM records read from file > ReadCoordsPdb(): --> 2574 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2574 (1631 C, 0 H, 441 O, 460 N, 12 S, 0 Q, 30 Metals) > INFO_mol: # residues: 323 (Avg. mol. weight: 109.2) > INFO_mol: # -- M.W. : 35258.1 g/mol. (35.26 kD) Estimated RoG : 19.77 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `temp_bcm_111.pdb' model #1, TOTAL RESIDUES: 323 > INFO_mol: Radius of Gyration : 24.5015 angstroms > INFO_mol: Center of Masses: x_cm(11.400), y_cm(45.084), z_cm(72.648) > INFO_res: HQKPIVRVFL PNKQRTVVPA RCGVTVRDSL KKALRGLIPE CCAVYRIQKK > INFO_res: PIGWDTDISW LTGEELHVEV LENVPLTSHQ KPIVRVFLPN KQRTVVPARC > INFO_res: GVTVRDSLKK ALRGLIPECC AVYRIQEKKP IGWDTDISWL TGEELHVEVL > INFO_res: ENVPLTTHQK PIVRVFLPNK QRTVVPARCG VTVRDSLKKA LRGLIPECCA > INFO_res: VYRIQKKPIG WDTDISWLTG EELHVEVLEN VPLTTHHQKP IVRVFLPNKQ > INFO_res: RTVVPARCGV TVRDSLKKAL RGLIPECCAV YRIKKPIGWD TDISWLTGEE > INFO_res: LHVEVLENVP L > INFO_res: > INFO_res: HIS MSE GLN LYS PRO ILE VAL ARG VAL PHE LEU PRO > INFO_res: ASN LYS GLN ARG THR VAL VAL PRO ALA ARG CYS GLY > INFO_res: VAL THR VAL ARG ASP SER LEU LYS LYS ALA LEU MSE > INFO_res: MSE ARG GLY LEU ILE PRO GLU CYS CYS ALA VAL TYR > INFO_res: ARG ILE GLN LYS LYS PRO ILE GLY TRP ASP THR ASP > INFO_res: ILE SER TRP LEU THR GLY GLU GLU LEU HIS VAL GLU > INFO_res: VAL LEU GLU ASN VAL PRO LEU THR SER HIS MSE GLN > INFO_res: LYS PRO ILE VAL ARG VAL PHE LEU PRO ASN LYS GLN > INFO_res: ARG THR VAL VAL PRO ALA ARG CYS GLY VAL THR VAL > INFO_res: ARG ASP SER LEU LYS LYS ALA LEU MSE MSE ARG GLY > INFO_res: LEU ILE PRO GLU CYS CYS ALA VAL TYR ARG ILE GLN > INFO_res: GLU LYS LYS PRO ILE GLY TRP ASP THR ASP ILE SER > INFO_res: TRP LEU THR GLY GLU GLU LEU HIS VAL GLU VAL LEU > INFO_res: GLU ASN VAL PRO LEU THR THR HIS MSE GLN LYS PRO > INFO_res: ILE VAL ARG VAL PHE LEU PRO ASN LYS GLN ARG THR > INFO_res: VAL VAL PRO ALA ARG CYS GLY VAL THR VAL ARG ASP > INFO_res: SER LEU LYS LYS ALA LEU MSE MSE ARG GLY LEU ILE > INFO_res: PRO GLU CYS CYS ALA VAL TYR ARG ILE GLN LYS LYS > INFO_res: PRO ILE GLY TRP ASP THR ASP ILE SER TRP LEU THR > INFO_res: GLY GLU GLU LEU HIS VAL GLU VAL LEU GLU ASN VAL > INFO_res: PRO LEU THR THR HIS HIS MSE GLN LYS PRO ILE VAL > INFO_res: ARG VAL PHE LEU PRO ASN LYS GLN ARG THR VAL VAL > INFO_res: PRO ALA ARG CYS GLY VAL THR VAL ARG ASP SER LEU > INFO_res: LYS LYS ALA LEU MSE MSE ARG GLY LEU ILE PRO GLU > INFO_res: CYS CYS ALA VAL TYR ARG ILE LYS LYS PRO ILE GLY > INFO_res: TRP ASP THR ASP ILE SER TRP LEU THR GLY GLU GLU > INFO_res: LEU HIS VAL GLU VAL LEU GLU ASN VAL PRO LEU > INFO_res: > INFO_res: 12 ALA 24 ARG 8 ASN 12 ASP 12 CYS 11 GLN > INFO_res: 21 GLU 16 GLY 9 HIS 20 ILE 32 LEU 24 LYS > INFO_res: 4 PHE 24 PRO 9 SER 21 THR 4 TYR 8 TRP > INFO_res: 40 VAL 12 MSE > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** x-mer, 4 [4] chains PdbStat> PdbStat> ** Model with _NO_ hydrogens, nothing to fix PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 N A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 N B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CA A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CA B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 C A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 C B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 O A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 O B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CB A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CB B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CG A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CG B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 SE A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 SE B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CE A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CE B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 N A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 N B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CA A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CA B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 C A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 C B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 O A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 O B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CB A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CB B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CG A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CG B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 SE A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 SE B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CE A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CE B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 N A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 N B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CA A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CA B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 C A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 C B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 O A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 O B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CB A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CB B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CG A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CG B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 SE A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 SE B] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CE A] _not_ in lib, will use as given PdbStat> (ToIUPAC) **WARN** Atom [MSE 186 CE B] _not_ in lib, will use as given PdbStat> > WRITER: Output file name ?:_ > WRITER: Coords, constraints, aco or sequence file? :_ > WRITER: ... backbone, heavy, full set? (back/heavy/all/select): > COORD_writer: Format (pdb/congen/RasMol) ? : > COORD_writer: * ---- Wrong typing BUDDY !! ----- * > COORD_writer: * Option NOT recognized, type again please * > COORD_writer: Format (pdb/congen/RasMol) ? : PdbStat> PdbStat> ** Model with _NO_ hydrogens, nothing to fix PdbStat> (ToPDB) **WARN** Atom [MSE 186 N A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 N B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CA A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CA B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 C A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 C B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 O A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 O B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CB A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CB B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CG A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CG B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 SE A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 SE B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CE A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CE B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 N A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 N B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CA A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CA B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 C A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 C B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 O A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 O B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CB A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CB B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CG A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CG B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 SE A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 SE B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CE A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CE B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 N A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 N B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CA A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CA B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 C A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 C B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 O A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 O B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CB A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CB B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CG A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CG B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 SE A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 SE B] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CE A] _not_ in lib, will use as given PdbStat> (ToPDB) **WARN** Atom [MSE 186 CE B] _not_ in lib, will use as given PdbStat> > WRITER: Output file name ?:_ > WRITER: Coords, constraints, aco or sequence file? :_ > WRITER: ... backbone, heavy, full set? (back/heavy/all/select): > COORD_writer: Format (pdb/congen/RasMol) ? : > COORD_writer: * ---- Wrong typing BUDDY !! ----- * > COORD_writer: * Option NOT recognized, type again please * > COORD_writer: Format (pdb/congen/RasMol) ? : PdbStat> PdbStat> *END* of program detected, BYE! ...