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 `PSR293_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 125 MET ASN ARG GLN GLN PHE ILE ASP TYR ALA GLN LYS LYS 1 > ReadCoordsPdb(): Counting models in file `PSR293_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(): I'm reading file PSR293_R3Cons_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2071 ATOM records read from file > ReadCoordsPdb(): --> 2071 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2071 (674 C, 1022 H, 185 O, 187 N, 3 S, 0 Q, 0 Metals) > INFO_mol: # residues: 125 (Avg. mol. weight: 118.4) > INFO_mol: # -- M.W. : 14800.6 g/mol. (14.80 kD) Estimated RoG : 13.78 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `PSR293_R3Cons_em_bcr3.pdb' model #1, TOTAL RESIDUES: 125 > INFO_mol: Radius of Gyration : 15.0782 angstroms > INFO_mol: Center of Masses: x_cm(2.738), y_cm(1.557), z_cm(-2.374) > INFO_res: MNRQQFIDYA QKKYDTKPDH PWEKFPDYAV FRHSDNDKWY ALLMDIPAEK > INFO_res: IGINGDKRVD VIDLKVQPEL VGSLRKKPGI YPAYHMNKEH WITVLLNGPL > INFO_res: GAKEIHSLIE DSFQLTRLEH HHHHH > INFO_res: > INFO_res: MET ASN ARG GLN GLN PHE ILE ASP TYR ALA GLN LYS > INFO_res: LYS TYR ASP THR LYS PRO ASP HIS PRO TRP GLU LYS > INFO_res: PHE PRO ASP TYR ALA VAL PHE ARG HIS SER ASP ASN > INFO_res: ASP LYS TRP TYR ALA LEU LEU MET ASP ILE PRO ALA > INFO_res: GLU LYS ILE GLY ILE ASN GLY ASP LYS ARG VAL ASP > INFO_res: VAL ILE ASP LEU LYS VAL GLN PRO GLU LEU VAL GLY > INFO_res: SER LEU ARG LYS LYS PRO GLY ILE TYR PRO ALA TYR > INFO_res: HIS MET ASN LYS GLU HIS TRP ILE THR VAL LEU LEU > INFO_res: ASN GLY PRO LEU GLY ALA LYS GLU ILE HIS SER LEU > INFO_res: ILE GLU ASP SER PHE GLN LEU THR ARG LEU GLU HIS > INFO_res: HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 6 ALA 5 ARG 5 ASN 11 ASP 5 GLN 7 GLU > INFO_res: 6 GLY 11 HIS 9 ILE 11 LEU 12 LYS 3 MET > INFO_res: 4 PHE 8 PRO 4 SER 3 THR 6 TYR 3 TRP > INFO_res: 6 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `temp.mr' opened for reading 0 SANI-RDC constraints read 172 ACO (dihedral) constraints read 1908 NOE-distance constraints (0 Ambiguous NOE/s) read 119 CHEMICAL SHIFT constraints detected -- not worked out 2080 TOTAL constraints read PdbStat> > WRITER: Output file name ?:_ > WRITER: Coords, constraints, aco or sequence file? :_ > WRITER_constr: Output format (congen | discover | impact | disman | diana | xplor | cns | rosetta)? :