Running PDBSTAT from Linux Ayuda is on: /farm/software/PdbStat/PdbStat-5.9 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2013 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.9-exp mar may 14 00:20:00 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 ...) 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 `ZR18_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 19-JUN-03 1PQX > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF STAPHYLOCOCCUS AUREUS PROTEIN > ReadCoordsPdb(): >> TITLE 2 SAV1430. NORTHEAST STRUCUTRAL GENOMICS CONSORTIUM TARGET > ReadCoordsPdb(): >> TITLE 3 ZR18. > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): Counting models in file `ZR18_NMR_em_bcr3.pdb'; Model: > ReadCoordsPdb(): After scanning there is(are) 10 model(s) > ReadCoordsPdb(): what model do you want [(1 to 10) or all] ?_ > ReadCoordsPdb(): I'm reading file ZR18_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1444 ATOM records read from file > ReadCoordsPdb(): --> 1444 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1444 (462 C, 708 H, 146 O, 124 N, 4 S, 0 Q, 0 Metals) > INFO_mol: # residues: 91 (Avg. mol. weight: 115.0) > INFO_mol: # -- M.W. : 10463.5 g/mol. (10.46 kD) Estimated RoG : 12.21 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `ZR18_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 91 > INFO_mol: Radius of Gyration : 13.9331 angstroms > INFO_mol: Center of Masses: x_cm(2.656), y_cm(0.664), z_cm(-0.826) > INFO_res: MKIISISETP NHNTMKITLS ESREGMTSDT YTKVDDSQPA FINDILKVEG > INFO_res: VKSIFHVMDF ISVDKENDAN WETVLPKVEA VFELEHHHHH H > INFO_res: > INFO_res: MET LYS ILE ILE SER ILE SER GLU THR PRO ASN HIS > INFO_res: ASN THR MET LYS ILE THR LEU SER GLU SER ARG GLU > INFO_res: GLY MET THR SER ASP THR TYR THR LYS VAL ASP ASP > INFO_res: SER GLN PRO ALA PHE ILE ASN ASP ILE LEU LYS VAL > INFO_res: GLU GLY VAL LYS SER ILE PHE HIS VAL MET ASP PHE > INFO_res: ILE SER VAL ASP LYS GLU ASN ASP ALA ASN TRP GLU > INFO_res: THR VAL LEU PRO LYS VAL GLU ALA VAL PHE GLU LEU > INFO_res: GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 3 ALA 1 ARG 5 ASN 7 ASP 1 GLN 9 GLU > INFO_res: 2 GLY 8 HIS 8 ILE 4 LEU 7 LYS 4 MET > INFO_res: 4 PHE 3 PRO 8 SER 7 THR 1 TYR 1 TRP > INFO_res: 8 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 179 ACO (dihedral) constraints read 1544 NOE-distance constraints (0 Ambiguous NOE/s) read 1723 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)? :