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 `SOR77_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 80 MET ALA ILE GLN SER LYS TYR SER ASN THR GLN VAL GLU > ReadCoordsPdb(): Counting models in file `SOR77_R3Cons_em_bcr3.pdb'; Model: > ReadCoordsPdb(): After scanning there is(are) 18 model(s) > ReadCoordsPdb(): what model do you want [(1 to 18) or all] ?_ > ReadCoordsPdb(): I'm reading file SOR77_R3Cons_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2526 ATOM records read from file > ReadCoordsPdb(): --> 2526 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2526 (782 C, 1272 H, 234 O, 232 N, 6 S, 0 Q, 0 Metals) > INFO_mol: # residues: 160 (Avg. mol. weight: 111.6) > INFO_mol: # -- M.W. : 17860.1 g/mol. (17.86 kD) Estimated RoG : 15.14 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `SOR77_R3Cons_em_bcr3.pdb' model #1, TOTAL RESIDUES: 160 > INFO_mol: Radius of Gyration : 16.7866 angstroms > INFO_mol: Center of Masses: x_cm(0.142), y_cm(0.130), z_cm(0.233) > INFO_res: MAIQSKYSNT QVESLIAEIL VVLEKHKAPT DLSLMALGNC VTHLLERKVP > INFO_res: SESRQAVAEQ FAKALAQSVK SNLEHHHHHH MAIQSKYSNT QVESLIAEIL > INFO_res: VVLEKHKAPT DLSLMALGNC VTHLLERKVP SESRQAVAEQ FAKALAQSVK > INFO_res: SNLEHHHHHH > INFO_res: > INFO_res: MET ALA ILE GLN SER LYS TYR SER ASN THR GLN VAL > INFO_res: GLU SER LEU ILE ALA GLU ILE LEU VAL VAL LEU GLU > INFO_res: LYS HIS LYS ALA PRO THR ASP LEU SER LEU MET ALA > INFO_res: LEU GLY ASN CYS VAL THR HIS LEU LEU GLU ARG LYS > INFO_res: VAL PRO SER GLU SER ARG GLN ALA VAL ALA GLU GLN > INFO_res: PHE ALA LYS ALA LEU ALA GLN SER VAL LYS SER ASN > INFO_res: LEU GLU HIS HIS HIS HIS HIS HIS MET ALA ILE GLN > INFO_res: SER LYS TYR SER ASN THR GLN VAL GLU SER LEU ILE > INFO_res: ALA GLU ILE LEU VAL VAL LEU GLU LYS HIS LYS ALA > INFO_res: PRO THR ASP LEU SER LEU MET ALA LEU GLY ASN CYS > INFO_res: VAL THR HIS LEU LEU GLU ARG LYS VAL PRO SER GLU > INFO_res: SER ARG GLN ALA VAL ALA GLU GLN PHE ALA LYS ALA > INFO_res: LEU ALA GLN SER VAL LYS SER ASN LEU GLU HIS HIS > INFO_res: HIS HIS HIS HIS > INFO_res: > INFO_res: 18 ALA 4 ARG 6 ASN 2 ASP 2 CYS 10 GLN > INFO_res: 14 GLU 2 GLY 16 HIS 6 ILE 20 LEU 12 LYS > INFO_res: 4 MET 2 PHE 4 PRO 16 SER 6 THR 2 TYR > INFO_res: 14 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** x-mer, 2 [2] chains PdbStat> > locate_file(): file `temp.mr' opened for reading 0 SANI-RDC constraints read 251 ACO (dihedral) constraints read 1484 NOE-distance constraints (0 Ambiguous NOE/s) read 1735 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)? :