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 `DRR147D_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP.PDB, 20 MODEL/S TEMP.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 155 MET GLY GLU THR VAL VAL ARG ASP ALA VAL THR ILE GLY 1 > ReadCoordsPdb(): Counting models in file `DRR147D_R3_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 DRR147D_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2439 ATOM records read from file > ReadCoordsPdb(): --> 2439 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2439 (767 C, 1215 H, 221 O, 232 N, 4 S, 0 Q, 0 Metals) > INFO_mol: # residues: 155 (Avg. mol. weight: 111.9) > INFO_mol: # -- M.W. : 17350.4 g/mol. (17.35 kD) Estimated RoG : 14.95 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `DRR147D_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 155 > INFO_mol: Radius of Gyration : 17.8184 angstroms > INFO_mol: Center of Masses: x_cm(2.363), y_cm(3.205), z_cm(-3.089) > INFO_res: MGETVVRDAV TIGKPAEQLY AVWRDLPGLP LLMTHLRSVE VLDDKRSRWT > INFO_res: VEAPAPLGAV SWEAELTADE PGKRIAWRSL PGARIENSGE VLFRPAPGAR > INFO_res: GTEVVVRLTY RPPGGSAGAV IARMFNQEPS QQLRDDLMRF KREQELGLEH > INFO_res: HHHHH > INFO_res: > INFO_res: MET GLY GLU THR VAL VAL ARG ASP ALA VAL THR ILE > INFO_res: GLY LYS PRO ALA GLU GLN LEU TYR ALA VAL TRP ARG > INFO_res: ASP LEU PRO GLY LEU PRO LEU LEU MET THR HIS LEU > INFO_res: ARG SER VAL GLU VAL LEU ASP ASP LYS ARG SER ARG > INFO_res: TRP THR VAL GLU ALA PRO ALA PRO LEU GLY ALA VAL > INFO_res: SER TRP GLU ALA GLU LEU THR ALA ASP GLU PRO GLY > INFO_res: LYS ARG ILE ALA TRP ARG SER LEU PRO GLY ALA ARG > INFO_res: ILE GLU ASN SER GLY GLU VAL LEU PHE ARG PRO ALA > INFO_res: PRO GLY ALA ARG GLY THR GLU VAL VAL VAL ARG LEU > INFO_res: THR TYR ARG PRO PRO GLY GLY SER ALA GLY ALA VAL > INFO_res: ILE ALA ARG MET PHE ASN GLN GLU PRO SER GLN GLN > INFO_res: LEU ARG ASP ASP LEU MET ARG PHE LYS ARG GLU GLN > INFO_res: GLU LEU GLY LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 15 ALA 16 ARG 2 ASN 7 ASP 5 GLN 14 GLU > INFO_res: 13 GLY 7 HIS 4 ILE 16 LEU 4 LYS 4 MET > INFO_res: 3 PHE 12 PRO 7 SER 7 THR 2 TYR 4 TRP > INFO_res: 13 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 656 ACO (dihedral) constraints read 1406 NOE-distance constraints (0 Ambiguous NOE/s) read 2062 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)? :