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 `CTR148A_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 88 MET THR ASP PHE LEU ALA GLY ILE ARG ILE VAL GLY GLU > ReadCoordsPdb(): Counting models in file `CTR148A_R3Cons_em_bcr3.pdb'; Model: > 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 CTR148A_R3Cons_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2846 ATOM records read from file > ReadCoordsPdb(): --> 2846 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2846 (884 C, 1440 H, 256 O, 256 N, 10 S, 0 Q, 0 Metals) > INFO_mol: # residues: 176 (Avg. mol. weight: 114.0) > INFO_mol: # -- M.W. : 20070.8 g/mol. (20.07 kD) Estimated RoG : 15.69 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `CTR148A_R3Cons_em_bcr3.pdb' model #1, TOTAL RESIDUES: 176 > INFO_mol: Radius of Gyration : 16.8683 angstroms > INFO_mol: Center of Masses: x_cm(-1.762), y_cm(-0.791), z_cm(0.196) > INFO_res: MTDFLAGIRI VGEDKNGMTN QITGVISKFD TNIRTIVLNA KDGIFTCNLM > INFO_res: IFVKNTDKLT TLMDKLRKVQ GVFTVERLSN LEHHHHHHMT DFLAGIRIVG > INFO_res: EDKNGMTNQI TGVISKFDTN IRTIVLNAKD GIFTCNLMIF VKNTDKLTTL > INFO_res: MDKLRKVQGV FTVERLSNLE HHHHHH > INFO_res: > INFO_res: MET THR ASP PHE LEU ALA GLY ILE ARG ILE VAL GLY > INFO_res: GLU ASP LYS ASN GLY MET THR ASN GLN ILE THR GLY > INFO_res: VAL ILE SER LYS PHE ASP THR ASN ILE ARG THR ILE > INFO_res: VAL LEU ASN ALA LYS ASP GLY ILE PHE THR CYS ASN > INFO_res: LEU MET ILE PHE VAL LYS ASN THR ASP LYS LEU THR > INFO_res: THR LEU MET ASP LYS LEU ARG LYS VAL GLN GLY VAL > INFO_res: PHE THR VAL GLU ARG LEU SER ASN LEU GLU HIS HIS > INFO_res: HIS HIS HIS HIS MET THR ASP PHE LEU ALA GLY ILE > INFO_res: ARG ILE VAL GLY GLU ASP LYS ASN GLY MET THR ASN > INFO_res: GLN ILE THR GLY VAL ILE SER LYS PHE ASP THR ASN > INFO_res: ILE ARG THR ILE VAL LEU ASN ALA LYS ASP GLY ILE > INFO_res: PHE THR CYS ASN LEU MET ILE PHE VAL LYS ASN THR > INFO_res: ASP LYS LEU THR THR LEU MET ASP LYS LEU ARG LYS > INFO_res: VAL GLN GLY VAL PHE THR VAL GLU ARG LEU SER ASN > INFO_res: LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 4 ALA 8 ARG 14 ASN 12 ASP 2 CYS 4 GLN > INFO_res: 6 GLU 12 GLY 12 HIS 16 ILE 16 LEU 14 LYS > INFO_res: 8 MET 10 PHE 4 SER 20 THR 14 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** x-mer, 2 [2] chains PdbStat> > locate_file(): file `CTR148A_R3Cons_em_bcr3.upl' opened for reading > CNSTR_rdr: Converting DYANA UPL input file > CNSTR_rdr: 2560 constraints read