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 `DHR29B_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 20-OCT-09 2KPU > ReadCoordsPdb(): >> TITLE NMR STRUCTURE OF YBBR FAMILY PROTEIN DHAF_0833 (RESIDUES 32-118) FROM > ReadCoordsPdb(): >> TITLE 2 DESULFITOBACTERIUM HAFNIENSE DCB-2: NORTHEAST STRUCTURAL GENOMICS > ReadCoordsPdb(): >> TITLE 3 CONSORTIUM TARGET DHR29B > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `DHR29B_NMR_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 DHR29B_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1522 ATOM records read from file > ReadCoordsPdb(): --> 1522 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1522 (477 C, 763 H, 148 O, 132 N, 2 S, 0 Q, 0 Metals) > INFO_mol: # residues: 96 (Avg. mol. weight: 112.3) > INFO_mol: # -- M.W. : 10779.0 g/mol. (10.78 kD) Estimated RoG : 12.46 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `DHR29B_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 96 > INFO_mol: Radius of Gyration : 16.9469 angstroms > INFO_mol: Center of Masses: x_cm(0.461), y_cm(0.324), z_cm(0.516) > INFO_res: SSQTLDRDPT LTLSLIAKNT PANSMIMTKL PSVRVKTEGY NPSINVNELF > INFO_res: AYVDLSGSEP GEHDYEVKVE PIPNIKIVEI SPRVVTLQLE HHHHHH > INFO_res: > INFO_res: SER SER GLN THR LEU ASP ARG ASP PRO THR LEU THR > INFO_res: LEU SER LEU ILE ALA LYS ASN THR PRO ALA ASN SER > INFO_res: MET ILE MET THR LYS LEU PRO SER VAL ARG VAL LYS > INFO_res: THR GLU GLY TYR ASN PRO SER ILE ASN VAL ASN GLU > INFO_res: LEU PHE ALA TYR VAL ASP LEU SER GLY SER GLU PRO > INFO_res: GLY GLU HIS ASP TYR GLU VAL LYS VAL GLU PRO ILE > INFO_res: PRO ASN ILE LYS ILE VAL GLU ILE SER PRO ARG VAL > INFO_res: VAL THR LEU GLN LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: > INFO_res: 3 ALA 3 ARG 6 ASN 4 ASP 2 GLN 8 GLU > INFO_res: 3 GLY 7 HIS 7 ILE 9 LEU 5 LYS 2 MET > INFO_res: 1 PHE 8 PRO 9 SER 7 THR 3 TYR 9 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 66 ACO (dihedral) constraints read 841 NOE-distance constraints (0 Ambiguous NOE/s) read 907 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)? :