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 `CSR4_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR 2JR2_R3EM.PDB, 20 MODEL/S 2JR2_R3EM.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 76 MET PRO ILE VAL SER LYS TYR SER ASN GLU ARG VAL GLU > ReadCoordsPdb(): Counting models in file `CSR4_R3_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 CSR4_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2448 ATOM records read from file > ReadCoordsPdb(): --> 2448 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2448 (762 C, 1242 H, 224 O, 214 N, 6 S, 0 Q, 0 Metals) > INFO_mol: # residues: 152 (Avg. mol. weight: 113.0) > INFO_mol: # -- M.W. : 17177.5 g/mol. (17.18 kD) Estimated RoG : 14.84 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `CSR4_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 152 > INFO_mol: Radius of Gyration : 16.1472 angstroms > INFO_mol: Center of Masses: x_cm(-0.662), y_cm(-0.408), z_cm(1.109) > INFO_res: MPIVSKYSNE RVEKIIQDLL DVLVKEEVTP DLALMCLGNA VTNIIAQVPE > INFO_res: SKRVAVVDNF TKALKQSVLE HHHHHHMPIV SKYSNERVEK IIQDLLDVLV > INFO_res: KEEVTPDLAL MCLGNAVTNI IAQVPESKRV AVVDNFTKAL KQSVLEHHHH > INFO_res: HH > INFO_res: > INFO_res: MET PRO ILE VAL SER LYS TYR SER ASN GLU ARG VAL > INFO_res: GLU LYS ILE ILE GLN ASP LEU LEU ASP VAL LEU VAL > INFO_res: LYS GLU GLU VAL THR PRO ASP LEU ALA LEU MET CYS > INFO_res: LEU GLY ASN ALA VAL THR ASN ILE ILE ALA GLN VAL > INFO_res: PRO GLU SER LYS ARG VAL ALA VAL VAL ASP ASN PHE > INFO_res: THR LYS ALA LEU LYS GLN SER VAL LEU GLU HIS HIS > INFO_res: HIS HIS HIS HIS MET PRO ILE VAL SER LYS TYR SER > INFO_res: ASN GLU ARG VAL GLU LYS ILE ILE GLN ASP LEU LEU > INFO_res: ASP VAL LEU VAL LYS GLU GLU VAL THR PRO ASP LEU > INFO_res: ALA LEU MET CYS LEU GLY ASN ALA VAL THR ASN ILE > INFO_res: ILE ALA GLN VAL PRO GLU SER LYS ARG VAL ALA VAL > INFO_res: VAL ASP ASN PHE THR LYS ALA LEU LYS GLN SER VAL > INFO_res: LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 10 ALA 4 ARG 8 ASN 8 ASP 2 CYS 6 GLN > INFO_res: 12 GLU 2 GLY 12 HIS 10 ILE 16 LEU 12 LYS > INFO_res: 4 MET 2 PHE 6 PRO 8 SER 6 THR 2 TYR > INFO_res: 22 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 212 ACO (dihedral) constraints read 1510 NOE-distance constraints (0 Ambiguous NOE/s) read 1722 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)? :