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 `HR4435B_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 83 MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET LEU PRO 1 > ReadCoordsPdb(): Counting models in file `HR4435B_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 HR4435B_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1332 ATOM records read from file > ReadCoordsPdb(): --> 1332 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1332 (423 C, 655 H, 121 O, 125 N, 8 S, 0 Q, 0 Metals) > INFO_mol: # residues: 83 (Avg. mol. weight: 116.7) > INFO_mol: # -- M.W. : 9684.0 g/mol. (9.68 kD) Estimated RoG : 11.79 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `HR4435B_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 83 > INFO_mol: Radius of Gyration : 12.4415 angstroms > INFO_mol: Center of Masses: x_cm(2.918), y_cm(1.724), z_cm(-0.205) > INFO_res: MGHHHHHHSH MLPPEQWSHT TVRNALKDLL KDMNQSSLAK ECPLSQSMIS > INFO_res: SIVNSTYYAN VSAAKCQEFG RWYKHFKKTK DMM > INFO_res: > INFO_res: MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET LEU > INFO_res: PRO PRO GLU GLN TRP SER HIS THR THR VAL ARG ASN > INFO_res: ALA LEU LYS ASP LEU LEU LYS ASP MET ASN GLN SER > INFO_res: SER LEU ALA LYS GLU CYS PRO LEU SER GLN SER MET > INFO_res: ILE SER SER ILE VAL ASN SER THR TYR TYR ALA ASN > INFO_res: VAL SER ALA ALA LYS CYS GLN GLU PHE GLY ARG TRP > INFO_res: TYR LYS HIS PHE LYS LYS THR LYS ASP MET MET > INFO_res: > INFO_res: 5 ALA 2 ARG 4 ASN 3 ASP 2 CYS 4 GLN > INFO_res: 3 GLU 2 GLY 9 HIS 2 ILE 6 LEU 8 LYS > INFO_res: 6 MET 2 PHE 3 PRO 10 SER 4 THR 3 TYR > INFO_res: 2 TRP 3 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 90 ACO (dihedral) constraints read 1190 NOE-distance constraints (0 Ambiguous NOE/s) read 1280 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)? :