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 `XCR50_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 09-OCT-04 1XPV > ReadCoordsPdb(): >> TITLE SOLUTION STRUCTURE OF NORTHEAST STRUCTURAL GENOMICS TARGET > ReadCoordsPdb(): >> TITLE 2 PROTEIN XCR50 FROM X. CAMPESTRIS > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): >> COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN XCC2852; > ReadCoordsPdb(): Counting models in file `XCR50_NMR_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 XCR50_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1194 ATOM records read from file > ReadCoordsPdb(): --> 1194 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1194 (388 C, 582 H, 112 O, 108 N, 4 S, 0 Q, 0 Metals) > INFO_mol: # residues: 78 (Avg. mol. weight: 111.3) > INFO_mol: # -- M.W. : 8679.7 g/mol. (8.68 kD) Estimated RoG : 11.52 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `XCR50_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 78 > INFO_mol: Radius of Gyration : 12.1170 angstroms > INFO_mol: Center of Masses: x_cm(-1.011), y_cm(1.725), z_cm(1.102) > INFO_res: MALTLYQRDD CHLCDQAVEA LAQARAGAFF SVFIDDDAAL ESAYGLRVPV > INFO_res: LRDPMGRELD WPFDAPRLRA WLDAAPHA > INFO_res: > INFO_res: MET ALA LEU THR LEU TYR GLN ARG ASP ASP CYS HIS > INFO_res: LEU CYS ASP GLN ALA VAL GLU ALA LEU ALA GLN ALA > INFO_res: ARG ALA GLY ALA PHE PHE SER VAL PHE ILE ASP ASP > INFO_res: ASP ALA ALA LEU GLU SER ALA TYR GLY LEU ARG VAL > INFO_res: PRO VAL LEU ARG ASP PRO MET GLY ARG GLU LEU ASP > INFO_res: TRP PRO PHE ASP ALA PRO ARG LEU ARG ALA TRP LEU > INFO_res: ASP ALA ALA PRO HIS ALA > INFO_res: > INFO_res: 15 ALA 7 ARG 10 ASP 2 CYS 3 GLN 3 GLU > INFO_res: 3 GLY 2 HIS 1 ILE 10 LEU 2 MET 4 PHE > INFO_res: 5 PRO 2 SER 1 THR 2 TYR 2 TRP 4 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `temp.dist' opened for reading > CNSTR_rdr: Converting DYANA UPL input file > CNSTR_rdr: 1565 constraints read