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 `UUR17A_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER LIPID BINDING PROTEIN 22-DEC-09 2KRT > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF A CONSERVED HYPOTHETICAL MEMBRANE > ReadCoordsPdb(): >> TITLE 2 LIPOPROTEIN OBTAINED FROM UREAPLASMA PARVUM: NORTHEAST > ReadCoordsPdb(): >> TITLE 3 STRUCTURAL GENOMICS CONSORTIUM TARGET UUR17A (139-239) > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `UUR17A_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 UUR17A_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2013 ATOM records read from file > ReadCoordsPdb(): --> 2013 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2013 (653 C, 997 H, 188 O, 173 N, 2 S, 0 Q, 0 Metals) > INFO_mol: # residues: 121 (Avg. mol. weight: 118.5) > INFO_mol: # -- M.W. : 14343.0 g/mol. (14.34 kD) Estimated RoG : 13.61 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `UUR17A_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 121 > INFO_mol: Radius of Gyration : 17.0403 angstroms > INFO_mol: Center of Masses: x_cm(0.074), y_cm(-1.195), z_cm(-0.132) > INFO_res: MLSQANEDFK KIVNNIRLKD TFDFKLAAFP NQNYDQLLPS QIYKNYYQGI > INFO_res: EIQQHKYQNE LDIKIINFLY PDGDFGSANK NGTLKLSLML TDKKNNQVYY > INFO_res: KLLEVSGFKS NPYLEHHHHH H > INFO_res: > INFO_res: MET LEU SER GLN ALA ASN GLU ASP PHE LYS LYS ILE > INFO_res: VAL ASN ASN ILE ARG LEU LYS ASP THR PHE ASP PHE > INFO_res: LYS LEU ALA ALA PHE PRO ASN GLN ASN TYR ASP GLN > INFO_res: LEU LEU PRO SER GLN ILE TYR LYS ASN TYR TYR GLN > INFO_res: GLY ILE GLU ILE GLN GLN HIS LYS TYR GLN ASN GLU > INFO_res: LEU ASP ILE LYS ILE ILE ASN PHE LEU TYR PRO ASP > INFO_res: GLY ASP PHE GLY SER ALA ASN LYS ASN GLY THR LEU > INFO_res: LYS LEU SER LEU MET LEU THR ASP LYS LYS ASN ASN > INFO_res: GLN VAL TYR TYR LYS LEU LEU GLU VAL SER GLY PHE > INFO_res: LYS SER ASN PRO TYR LEU GLU HIS HIS HIS HIS HIS > INFO_res: HIS > INFO_res: > INFO_res: 4 ALA 1 ARG 13 ASN 8 ASP 9 GLN 5 GLU > INFO_res: 5 GLY 7 HIS 8 ILE 14 LEU 13 LYS 2 MET > INFO_res: 7 PHE 4 PRO 6 SER 3 THR 9 TYR 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 128 ACO (dihedral) constraints read 2310 NOE-distance constraints (0 Ambiguous NOE/s) read 2438 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)? :