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 `temp_bcm_111.pdb' opened for reading > ReadCoordsPdb(): >> MODEL 1 1 > ReadCoordsPdb(): >> REMARK FAMILY or FILE: ./S_2KCZ_pdb_9_1_0008.pdb > ReadCoordsPdb(): >> ATOM 1 N MET A 1 -3.568 0.211 22.628 1.00 0.00 > ReadCoordsPdb(): >> ATOM 2 CA MET A 1 -3.723 1.496 21.907 1.00 0.00 > ReadCoordsPdb(): >> ATOM 3 C MET A 1 -2.711 2.514 22.414 1.00 0.00 > ReadCoordsPdb(): Counting models in file `temp_bcm_111.pdb'; Model: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 > ReadCoordsPdb(): After scanning there is(are) 18 model(s) > ReadCoordsPdb(): what model do you want [(1 to 18) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file temp_bcm_111.pdb > ReadCoordsPdb(): Reading a total of (18) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 43902 ATOM records read from file > ReadCoordsPdb(): --> 43902 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > ReadCoordsPdb(): ** monomer, 1 [1] chains ** PdbStat> PdbStat> > WRITER: Output file name ?:_ > WRITER: Coords, constraints, aco or sequence file? :_ > WRITER: ... backbone, heavy, full set? (back/heavy/all/select): > WRITER: What model ?_ : > WRITER: -- All models to be written > COORD_writer: Format (pdb/congen/RasMol) ? : PdbStat> PdbStat> > WRITER: Output file name ?:_ > WRITER: Coords, constraints, aco or sequence file? :_ > WRITER: ... backbone, heavy, full set? (back/heavy/all/select): > WRITER: What model ?_ : > WRITER: -- All models to be written > COORD_writer: Format (pdb/congen/RasMol) ? : PdbStat> PdbStat> *END* of program detected, BYE! ...