Protein.m

Protein data import function. Parses PDB and BMRB data, runs a J-coupling guess, a CSA guess and outputs Spinach data structures. Syntax:

             [sys,inter]=protein(pdb_file,bmrb_file,subset)

Parameters:

       pdb_file - string containing the name of the PDB file

      bmrb_file - string containing the name of the BMRB file

         subset - 'backbone' imports protein backbone up to
                  CB and HB, 'backbone-minimal' only imports
                  the backbone, 'backbone-hsqc' is the same
                  as backbone, but with GLN and ASN side chain
                  amide groups included, 'all' imports every-
                  thing that is assigned in BMRB. If a list of
                  numbers is supplied, spins with those num-
                  bers in the PDB file are imported, but only
                  if they are assigned in the PDB.

Note: unassigned atom coordinates are used internally for the J-coupling prediction procedure, but these atoms are not passed to Spinach.

Note: watch carefully the output of this function, it would inform you if it has to skip an atom or a coupling for any reason.

More information is available in the protein getting started manual.