Protein.m

Protein data import function.

Syntax

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

Description

This function parses PDB and BMRB data, runs a J-coupling guess using guess_j_pro.m function, then a backbone CSA guess using guess_csa_pro.m function, and outputs sys and inter data structures that are required to run by create.m gateway function in Spinach.

Arguments

           pdb_file - a character string containing the name of the PDB file
   
          bmrb_file - a character string containing the name of the BMRB file
   
     options.select - '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 everything that is assigned in BMRB. If a list of
                      numbers is supplied, spins with those numbers in the PDB file are imported, but only
                      if they are assigned in the PDB.
  
    options.pdb_mol - the number of molecule if there are multiple molecules in the pdb file 
  
    options.noshift - 'keep' places unassigned atoms between -1 and 0 ppm, 'ignore' removes them from the system

Returns

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.