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

The following subfields of sys and inter data structures are set by this function:

    sys.isotopes          - Nspins x 1 cell array of strings

    sys.labels            - Nspins x 1 cell array of strings containing standard IUPAC protein atom labels

    inter.coordinates     - Nspins x 3 matrix, Angstrom.

    inter.zeeman.iso      - Nspins x 1 cell array of numbers, ppm. Isotropic chemical shifts go here.

    inter.zeeman.matrix   - Nspins x 1 cell array of 3x3 matrices, ppm. Chemical shift anisotropies go here.

    inter.coupling.scalar - Nspins x Nspins cell array of scalar couplings, all in Hz.

Notes

1. Unassigned atom coordinates are used internally for the J-coupling prediction procedure even if options.noshift is set to 'ignore'.
2. Watch carefully the output of this function, it would inform you if it sees anything strange in the data supplied. Protein datasets available from major databases are rarely free of errors.
3. More information is available in the protein getting started manual.