protein.m

Protein data import function. Parses PDB and BMRB data, runs a J-coupl- ing guess, a CSA guess and outputs Spinach data structures.

Syntax

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

Arguments

pdb_file   - string containing the name of the PDB file

      bmrb_file   - 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 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.

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, 'delete' removes them from the system

options.deuterate - a cell array of character strings, replaces
                    protons with the specified PDB identifiers
                    with deuterons; 'non-Me' deuterates every-
                    thing except methyl groups

options.nh_csa    - peptide bond CSAs differ across literature,
                    the following options are available:

         'bax' for H:[6.00 0.00 -6.00], N:[-108.0 62.0 46.0] ppm
         'tcb' for H:[7.00 0.00 -7.00], N:[-125.0 45.0 80.0] ppm
         'pol' for H:[6.66 0.66 -7.33], N:[ -92.4 34.7 57.7] ppm

                    the default is 'tcb'.

Outputs

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 coup-
                           lings, all in Hz.

   aux.pdb_aa_num        - pdb amino acid number for each spin

   aux.pdb_aa_typ        - pdb amino acid type for each spin

ilya.kuprov@weizmann.ac.il
zenawi.welderufael@soton.ac.uk
andras_boeszoermenyi@hms.harvard.edu
matt.walker@soton.ac.uk
mariagrazia.concilio@sjtu.edu.cn