Read pdb pro.m

Reads protein PDB data.

Syntax

    [aa_num,aa_typ,pdb_id,coords]=read_pdb_pro(pdb_file_name,instance)

Description

This function reads the coordinates of all atoms from the user-specified PDB file and returns, for each atom, the amino acid number, the amino acid type, the PDB label and the Cartesian coordinates.

Arguments

    pdb_file_name - a character string giving the name of the PDB file

    instance      - the number of molecule to read from a PDB file
                    containing multiple molecules

Returns

    aa_num  - nspins x 1 vector giving the number of the amino acid to which each spin belongs

    aa_typ  - nspins x 1 cell array of strings giving the PDB identifier of the amino acid to 
              which each spin belongs (e.g. 'TYR')

    pdb_id   - nspins x 1 cell array of strings giving the PDB identifier of the protein atom 
             type to which each spin belongs (e.g. 'HE2')

    coords  - nspins x 1 cell array of 3-vectors giving cartesian coordinates of each spin in Angstrom

Examples

The output may be used, for example, to guess J-couplings:

    % Parse the PDB file
    [pdb_aa_num,pdb_aa_typ,pdb_atom_id,pdb_coords]=read_pdb_pro('1D3Z.pdb',1);

    % Guess the J-couplings
    jmatrix=guess_j_pro(pdb_aa_num,pdb_aa_typ,pdb_atom_id,pdb_coords);

Notes

1. 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.
2. More information is available in the protein getting started manual.

See also

protein.m, nuclacid.m, guess_j_pro.m

Revision 3284, authors: Ilya Kuprov