guess_csa_pro.m

Guesses reasonable amide bond nitrogen and carbon CSA tensors (anisotropic parts only), given the local protein geometry. While this function is certainly not a replacement for the accurate experimentally measured values of these parameters, it provides serviceable substitutes that are useful for testing. The literature sources used for the estimates are:

http://dx.doi.org/10.1007/s10858-006-9037-6

http://pubs.acs.org/doi/abs/10.1021/ja00083a028

Direct calls to this function are discouraged; it is invoked by protein.m during protein data import.

Syntax

    CSAs=guess_csa_pro(aa_nums,pdb_ids,coords,options)

Parameters

aa_nums        - vector of amino acid numbers

pdb_ids        - cell array of PDB atom identifiers

coords         - cell array of coordinate vectors

options.nh_csa - 'tcb' for Tjandra, Curtis, and Bodenhausen, 'bax'
                for Cornilescu and Bax, and 'pol' for Case, Polenova,
                and Gronenborn eigenvalues and orientations of the CSA
                tensors

Outputs

    CSAs      - nspins x 1 cell array containing chemical shift anisotropy tensors in ppm where
                the function could make a guess of the CSA tensor, and empty cells where it could not.

Examples

The function accepts, for example, the output of read_pdb_pro.m:

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

    % Guess chemical shift anisotropies
    CSAs=guess_csa_pro(pdb_aa_num,pdb_atom_id,pdb_coords);

Notes

These CSAs are very approximate. For accurate relaxation analysis, supply your own tensors. This is an auxiliary function called by protein.m; direct calls are discouraged.

See also

protein.m, read_pdb_pro.m, awg_interface.m, bootstrap.m, gslice.m, guess_j_nuc.m, guess_j_pro.m, py_run.m, retrieve_file.m, spinach2hiper.m, Import,_export,_and_visualisation, Spin_system_specification

Version 2.5, authors: Ilya Kuprov, Zenawi Welderufael