Nuclacid.m

Nucleic acid data import function. This function parses PDB and chemical shift data, runs a J-coupling guess using guess_j_nuc.m function and outputs sys and inter data structures that are required by create.m gateway function in Spinach.

Syntax

    [sys,inter]=nuclacid(pdb_file,shift_file,options)

Arguments

           pdb_file - a character string containing the name of the PDB file
   
         shift_file - a character string containing the name of the chemical 
                      shift file, ASCII formatted as [residue_number atom_id shift],
                      see example.txt in examples/nmr_nucleic 
      
  options.deut_list - a cell array of strings, specifying which atoms should be
                      assumed to be deuterated, for example {'ADE:H2pp'}
  
    options.noshift - 'keep' places unassigned atoms between -1 and 0 ppm, 'delete' removes them from the system

When an atom is deuterated, J-couplings are reduced appropriately.

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

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

Examples

Below is a typical use case for this function. This script calculates the HSQC spectrum of the example RNA hairpin.

    % Import RNA data
    options.noshift='keep';
    options.deut_list={'GUA:H1','GUA:H21','GUA:H22','CYT:H41',...
                       'CYT:H42','URI:H3','ADE:H61','ADE:H62'};
    [sys,inter]=nuclacid('example.pdb','example.txt',options);
    
    % Magnet field
    sys.magnet=11.7395;
    
    % Tolerances
    sys.tols.inter_cutoff=5.0;
    sys.disable={'krylov'};
    
    % Basis set
    bas.formalism='sphten-liouv';
    bas.approximation='IK-1';
    bas.connectivity='scalar_couplings';
    bas.level=4; bas.space_level=1;
    
    % Relaxation theory
    inter.relaxation={'damp'};
    inter.rlx_keep='diagonal';
    inter.equilibrium='zero';
    inter.damp_rate=5.0;
    
    % Sequence parameters
    parameters.J=90;
    parameters.sweep=[7500 4500];
    parameters.offset=[16250 4250];
    parameters.npoints=[128 256];
    parameters.zerofill=[1024 1024];
    parameters.spins={'13C','1H'};
    parameters.decouple_f1={'1H','2H'};
    parameters.decouple_f2={'13C','2H'};
    parameters.axis_units='ppm';
    
    % Create the spin system structure
    spin_system=create(sys,inter);
    
    % Build the basis
    spin_system=basis(spin_system,bas);
    
    % Simulation
    fid=liquid(spin_system,@hsqc,parameters,'nmr');
    save('hsqc_rna.mat','spin_system','parameters','fid');
    
    % Apodization
    fid.pos=apodization(fid.pos,'cosbell-2d');
    fid.neg=apodization(fid.neg,'cosbell-2d');
    
    % F2 Fourier transform
    f1_pos=fftshift(fft(fid.pos,parameters.zerofill(2),1),1);
    f1_neg=fftshift(fft(fid.neg,parameters.zerofill(2),1),1);
    
    % Form States signal
    fid=f1_pos+conj(f1_neg);
    
    % F1 Fourier transform
    spectrum=fftshift(fft(fid,parameters.zerofill(1),2),2);
    
    % Destreaking
    spectrum=destreak(spectrum);
    
    % Plotting
    plot_2d(spin_system,real(spectrum),parameters,20,[0.1 0.5 0.1 0.5],2,256,6,'positive');
         

Further examples are available in examples/nmr_nucleic directory.

Notes

1. Unassigned atom coordinates are used internally for the J-coupling prediction procedure even if options.noshift is set to 'delete'.
2. Deleting unassigned atoms removes them from the dipolar coupling network. Relaxation properties, such as Overhauser effects, may be distorted as a result.
3. Watch carefully the output of this function, it would inform you if it sees anything strange in the data supplied. Nucleic acid datasets available from major databases are rarely free of errors.

See also

Protein and nucleic acid import

Protein NMR simulations

Version 2.5, authors: Ilya Kuprov, Zenawi Welderufael