Difference between revisions of "Protein.m"

Revision as of 15:13, 5 April 2026

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

@@ Line 1: / Line 1: @@
 {{DISPLAYTITLE:protein.m}} __NOTOC__
-Protein data import 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''.
+Protein data import function. Parses PDB and BMRB data, runs a J-coupl-
+ing guess, a CSA guess and outputs Spinach data structures.
-The function runs rather a lot of internal heuristics. Symmetry-related methyl group protons (listed once in BMRB) are replicated using PDB coordinates; unassigned capping groups on C- and N-termini are ignored; all oxygen and sulphur atoms are removed; symmetry-related carbons and protons in PHE and TYR aromatic rings (listed once in BMRB) are replicated using PDB coordinates; protons of deuterated or exchanging groups, such as –OH or –NH3+, are ignored; magnetically equivalent –CH2– group protons (listed once in BMRB) are replicated using PDB coordinates. Please refer to the function source code for the precise details of these post-processing steps.
 ==Syntax==
-[sys,inter,aux]=protein(pdb_file,bmrb_file,options)
+ [sys,inter,aux]=protein(pdb_file,bmrb_file,options)
 ==Arguments==
-pdb_file   - string containing the name of the PDB file
+ pdb_file   - string containing the name of the PDB file
         bmrb_file   - string containing the name of the BMRB file
@@ Line 47: / Line 46: @@
 ==Outputs==
-sys.isotopes          - Nspins x 1 cell array of strings
+ sys.isotopes          - Nspins x 1 cell array of strings
      sys.labels            - Nspins x 1 cell array of strings containing
@@ Line 72: / Line 71: @@
   matt.walker@soton.ac.uk
   mariagrazia.concilio@sjtu.edu.cn
-==Examples==
-Below is a typical use case for this function. This script calculates the NOESY spectrum of ubiquitin.
-     % Protein data import
-     options.select='all';
-     options.pdb_mol=1;
-     options.noshift='delete';
-     [sys,inter]=protein('1D3Z.pdb','1D3Z.bmrb',options);
-     % Magnet field
-     sys.magnet=21.1356;
-     % Tolerances
-     sys.tols.inter_cutoff=2.0;
-     sys.disable={'krylov'};
-     % Relaxation theory
-     inter.relaxation={'redfield'};
-     inter.rlx_keep='secular';
-     inter.equilibrium='zero';
-     inter.tau_c=5e-9;
-     % Basis set
-     bas.formalism='sphten-liouv';
-     bas.approximation='IK-1';
-     bas.connectivity='scalar_couplings';
-     bas.level=4; bas.space_level=3;
-     % Create the spin system structure
-     spin_system=create(sys,inter);
-     % Kill carbons and nitrogens (protein assumed unlabelled)
-     spin_system=kill_spin(spin_system,strcmp('13C',spin_system.comp.isotopes));
-     spin_system=kill_spin(spin_system,strcmp('15N',spin_system.comp.isotopes));
-     % Build the basis
-     spin_system=basis(spin_system,bas);
-     % Sequence parameters
-     parameters.tmix=0.065;
-     parameters.offset=4250;
-     parameters.sweep=[10750 10750];
-     parameters.npoints=[512 512];
-     parameters.zerofill=[2048 2048];
-     parameters.spins={'1H'};
-     parameters.axis_units='ppm';
-     parameters.rho0=state(spin_system,'Lz','1H','cheap');
-     % Simulation
-     fid=liquid(spin_system,@noesy,parameters,'nmr');
-     save('noesy_ubiquitin_theo.mat','spin_system','parameters','fid');
-     % Apodization
-     fid.cos=apodization(fid.cos,'gaussian-2d',5);
-     fid.sin=apodization(fid.sin,'gaussian-2d',5);
-     % F2 Fourier transform
-     f1_cos=real(fftshift(fft(fid.cos,parameters.zerofill(2),1),1));
-     f1_sin=real(fftshift(fft(fid.sin,parameters.zerofill(2),1),1));
-     % States signal
-     f1_states=f1_cos-1i*f1_sin;
-     % F1 Fourier transform
-     spectrum=fftshift(fft(f1_states,parameters.zerofill(1),2),2);
-     % Destreaking
-     spectrum=destreak(spectrum);
-     % Plotting
-     plot_2d(spin_system,-real(spectrum),parameters,20,[0.01 0.05 0.01 0.05],2,256,6,'positive');
-Further examples are available in examples/nmr_proteins directory.
-==Notes==
-# Unassigned atom coordinates are used internally for the J-coupling prediction procedure even if options.noshift is set to 'delete'.
-# Deleting unassigned atoms removes them from the dipolar coupling network. Relaxation properties, such as Overhauser effects, may be distorted as a result.
-# 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.
-# More information is available in the protein [[Protein NMR simulations|getting started]] manual.
-==See also==
-[[nuclacid.m]], [[guess_csa_pro.m]], [[guess_j_pro.m]]
-''Version 2.2, authors: [[Ilya Kuprov]], [[Zenawi Welderufael]], [[Andras Boeszoermenyi]]''
-==Parameters==
-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, 'delete' removes them from the system
-     options.deuterate - a cell array of character strings, replaces protons with the specified PDB identifiers
-                         with deuterons

Difference between revisions of "Protein.m"

Revision as of 15:13, 5 April 2026

Syntax

Arguments

Outputs

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