Difference between revisions of "Read pdb pro.m"

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Reads protein PDB data.
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{{DISPLAYTITLE:read_pdb_pro.m}} __NOTOC__
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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.
  
 
==Syntax==
 
==Syntax==
  
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     [aa_num,aa_typ,pdb_id,coords]=read_pdb_pro(pdb_file_name,instance)
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     [aa_num,aa_typ,pdb_id,coords]=read_pdb_pro(pdb_file_name,mod_id)
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==Description==
 
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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==
 
==Arguments==
  
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     pdb_file_name - a character string giving the name of the PDB file
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     pdb_file_name - a character string with the file name
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     instance      - the number of molecule to read from a PDB file
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     mod_id        - the number of model that should be
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                    containing multiple molecules
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                    read from the pdb file
  
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==Returns==
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==Outputs==
  
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     aa_num  - nspins x 1 vector giving the number of the amino acid to which each spin belongs
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     aa_num  - nspins x 1 vector giving the number of  
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              the amino acid to which each spin belongs
 
   
 
   
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     aa_typ  - nspins x 1 cell array of strings giving the PDB identifier of the amino acid to  
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     aa_typ  - nspins x 1 cell array of strings giving  
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              the PDB identifier of the amino acid to  
 
               which each spin belongs (e.g. 'TYR')
 
               which each spin belongs (e.g. 'TYR')
 
   
 
   
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     pdb_id   - nspins x 1 cell array of strings giving the PDB identifier of the protein atom  
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     pdb_id - nspins x 1 cell array of strings giving  
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              type to which each spin belongs (e.g. 'HE2')
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              the PDB identifier of the protein atom  
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              type to which each spin belongs (e.g. 'HE2')
 
   
 
   
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     coords  - nspins x 1 cell array of 3-vectors giving cartesian coordinates of each spin in Angstrom
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     coords  - nspins x 1 cell array of 3-vectors giving  
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              Cartesian coordinates of each spin in Angstrom
  
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==Examples==
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==See also==
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The output may be used, for example, to guess J-couplings:
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[[Import,_export,_and_visualisation#Data_import|Data import]]
  
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    % Parse the PDB file
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[[Protein NMR simulations]]
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    [pdb_aa_num,pdb_aa_typ,pdb_atom_id,pdb_coords]=read_pdb_pro('1D3Z.pdb',1);
 
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    % Guess the J-couplings
 
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    jmatrix=guess_j_pro(pdb_aa_num,pdb_aa_typ,pdb_atom_id,pdb_coords);
 
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==Notes==
 
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# 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.
 
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# More information is available in the protein [[Protein NMR simulations|getting started]] manual.
 
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==See also==
 
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[[protein.m]], [[nuclacid.m]], [[guess_j_pro.m]]
 
  
  
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''Revision 3284, authors: [[Ilya Kuprov]]''
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''Version 2.8, authors: [[Ilya Kuprov]]''

Revision as of 16:33, 2 July 2023

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.

Syntax

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

Arguments

    pdb_file_name - a character string with the file name

    mod_id        - the number of model that should be
                    read from the pdb file

Outputs

    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

See also

Data import

Protein NMR simulations


Version 2.8, authors: Ilya Kuprov

Retrieved from "https://spindynamics.org/wiki/index.php?title=Read_pdb_pro.m&oldid=4840"