Difference between revisions of "Read pdb pro.m"

Latest revision as of 10:58, 18 September 2026

Reads a PDB file and returns amino acid numbers, the amino acid types, PDB atom identifiers, and Cartesian coordinates.

Syntax

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

Parameters

    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

    pdb_ser - nspins x 1 vector giving the PDB atom serial
              number of each spin

c2spinach.m, cyprinol.m, fatty_acid.m, g2spinach.m, gissmo2spinach.m, gparse.m, karplus_fit.m, killcross.m, killdiag.m, merge_inp.m, methyl_group.m, nuclacid.m, ocparse.m, oparse.m, parsexml.m, protein.m, read_bmrb.m, read_pdb_nuc.m, v2spinach.m, weblab2nqi.m, x2spinach.m, Import,_export,_and_visualisation, Protein NMR simulations

Version 2.8, authors: Ilya Kuprov

Difference between revisions of "Read pdb pro.m"

Latest revision as of 10:58, 18 September 2026

Syntax

Parameters

Outputs

See also

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@@ Line 1: / Line 1: @@
-Reads protein PDB data.
+{{DISPLAYTITLE:read_pdb_pro.m}} __NOTOC__
+Reads a PDB file and returns amino acid numbers, the amino acid types, PDB atom identifiers, and Cartesian coordinates.
 ==Syntax==
-      [aa_num,aa_typ,pdb_id,coords]=read_pdb_pro(pdb_file_name,instance)
+      [aa_num,aa_typ,pdb_id,coords,pdb_ser]=read_pdb_pro(pdb_file_name,mod_id)
-==Description==
+==Parameters==
-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 with the file name
-      pdb_file_name - a character string giving the name of the PDB file
+      mod_id        - the number of model that should be
+                     read from the pdb file
-      instance      - the number of molecule to read from a PDB file
-                     containing multiple molecules
-==Returns==
+==Outputs==
-      aa_num  - nspins x 1 vector giving the number of the amino acid to which each spin belongs
+      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
+      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
+      pdb_id  - nspins x 1 cell array of strings giving
-              type to which each spin belongs (e.g. 'HE2')
+               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
+      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
+      pdb_ser - nspins x 1 vector giving the PDB atom serial
-     jmatrix=guess_j_pro(pdb_aa_num,pdb_aa_typ,pdb_atom_id,pdb_coords);
+               number of each spin
-==Notes==
-# 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==
-[[protein.m]], [[nuclacid.m]], [[guess_j_pro.m]]
+[[c2spinach.m]], [[cyprinol.m]], [[fatty_acid.m]], [[g2spinach.m]], [[gissmo2spinach.m]], [[gparse.m]], [[karplus_fit.m]], [[killcross.m]], [[killdiag.m]], [[merge_inp.m]], [[methyl_group.m]], [[nuclacid.m]], [[ocparse.m]], [[oparse.m]], [[parsexml.m]], [[protein.m]], [[read_bmrb.m]], [[read_pdb_nuc.m]], [[v2spinach.m]], [[weblab2nqi.m]], [[x2spinach.m]], [[Import,_export,_and_visualisation]], [[Protein NMR simulations]]
-''Revision 3284, authors: [[Ilya Kuprov]]''
+''Version 2.8, authors: [[Ilya Kuprov]]''