Read pdb pro.m - Revision history

Kuprov: sync with Spinach main 3975f139: pdb_ser output

2026-09-18T09:58:52Z

sync with Spinach main 3975f139: pdb_ser output

Kuprov: Update function See also links and function index membership

2026-06-06T18:40:45Z

Update function See also links and function index membership

Kuprov: Rename Arguments section heading to Parameters

2026-06-05T17:51:48Z

Rename Arguments section heading to Parameters

Kuprov: Normalise sequential blank lines

2026-04-25T11:29:34Z

Normalise sequential blank lines

Kuprov at 15:34, 2 July 2023

2023-07-02T15:34:53Z

Kuprov at 15:33, 2 July 2023

2023-07-02T15:33:25Z

Admin: /* Notes */

2016-08-13T15:24:42Z

‎Notes

Admin: Created page with "Reads protein PDB data. ==Syntax== [aa_num,aa_typ,pdb_id,coords]=read_pdb_pro(pdb_file_name,instance) ==Description== This function reads the coordinates of all atoms ..."

2016-08-13T15:22:16Z

Created page with "Reads protein PDB data. ==Syntax== [aa_num,aa_typ,pdb_id,coords]=read_pdb_pro(pdb_file_name,instance) ==Description== This function reads the coordinates of all atoms ..."

New page

Reads protein PDB data.

==Syntax==

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

==Description==
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 giving the name of the PDB file

instance - the number of molecule to read from a PDB file
containing multiple molecules

==Returns==

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

==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
jmatrix=guess_j_pro(pdb_aa_num,pdb_aa_typ,pdb_atom_id,pdb_coords);

==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 getting started manual.

==See also==
[[protein.m]], [[nuclacid.m]], [[guess_j_pro.m]]

''Revision 3284, authors: [[Ilya Kuprov]]''

@@ Line 4: / Line 4: @@
 ==Syntax==
-      [aa_num,aa_typ,pdb_id,coords]=read_pdb_pro(pdb_file_name,mod_id)
+      [aa_num,aa_typ,pdb_id,coords,pdb_ser]=read_pdb_pro(pdb_file_name,mod_id)
 ==Parameters==
@@ Line 28: / Line 28: @@
       coords  - nspins x 1 cell array of 3-vectors giving
                 Cartesian coordinates of each spin in Angstrom
 ==See also==

@@ Line 30: / Line 30: @@
 ==See also==
-[[Import,_export,_and_visualisation#Data_import|Data import]]
+[[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]]''

@@ Line 6: / Line 6: @@
       [aa_num,aa_typ,pdb_id,coords]=read_pdb_pro(pdb_file_name,mod_id)
-==Arguments==
+==Parameters==
       pdb_file_name - a character string with the file name

← Older revision		Revision as of 11:29, 25 April 2026
Line 33:		Line 33:

	[[Protein NMR simulations]]		[[Protein NMR simulations]]
−

	''Version 2.8, authors: [[Ilya Kuprov]]''		''Version 2.8, authors: [[Ilya Kuprov]]''

@@ Line 1: / Line 1: @@
 {{DISPLAYTITLE:read_pdb_pro.m}} __NOTOC__
-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.
+Reads a PDB file and returns amino acid numbers, the amino acid types, PDB atom identifiers, and Cartesian coordinates.
 ==Syntax==

@@ Line 1: / Line 1: @@
-Reads protein PDB data.
+{{DISPLAYTITLE:read_pdb_pro.m}} __NOTOC__
 ==Syntax==
-      [aa_num,aa_typ,pdb_id,coords]=read_pdb_pro(pdb_file_name,instance)
+      [aa_num,aa_typ,pdb_id,coords]=read_pdb_pro(pdb_file_name,mod_id)
 ==Arguments==
-      pdb_file_name - a character string giving the name of the PDB file
+      pdb_file_name - a character string with the file name
-−
-      instance      - the number of molecule to read from a PDB file
+      mod_id        - the number of model that should be
-                     containing multiple molecules
+                     read from the pdb file
-==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
-      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
                 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
-      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
-==Examples==
+==See also==
-The output may be used, for example, to guess J-couplings:
+[[Import,_export,_and_visualisation#Data_import|Data import]]
-     % Parse the PDB file
+[[Protein NMR simulations]]
-''Revision 3284, authors: [[Ilya Kuprov]]''
+''Version 2.8, authors: [[Ilya Kuprov]]''

@@ Line 38: / Line 38: @@
 ==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 getting started manual.
+# More information is available in the protein [[Protein NMR simulations|getting started]] manual.
 ==See also==