Nuclacid.m - Revision history

Kuprov: Update function See also links and function index membership

2026-06-06T18:39:16Z

Update function See also links and function index membership

Kuprov: Rename Arguments section heading to Parameters

2026-06-05T17:50:42Z

Rename Arguments section heading to Parameters

Kuprov: Normalise preformatted blank lines in function documentation blocks

2026-06-05T16:41:19Z

Normalise preformatted blank lines in function documentation blocks

Kuprov: Normalise sequential blank lines

2026-04-25T11:27:51Z

Normalise sequential blank lines

Kuprov: Restore pre-bulk-edit wiki content

2026-04-05T14:49:32Z

Restore pre-bulk-edit wiki content

Kuprov: Sync syntax/arguments/outputs with current Spinach source

2026-04-05T14:06:17Z

Sync syntax/arguments/outputs with current Spinach source

Kuprov at 15:52, 21 October 2020

2020-10-21T15:52:20Z

Kuprov: /* See also */

2020-10-21T15:52:07Z

‎See also

Kuprov: /* See also */

2020-10-21T15:51:57Z

‎See also

Kuprov at 15:51, 21 October 2020

2020-10-21T15:51:25Z

@@ Line 111: / Line 111: @@
 ==See also==
-[[Spin_system_specification#Protein_and_nucleic_acid_import|Protein and nucleic acid import]]
+[[guess_j_nuc.m]], [[create.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]], [[ocparse.m]], [[oparse.m]], [[parsexml.m]], [[protein.m]], [[read_bmrb.m]], [[read_pdb_nuc.m]], [[read_pdb_pro.m]], [[v2spinach.m]], [[weblab2nqi.m]], [[x2spinach.m]], [[Import,_export,_and_visualisation]], [[Spin_system_specification]], [[Protein NMR simulations]]
 ''Version 2.5, authors: [[Ilya Kuprov]], [[Zenawi Welderufael]]''

@@ Line 6: / Line 6: @@
       [sys,inter]=nuclacid(pdb_file,shift_file,options)
-==Arguments==
+==Parameters==
              pdb_file - a character string containing the name of the PDB file

@@ Line 9: / Line 9: @@
              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

← Older revision		Revision as of 11:27, 25 April 2026
Line 114:		Line 114:

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

	''Version 2.5, authors: [[Ilya Kuprov]], [[Zenawi Welderufael]]''		''Version 2.5, authors: [[Ilya Kuprov]], [[Zenawi Welderufael]]''

@@ Line 1: / Line 1: @@
 {{DISPLAYTITLE:nuclacid.m}} __NOTOC__
 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)
+     [sys,inter]=nuclacid(pdb_file,shift_file,options)
 ==Arguments==
-pdb_file - a character string containing the name
+            pdb_file - a character string containing the name of the PDB file
-                      of the PDB file
-         shift_file - a character string containing the name
+When an atom is deuterated, J-couplings are reduced appropriately.
-  options.deut_list - a cell array of strings, specifying which
+==Returns==
-                      atoms should be assumed to be deuterated,
+The following subfields of sys and inter data structures are set by this function:
-    options.noshift - 'keep' places unassigned atoms between -1
+     sys.isotopes          - Nspins x 1 cell array of strings
-                       and 0 ppm, 'delete' removes them from the
-                       system
+     sys.labels            - Nspins x 1 cell array of strings containing standard IUPAC protein atom labels
-−
+     inter.coordinates     - Nspins x 3 matrix, Angstrom.
- Returns:
+     inter.zeeman.scalar   - Nspins x 1 cell array of numbers, ppm. Isotropic chemical shifts go here.
-−
-    sys.isotopes          - Nspins x 1 cell array of strings
+     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.
@@ Line 119: / Line 104: @@
 Further examples are available in examples/nmr_nucleic 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.
@@ Line 127: / Line 111: @@
 ==See also==
 [[Spin_system_specification#Protein_and_nucleic_acid_import|Protein and nucleic acid import]]
@@ Line 134: / Line 117: @@
 ''Version 2.5, authors: [[Ilya Kuprov]], [[Zenawi Welderufael]]''

← Older revision		Revision as of 15:52, 21 October 2020
Line 1:		Line 1:
−	{{DISPLAYTITLE:~~nucleacid~~.m}} __NOTOC__	+	{{DISPLAYTITLE:nuclacid.m}} __NOTOC__
	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''.		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''.