Protein.m - Revision history

Kuprov: Update function See also links and function index membership

2026-06-06T18:40:17Z

Update function See also links and function index membership

Kuprov: Rename Arguments section heading to Parameters

2026-06-05T17:51:27Z

Rename Arguments section heading to Parameters

Kuprov at 17:03, 5 June 2026

2026-06-05T17:03:57Z

Kuprov: Normalise preformatted blank lines in function documentation blocks

2026-06-05T16:41:24Z

Normalise preformatted blank lines in function documentation blocks

Kuprov at 16:35, 5 June 2026

2026-06-05T16:35:40Z

Kuprov: Add missing Version/authors metadata and remove raw author emails

2026-06-05T16:26:43Z

Add missing Version/authors metadata and remove raw author emails

Kuprov: Normalise sequential blank lines

2026-04-25T11:28:53Z

Normalise sequential blank lines

Kuprov: Restore pre-bulk-edit wiki content

2026-04-05T14:49:47Z

Restore pre-bulk-edit wiki content

Kuprov: Normalise remaining wiki page to current Spinach source header

2026-04-05T14:13:59Z

Normalise remaining wiki page to current Spinach source header

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

2026-04-05T14:03:54Z

Sync syntax/arguments/outputs with current Spinach source

@@ Line 152: / Line 152: @@
 ==See also==
-[[nuclacid.m]], [[guess_csa_pro.m]], [[guess_j_pro.m]]
+[[nuclacid.m]], [[guess_csa_pro.m]], [[guess_j_pro.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]], [[read_bmrb.m]], [[read_pdb_nuc.m]], [[read_pdb_pro.m]], [[v2spinach.m]], [[weblab2nqi.m]], [[x2spinach.m]], [[Import,_export,_and_visualisation]]
 ''Version 2.2, authors: [[Ilya Kuprov]], [[Zenawi Welderufael]], [[Andras Boeszoermenyi]], [[Matt Walker]], [[Maria Grazia Concilio]]''

@@ Line 9: / Line 9: @@
       [sys,inter,aux]=protein(pdb_file,bmrb_file,options)
-==Arguments==
+==Parameters==
           pdb_file   - string containing the name of the PDB file

← Older revision		Revision as of 17:03, 5 June 2026
Line 153:		Line 153:

	[[nuclacid.m]], [[guess_csa_pro.m]], [[guess_j_pro.m]]		[[nuclacid.m]], [[guess_csa_pro.m]], [[guess_j_pro.m]]
−
−
−	~~==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~~

	''Version 2.2, authors: [[Ilya Kuprov]], [[Zenawi Welderufael]], [[Andras Boeszoermenyi]], [[Matt Walker]], [[Maria Grazia Concilio]]''		''Version 2.2, authors: [[Ilya Kuprov]], [[Zenawi Welderufael]], [[Andras Boeszoermenyi]], [[Matt Walker]], [[Maria Grazia Concilio]]''

@@ Line 12: / Line 12: @@
           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
@@ Line 24: / Line 24: @@
                        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
 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'.
@@ Line 48: / Line 48: @@
      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
@@ Line 160: / Line 160: @@
             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
@@ Line 166: / Line 166: @@
                           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

@@ Line 7: / Line 7: @@
 ==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
+        bmrb_file   - string containing the name of the BMRB file
- options.select    - 'backbone' imports protein backbone up to
+  options.select    - 'backbone' imports protein backbone up to
-                     CB and HB, 'backbone-minimal' only imports
+                      CB and HB, 'backbone-minimal' only imports
-                     the backbone, 'backbone-hsqc' is the same
+                      the backbone, 'backbone-hsqc' is the same
-                     as backbone, but with GLN and ASN side chain
+                      as backbone, but with GLN and ASN side chain
-                     amide groups included, 'all' imports every-
+                      amide groups included, 'all' imports every-
-                     thing that is assigned in BMRB. If a list of
+                      thing that is assigned in BMRB. If a list of
-                     numbers is supplied, spins with those num-
+                      numbers is supplied, spins with those num-
-                     bers in the PDB file are imported, but only
+                      bers in the PDB file are imported, but only
-                     if they are assigned in the PDB.
+                      if they are assigned in the PDB.
- options.pdb_mol   - the number of molecule if there are multiple
+  options.pdb_mol   - the number of molecule if there are multiple
-                     molecules in the pdb file
+                      molecules in the pdb file
- options.noshift   - 'keep' places unassigned atoms between -1 and
+  options.noshift   - 'keep' places unassigned atoms between -1 and
 ppm, 'delete' removes them from the system
- options.deuterate - a cell array of character strings, replaces
+  options.deuterate - a cell array of character strings, replaces
-                     protons with the specified PDB identifiers
+                      protons with the specified PDB identifiers
-                     with deuterons; 'non-Me' deuterates every-
+                      with deuterons; 'non-Me' deuterates every-
-                     thing except methyl groups
+                      thing except methyl groups
- options.nh_csa    - peptide bond CSAs differ across literature,
+  options.nh_csa    - peptide bond CSAs differ across literature,
-                     the following options are available:
+                      the following options are available:
            'bax' for H:[6.00 0.00 -6.00], N:[-108.0 62.0 46.0] ppm
@@ Line 47: / Line 47: @@
 ==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 67: / Line 67: @@
      aux.pdb_aa_typ        - pdb amino acid type for each spin
 ==Examples==
@@ Line 159: / Line 154: @@
 [[nuclacid.m]], [[guess_csa_pro.m]], [[guess_j_pro.m]]
 ==Parameters==
@@ Line 179: / Line 173: @@
       options.deuterate - a cell array of character strings, replaces protons with the specified PDB identifiers
                           with deuterons

← Older revision		Revision as of 11:28, 25 April 2026
Line 158:		Line 158:

	[[nuclacid.m]], [[guess_csa_pro.m]], [[guess_j_pro.m]]		[[nuclacid.m]], [[guess_csa_pro.m]], [[guess_j_pro.m]]
−

	''Version 2.2, authors: [[Ilya Kuprov]], [[Zenawi Welderufael]], [[Andras Boeszoermenyi]]''		''Version 2.2, authors: [[Ilya Kuprov]], [[Zenawi Welderufael]], [[Andras Boeszoermenyi]]''