Version 1.0 minor fixes to Commented_Example.nef
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Updatedversion number in COmmented_Example to 1.0
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Fixed inconsistencies
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Added some alternative cases for optional values
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Regularised spacing
Version 1.0
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Fixed typos and improved documentation
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This is version 1.0, the first official version.
Proposal rename_to_index
- rename 'index_id'and 'ordinal' to just 'index', and rename and 'run_ordinal' to 'run_number' This proposal deliberately undoes several prior proposals. It arose out of discussion on those proposals.
Proposal new_isotope_specification
- Added _nef_chemical_shift.element and _nef_chemical_shift.isotope_number columns to specify isotope and elements with two letter element codes.
Proposal change_sequence_linking
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Changed rules for 'break' linking type, making it simper t0 specify sequences with breaks
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Removed 'nonlinear' linking type - now using 'single' for all residue types instead.
Proposal new_residue_variants
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Change variant specification from RCSB codes to form tha lista added and subtracted atoms
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Add _nef_sequence.cis_peptide column to specify peptide obnd cis/trans state.
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Add specifications/Residue_Variants.txt listing all supported standard residue variants
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Add example of non-stadard modified residue
Proposal add_nef_sequence_ordinal
- Add ordinal column to nef_sequence loop to recflect the (significant) line order.
Proposal multiple changes
- Add program_specific_raw_data saveframe
- Change nonsereospecific wildcards from X/Y (upper case) to x/y (lower case)
- Tighten allowed wildcards
- Improve consistency of COmmented_Example
Proposal remove_chemical_shift_units
- Remove _nef_chemical_shift_list.atom_chemical_shift_units tag
Proposal ordinal_to_index_id
- change 'ordinal' to 'index_id' (preserving _nef_run_history.run_ordinal, which does signify an ordering)
Proposal residue_type_to_name
Proposal residue_type_to_name
- change 'residue_type' to 'residue_name' in all occurrences and tags
Version 0.2
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Version 0.2 (unfortunately named) is the final, cleaned-up version before proposing the changes that will define the first release version, 1.0.
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Version 0.2 has a proper specifications file mmcif_nef.dic.
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A wide range of test data have been added.
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The Commented_Example file has been reorganised, expanded with additional examples, and cleaned of errors and inconsistencies.
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The overview document has been modified to clarify confusion on a number of points.
Version 0.8
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Updated charter to reflect the discussion at the Rutgers 7/11-9/1 2015 meeting.
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Basic format rules
- Datablock name must now start with 'nef_'
- All sf_framecode must now start with the name of the corresponding sf_category
- '?' is no longer supported to mean 'not set' - all unset parameters must now be given as '.', which translates as null (None)
- mandatory and optional tags and key columns for loops defined and given in Commented_Example.nef
- The convention of starting references to saveframes with a '$' is NOT supported any longer.
- added ordinal column to peak and restraint lists to provide unique identifier for each line
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Added new tags
- Added restraint_origin tag to _nef_dihedral_restraint_list, _nef_distance_restraint_list, _nef_rdc_restraint_list
- Added _nef_rdc_restraint.distance_dependent and _nef_rdc_restraint.scale
- Explicitly expanded _nef_peak loop to support up to 15D peaks
- _nef_nmr_meta_data.uuid, uniquely identifying the specific version of the data
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Further changes
- Changed atomset wildcard from '#' (e.g. ALA HB#) to '%' (e.g. ALA HB%)
- Changed specification of sequence and amino acid variants.
Version 0.7
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Global nef name space. All tags now start with 'nef'.
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RCSB Amino acid variant codes
The RCSB variant codes consist of three parts, connected by underscores:
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The amino acid three-letter code
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the backbone linking, with twelve alternatives:
- 'LL' : L-amino acid, middle position
- 'LSN3' : L-amino acid, N-terminal -NH3+
- 'LEO2' : L-amino acid, C-terminal COO-
- 'LEO2H' : L-amino acid, C-terminal COOH
- 'LFZW' : L-amino acid, free zwitterion
- 'LFOH' : L-amino acid, free COOH,NH2 form
And six equivalent forms starting with 'D' for D-amino acids.
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The side chain protonation state.
The default is the fully protonated form (no third field).
A missing proton is indicated by DHxy, where Hxy is the proton name.
For NEF the standard forms are with charged Glutamate, Aspartate, Lysine,
and Arginine side chains and charged N and C termini. These need not be
indicated. The cases you might want to indicate (enclosed in '\*\* in the table)
are protonated Aspartate, di-sulfide or deprotonated Cysteine, protonated
Glutamate, double protonated Histidine, neutral HE-protonated Histidine,
neutral Lysine, and O-linked (or deprotonated) Serine, Threonine, or
Tyrosine. These are the codes that programs should consider using.
You would also want to indicate cis-Proline, but there are no RCSB codes
for that situation (as far as we could tell), so we invented them (John
Westbrook!?).
The more common variant codes are given in the table below. I have omitted
free amino acid forms and side chain deprotonated ARG and TRP.
Non-standard variant codes that should be used where relevant, are enclosed in '\*\*'.
In all other cases, the short three-letter residue-type will suffice.
```
**Table 1:** *PDB amino-acids variant codes (sorted)*
Description Residue-type Middle N-terminal-NH3+ C-terminal COO- C-terminal COOH
Alanine ALA ALA_LL ALA_LSN3 ALA_LEO2 ALA_LEO2H
protonated Arginine ARG ARG_LL ARG_LSN3 ARG_LEO2 ARG_LEO2H
Asparagine ASN ASN_LL ASN_LSN3 ASN_LEO2 ASN_LEO2H
de-protonated Aspartate ASP ASP_LL_DHD2 ASP_LSN3_DHD2 ASP_LEO2_DHD2 ASP_LEO2H_DHD2
protonated Aspartate ASP *ASP_LL* *ASP_LSN3* *ASP_LEO2* ASP_LEO2H
Free cysteine CYS CYS_LL CYS_LSN3 CYS_LEO2 CYS_LEO2H
S_S or S- cysteine CYS *CYS_LL_DHG* *CYS_LSN3_DHG* *CYS_LEO2_DHG* CYS_LEO2H_DHG
Glutamine GLN GLN_LL GLN_LSN3 GLN_LEO2 GLN_LEO2H
protonated Glutamate GLU *GLU_LL* *GLU_LSN3* *GLU_LEO2* GLU_LEO2H
de-protonated Glutamate GLU GLU_LL_DHE2 GLU_LSN3_DHE2 GLU_LEO2_DHE2 GLU_LEO2H_DHE2
Glycine GLY GLY_LL GLY_LSN3 GLY_LEO2 GLY_LEO2H
HD-protonated Histidine HIS HIS_LL_DHE2 HIS_LSN3_DHE2 HIS_LEO2_DHE2 HIS_LEO2H_DHE2
HD,HE protonated Histidine HIS *HIS_LL* *HIS_LSN3* *HIS_LEO2* HIS_LEO2H
HE-protonated Histidine HIS *HIS_LL_DHD1* *HIS_LSN3_DHD1* *HIS_LEO2_DHD* HIS_LEOH2_DHD1
Isoleucine ILE ILE_LL ILE_LSN3 ILE_LEO2 ILE_LEO2H
Leucine LEU LEU_LL LEU_LSN3 LEU_LEO2 LEU_LEO2H
protonated Lysine LYS LYS_LL LYS_LSN3 LYS_LEO2 LYS_LEO2H
neutral Lysine LYS *LYS_LL_DHZ3* *LYS_LSN3_DHZ3* *LYS_LEO2_DHZ3* LYS_LEO2H_DHZ3
Methionine MET MET_LL MET_LSN3 MET_LEO2 MET_LEO2H
Phenylalanine PHE PHE_LL PHE_LSN3 PHE_LEO2 PHE_LEO2H
Proline PRO PRO_LL PRO_LSN3 PRO_LEO2 PRO_LEO2H
cis Proline PRO *PRO_LL_CIS* *PRO_LSN3_CIS* *PRO_LEO2_CIS* PRO_LEO2H_CIS
Serine SER SER_LL SER_LSN3 SER_LEO2 SER_LEO2H
O-linked-Serine SER *SER_LL_DHG* *SER_LSN3_DHG* *SER_LEO2_DHG* SER_LEO2H_DHG
Threonine THR THR_LL THR_LSN3 THR_LEO2 THR_LEO2H
O-linked Threonine THR *THR_LL_DHG1* *THR_LSN3_DHG1* *THR_LEO2_DHG1* THR_LEO2H_DHG1
Tryptophan TRP TRP_LL TRP_LSN3 TRP_LEO2 TRP_LEO2H
Tyrosine TYR TYR_LL TYR_LSN3 TYR_LEO2 TYR_LEO2H
O-linked or O- Tyrosine TYR *TYR_LL_DHH* *TYR_LSN3_DHH* *TYR_LEO2_DHH TYR_LEO2H_DHH
Valine VAL VAL_LL VAL_LSN3 VAL_LEO2 VAL_LEO2H
```
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Indirect magnetisation transfer
We have added a new tag to the spectrum_dimension_transfer loop, so that it becomes e.g.
loop_ _nef_spectrum_dimension_transfer.dimension_1 _nef_spectrum_dimension_transfer.dimension_2 _nef_spectrum_dimension_transfer.transfer_type _nef_spectrum_dimension_transfer.is_indirect 1 3 through-space true 2 3 onebond false stop_The is_indirect tag would be used for transfers that are relayed through other nuclei. The relevant cases are the ChhC NOESY (used in solid state NMR) or 3D CCH HSQC-NOESY-HSQC, where the transfer being measured is a proton-proton NOESY, but the nucleus observed is actually carbon.
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We have added a proposal for representing tensors (for use in e.g. RDC restraint lists), including a format for the tensor value, and a system of dummy residues to hold the tensor orientation. Please see the Questions document for details