Hi Edward,
Sorry for the delayed response. The file looks like a good start. I have
provided answers below.
Thanks,
Eldon
Edward d'Auvergne wrote:
Dear Eldon,
relax is now producing NMR-STAR dictionary files containing relaxation
data (one truncated example is attached), although these are obviously
far from complete. I have a few questions as this does not work for
all molecule types. For example if you have a protein or RNA system
and have collected both 15N and 13C R1 relaxation data. Should these
go into 2 separate heteronucl_T1_relaxation saveframes?
In the past 15N and 13C relaxation data would be put in separate
saveframes, but if the new 'coherence_type' values are used all data of
the same coherence type could be included in one table. The atom names
are required.
Or if you are
studying a protein with 15N labelling and have data for both the
backbone amide and the Trp indole ring?
Here, the data can be in the same table for sure, you just need to
provide the atom name as a value to the tag _T1.Atom_ID. This tag should
have the value of 'N' for backbone nitrogen in any case. We do not
assume an atom name. This will be especially true if you use the new
values for coherence type (Iz, etc.) we have discussed.
And is there more information
on how to construct the molecular entities other than at
http://www.bmrb.wisc.edu/deposit/mol_assembly/?
More information on required tags and their descriptions is available here:
http://www.bmrb.wisc.edu/dictionary/3.1html_frame/frame_index.html
I can try to put together more examples and send them to you this weekend.
Also, for submission, should relax produce the full set of records for
this data, so for example all of:
The required tags are annotated below.
loop_
_T1.ID should be provided as a counter
_T1.Assembly_atom_ID not needed
_T1.Entity_assembly_ID not abosolutely required always has a value
of 1
_T1.Entity_ID required particularly for molecular
assemblies that have more than one entity (heterodimers, complexes, etc.)
_T1.Comp_index_ID required, this is the residue sequence number
_T1.Seq_ID not needed
_T1.Comp_ID required, residue type
_T1.Atom_ID required, this is the atom name and allows
for things like backbone nitrogen and sidechain nitrogen data to be listed in
the same table.
_T1.Atom_type not absolutely required but useful to
distinguish CA from calcium.
_T1.Atom_isotope_number not required, but useful to distinguish 1H
from 2H relaxation
_T1.Val required
_T1.Val_err required in general
_T1.Resonance_ID not needed
_T1.Auth_entity_assembly_ID not needed
_T1.Auth_seq_ID not needed
_T1.Auth_comp_ID not needed
_T1.Auth_atom_ID not needed
_T1.Entry_ID not needed
_T1.Heteronucl_T1_list_ID required, particularly for entries
with more than one T1/R1 table
for R1 data? Or can a subset of these be filled out for submission?
Only the required tags above are needed. The others can be left out
And for missing entries, should this be represented as the character
'.' or '?', as both seem to be used in the file bmr15437_3.str.gz
The use of a '?' is clearer to read. Either is allowed. By definition,
',' means null and '?' means 'should have a value, but I do not have a
value to enter'.
(https://gna.org/task/?6438)?
Cheers,
Edward
Re: BMRB heteronuclear relaxation records together with multiple spin types.