Re: export -- February 21, 2011 - 18:38

Hi,

Yes, I think it would be very useful to have depositors of relaxation 
data (1) provide chemical shifts if they made the assignments as part of 
their research (would be included in the relaxation entry), (2) provide 
an existing BMRB entry accession code, if they used chemical shifts from 
that entry for their research (these data could be from their group or 
from another group), or (3) describe where the chemical shift 
assignments were obtained and why they cannot be published, if they 
cannot be made public (rare, but possible).

Eldon

On 2/21/11 11:30 AM, Edward d'Auvergne wrote:
> On 21 February 2011 18:02, Eldon Ulrich<elu@xxxxxxxxxxxxx>  wrote:
> > Hi,
> >
> > > The chemical shifts are deposited seperately into the BMRB.  Eldon, is
> > > there a way to associate 2 BMRB entries, so that relax can
> > > automatically read in chemical shifts for a given model-free BMRB
> > > deposition?
> >
> > There are two ways to associate one or more BMRB entries. The first is to
> > use the 'Related_entries' tags.
> >
> > loop_
> > _Related_entries.Database_name
> > _Related_entries.Database_accession_code
> > _Related_entries.Relationship
> > _Related_entries.Entry_ID
> > stop_
> >
> > This is used often in BMRB entries.
>
> Hi,
>
> This is quite useful, and could be added to relax.  Do you think that
> all relaxation data should have deposited chemical shifts?
> Considering this is a requirement for publication of structures, do
> you think it would be reasonable to force relax users to supply a
> chemical shift BMRB deposition number?
>
>
> > The second method is to define a set of two or more BMRB entries as a
> > 'study'. This method has not been used in BMRB entries but the tags exist
> > and could be used. This would be a more formal method of grouping entries.
> >
> > loop_
> > _Study_list.Sf_category
> > _Study_list.Sf_framecode
> > _Study_list.Entry_ID
> > _Study_list.ID
> > stop_
> >
> > loop_
> > _Study.ID
> > _Study.Name
> > _Study.Type
> > _Study.Details
> > _Study.Entry_ID
> > _Study.Study_list_ID
> > stop_
> >
> > loop_
> > _Study_keyword.Study_ID
> > _Study_keyword.Keyword
> > _Study_keyword.Entry_ID
> > _Study_keyword.Study_list_ID
> > stop_
> >
> > loop_
> > _Study_entry_list.Study_ID
> > _Study_entry_list.BMRB_accession_code
> > _Study_entry_list.BMRB_entry_description
> > _Study_entry_list.Details
> > _Study_entry_list.Entry_ID
> > _Study_entry_list.Study_list_ID
> > stop_
>
> This looks quite interesting!  I might consider adding this after the
> BMRB-relax integration paper is written.  Would this be in a separate
> deposition file?  Is is part of a separate deposition used to link
> previous depositions together?  Or should it be added to the file
> relax produces with the relaxation data and model-free saveframes?
>
> Cheers,
>
> Edward