Re: export -- February 24, 2011 - 10:20

Hi,

For this I could create one user function:

bmrb.cs_entry()

Running this in relax would be compulsory before a n NMR-STAR file
could be created.  It would then accept as an argument one of three
things:

1)  The entry ID.

2)  A flag saying that chemical shifts will be deposited as a separate
file, but in the same deposition.

3)  A text string "describing where the chemical shift assignments
were obtained and why they cannot be published, if they cannot be made
public."

My question is, could you give NMR-STAR saveframe examples for these
three situations?  If I have a template, I will then be able to add
these to the NMR-STAR file created by relax.

Cheers,

Edward



On 21 February 2011 18:40, Eldon Ulrich <elu@xxxxxxxxxxxxx> wrote:
> 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