Re: BMRB deposition of model-free results. -- January 11, 2011 - 16:17

Hi,

That's great!  The only thing is that this code is currently in a
branch and not within a released relax version.  I will try to merge
this branch into the main line soon, and release a new version of
relax with BMRB support.  We should have this project terminated very
soon, and the paper written up.

Cheers,

Edward



On 7 January 2011 20:41, Eldon Ulrich <elu@xxxxxxxxxxxxx> wrote:
> Hi,
>
> I am presenting a poster at the Keystone Symposium next week and included
> under new developments related to BMRB a link to the new release of relax,
> the butterfly logo, a list of the relax developer names and a statement that
> the experimental data and derived relaxation parameters can be exported in
> NMR-STAR format.
>
> Thank you very much,
> Eldon
>
> On 12/31/10 9:10 AM, Edward d'Auvergne wrote:
> > Dear Eldon,
> >
> > I have now closed the task for the relax-BMRB integration
> > (https://gna.org/task/?6438) as relax fully supports the writing of
> > NMR-STAR v3.1 files (as well as the reading of that data).  There are
> > still problems with this file and the ADIT-NMR system.  This can be
> > tested with the file attached to the task
> > (https://gna.org/support/download.php?file_id=11684).
> >
> > The new ADIT-NMR system appears to have a few additional problems with
> > this file.  For example it no longer automatically determines what is
> > in the file, so if you don't select all of the correct saveframes
> > (something a user might have problems with, for example knowing about
> > ticking the Chemical shift anisotropy) these will not appear in
> > ADIT-NMR.  I have a few more comments below about the existing
> > problems.  But now that this is complete (well, a little more
> > polishing may be required), hopefully I'll now have some time to write
> > this work up as a paper.  The Bmrblib package
> > (https://gna.org/projects/bmrblib) is currently only in the source
> > code repository, but if you would like a release of this library for
> > the BMRB, this can be done.
> >
> > I wish you a happy new year!
> >
> > Regards,
> >
> > Edward
> >
> >
> > On 22 November 2010 19:59, Edward d'Auvergne<edward@xxxxxxxxxxxxx>  wrote:
> > [snip]
> > > There are a few problems remaining:
> > >
> > > 1)  The first issue is that there is a piece of information currently
> > > missing - the XH bond lengths and XH unit vectors.  I think we
> > > discussed how to store this data in the NMR-STAR file, but
> > > unfortunately I have forgotten how to do this.  Would you remember the
> > > saveframes and tags that this goes into?
> >
> > I have temporarily solved this by creating a new tag called
> > Model_free.Bond_length_val.  This is to match all of the other
> > Model_free tags, and the idea is taken from the RDC saveframe.  Is
> > there a better solution to this problem?
> >
> >
> > > 2)  A few saveframes seem to be ignored by the production ADIT-NMR
> > > system including:
> > >
> > > - The method saveframes.
> > > - The auto_relaxation saveframes.
> > > - The model_free saveframes.
> > > - The tensor saveframes.
> >
> > These are still ignored in the new ADIT-NMR system.
> >
> >
> > > 3)  Some saveframes have problems:
> > >
> > > - For the relax software saveframe tag _Software.Version, ADIT-NMR
> > > expects 31 characters or less.  Can this be increased?  The relax
> > > version in this case is a repository checkout, so the version info is
> > > quite detailed.
> > > - The chemical_shift and heteronucl_NOE saveframes are expecting a
> > > "Deposited data file name", but this is coming from the temp_bmrb
> > > complete file.  Should this be automatically handled so the user has
> > > almost nothing to do in the deposition process?
> >
> > These problems also still exist.  How should we solve these?