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?
Re: BMRB deposition of model-free results.