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<[email protected]> 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?
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