Hi Troels,
The support for handling relaxation dispersion data for BMRB
deposition has been a long running issue. I have included Eldon
Ulrich from the BMRB in the CC list as he would be the person to
discuss this with (note this is the relax-devel public mailing list
which is permanently archived). Since discussions at the ENC
conference in 2009, Eldon and I have jointly developed both the
support in relax and the required NMR-STAR saveframes and tags for
fully and properly supporting the deposition and reading of model-free
data. This includes the base relaxation data and its metadata, all
parameters used such as CSA and dipolar coupling information, the
diffusion tensor, and the internal model-free motions (as well as
citations, the molecular assembly, experimental details, etc). See
http://www.nmr-relax.com/api/3.3/specific_analyses.model_free.api.Model_free-class.html#bmrb_write
and
http://www.nmr-relax.com/api/3.3/specific_analyses.model_free.api-pysrc.html#Model_free.bmrb_write.
As for relaxation dispersion data, I think I have discussed this with
Eldon in person (and possibly also with Art Palmer). But the
relaxation dispersion analysis in relax was at the time not in a
useful state, unlike today where relax is now probably faster and more
comprehensive than all other dispersion software out there. I do not
know the current state of the BMRB database with respect to relaxation
dispersion data, but Eldon should be able to help. If the support is
not currently there, then we would need to follow the same development
path as with the model-free analysis. This would involve joint
discussions with Eldon about what NMR-STAR saveframes and tags need to
be developed to support the data. These would then have to be added
to the BMRB. And we would need to extend both relax and the bmrblib
library (https://gna.org/projects/bmrblib/), which used to be part of
relax and which uses Jurgen Doreleijers' Pystarlib library
(https://code.google.com/p/pystarlib/). The STAR format is relatively
simple (http://www.bmrb.wisc.edu/formats.html) but Jurgen's library
handles that part for you. Troels, your coding skill are now so
advanced that you should have no problem adding this support to the
relaxation dispersion analysis in relax and to also extend the brmblib
which is really also a part of relax. It would only be a couple of
weeks to a month to develop. The hardest part may be to discuss and
have all the required tags added to the BMRB itself.
However for you Troels, I would recommend that you consider this for a
later project, as I know you have some other important deadlines to
meet first. I believe there is strong interest on the side of the
BMRB to have this type of data deposited, and with relax we have the
best starting point for this. Kaare Teilum has a lot of high quality
CPMG and R1rho data which could form the basis of the initial BMRB
depositions. From Kaare's point of view, I don't know how beneficial
this would be. Anyway, you should discuss this with your supervisor
Kaare and determine if this short project is worth your time, after
your other deadlines have been met.
Regards,
Edward
On 3 October 2014 18:31, Troels E. Linnet
<NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
Update of task #7858 (project relax):
Status: In Progress => Gone walkabout
_______________________________________________________
Follow-up Comment #6:
This feature will not be implemented, as it requires a large re-write of
data
structures.
To implement the funvtion, it would require a re-write of the relax_data
bmrb_write(star) function, and proper handling of cdp.ri_ids.
It was also not readily possible to find examples of submitted CPMG data in
the BMRB database.
This makes it hard to develop, and even ensure that BMRB would accept the
format.
_______________________________________________________
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<http://gna.org/task/?7858>
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Re: [task #7858] Make it possible to submit CPMG experiments for BMRB