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. _______________________________________________________ Reply to this item at: <http://gna.org/task/?7858> _______________________________________________ Message sent via/by Gna! http://gna.org/ _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@xxxxxxx To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel