Chris MacRaild wrote:
On Dec 3, 2007 10:47 PM, Gary Thompson <garyt@xxxxxxxxxxxxxxx> wrote:
on an aside should we start supporting the ccpn datamodel?
Support of the CCPN data model (http://www.ccpn.ac.uk/ccpn/data-model)
can of course be added to relax, and would be a welcome addition.
Well for the 1.3 line anyway. Can you envisage a practical use for
this? Is there a specific application? Do you mean for the structure
reader? Or for the spectral side of things?
both... It should be possible to set things up so you extract relaxation
parameters from the datamodel and return the results back to the
datamodel...
Is the datamodel really ready for that? Last we talked to Tim & Rasmus
about this, there was nowhere in the datamodel for results of a
model-free analysis. That was a long time ago, but I get the
impression they have been busy with things other than that - correct
me if I'm wrong.
I think this was a while back they do now have this idea of a
measurement list and I guess that where it would go. However, we would
have to talk to the cambridge people more before we went that far. The
mention of it was certainly along the lines that it something we should
plan for ...
It raises a few curly, if pedantic, issues: eg. to
what element of the molecular system does an order parameter belong?
In the case of amide relaxation, it should be the amide bond vector,
in the case of methyls, it belongs to the symetry axis. Are these even
meaningful concepts in the datamodels representation of the molecular
system? (It becomes even more tricky if we consider relaxation of
nuclei with non-colinear sources of relaxation!)
well the measurement list does define measurements for DipolarRelaxation
in terms of sets of resonances (ccpn class DipolarRelaxation) but only
defines the relaxation as being between 2 nuclei ;-)!!
On a more parctical note, I wouldn't be encouraging anyone to use
Analysis to determine relaxation rates. Neither the peak integration
nor rate-fitting routines were up to the job, last I played with them
(Again, this may have changed recently, but I've missed it in the
release notes if it has).
Indeed I would agree. I have't tested there latest software, so this
should not seen as a suggestion that the software is currenly up to the
job (though i would like to be proved wrong)
None of my negativity is meant to imply that this is a bad idea,
however. It would be great if Analysis and the data model were up to
suplying relax with data, and vice-versa. I'd just point out it there
is more work to be done than just some import/export functions in
relax (otherwise I might have done it myself 18 months ago!)
True the suggestion is that it is something that we should keep in sight
and investigate (and if we work at it it might help debug the datamodel
and get things going I would expect that there is a need for a good
'strawman' and relax fits the required feature set quite well)
regards
gary
Cheers,
Chris
_______________________________________________
relax (http://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
.
--
-------------------------------------------------------------------
Dr Gary Thompson
Astbury Centre for Structural Molecular Biology,
University of Leeds, Astbury Building,
Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024
email: garyt@xxxxxxxxxxxxxxx Fax +44-113-2331407
-------------------------------------------------------------------
Re: [Fwd: Re: CCPN data model.]