Hi,
Please see below.
On 8 March 2011 12:09, Sébastien Morin <sebastien.morin@xxxxxxxxx> wrote:
Hi Eldon and Edward,
Currently, from what I understand from the BMRB storage format, Rex values
derived from model-free analysis are stored in the "T2 relaxation" frame
under "_Rex_value" and "_Rex_error" tags.
Those are the old v2.1 tags. For the values from a model-free
analysis they are now called _Order_param.Rex_val and
_Order_param.Rex_val_fit_err. I'm not sure if you can use the
model-free Rex values in the _Auto_relaxation.Rex_val tag though. I'm
guessing these tags are for experimentally measured Rex values rather
than fitted via a specific theory values.
Generally, these values will be scaled and deposited for a single magnetic
field. Hence, I wonder:
* If there should be some automatic scaling of the data so that Rex values
scaled to other magnetic fields could be readily available in the BMRB file.
This would, of course, need the user to confirm that values should be
scaled, for example, assuming a fast exchange regime... Moreover, in the
case where some R2 values are deposited but were not used in the model-free
analysis (for example, in case of inconsistency as in Morin and Gagné, 2009,
Biophys.J. 96: 4681–4691), no Rex should be associated with this particular
magnetic field...
If the values are from model-free analysis, this analysis assumes fast
exchange and hence quadratic scaling. So if you used the model-free
Rex values in the relaxation saveframes, you could scale these and
have different Rex values per Auto_relaxation saveframe, as each of
these saveframes corresponds to a different magnetic field strength.
But I don't think we should use the _Auto_relaxation.Rex_val tag.
* If the magnetic field independent value should be stored somewhere else. I
guess that Edward has already discussed this before in some post..?
Any idea / comment ?
I have only recently noticed this problem with the scanning of the
entire BMRB. But I think we need a tag identifying the frequency of
the Rex data in the Order_parameter saveframe. For example:
_Order_parameter_list.Rex_frequency_1H
This is modelled on the
_Auto_relaxation_list.Spectrometer_frequency_1H tag. Alternatively
the Rex values could be the sigma_Rex field strength independent
value, though none of the current data is in this notation.
Regards,
Edward
Re: Rex in the BMRB