Hi,
Sorry, I was out of the office this morning and have just read through
the email string. It will take me a little time to digest this all. A
couple of general comments:
1. We have tried in NMR-STAR to avoid having tag values that take on
special formats and syntax. The _Auto_relaxation.Delay_interleaving
might be handled like this if this information was to be included with
the experimental data (see below for other comment):
loop_
_Auto_relaxation.Delay_ordinal
_Auto_relaxation.Delay_value
1 300
2 20
3 1000
4 10
5 15000
stop_
This preserves the values and from the order indicates the interleaving.
A general tag _Auto_relaxation.Delay_interleaving with values of yes/no
could be used as a flag.
2. Information like relaxation delays might be more appropriate in a
save frame where the acquisition parameters used in carrying out an
experiment were listed. The design for this in the NMR-STAR dictionary
may need to be revised or extended, but looks like this:
loop_
_Spectral_acq_param.ID
_Spectral_acq_param.Acquisition_dimension_ID
_Spectral_acq_param.Name
_Spectral_acq_param.Val
_Spectral_acq_param.Entry_ID
_Spectral_acq_param.NMR_spec_expt_ID
1 1 'relaxation delay 1' 300 3452 1
2 1 'relaxation delay 2' 20 3452 1
3 1 'relaxation delay 3' 1000 3452 1
4 1 'relaxation delay 4' 10 3452 1
5 1 'relaxation delay 5' 1500 3452 1
stop_
In this construct a tag is not needed for every parameter that needs to
be defined. The parameter name is the value to a tag and then a value
provided. As currently implemented, the order in which the parameters
are executed is not captured with an 'ordinal' tag.
If the delay information is being extracted from the acquisition files,
I would lean towards putting the information into the NMR_spec_expt save
frame and then linking the experiment to the data set save frame. If the
depositor is being asked to provide the information, then it is
trickier. Something to think about.
I think the Rex_frequency_1H information request was mentioned earlier.
Was it suggested that a tag like this should also be included in another
save frame?
Cheers,
Eldon
On 3/8/11 7:01 AM, Sébastien Morin wrote:
* 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.
I would suggest that the values are stored as both field dependent
Rex and
field independent sigma_Rex. The former would be useful for human
perception
and comparison with the amplitude of the R2 data, and should
definitely be
associated to a magnetic field (!). The latter would be better for
direct
comparison between different systems / proteins...
Then we could have the new tags:
_Order_parameter_list.Rex_frequency_1H
_Order_param.Sigma_rex_val
_Order_param.Sigma_rex_val_fit_err
And keep the old tags:
_Order_param.Rex_val
_Order_param.Rex_val_fit_err
These 5 should cover everything.
Regards,
Edward
That sounds very good.
Séb :)
Re: Rex in the BMRB