Hi,
I've been thinking about the options for this, and think that you have
covered all the standard relaxation rates for a two spin system. I
just wonder, how do you identify which nucleus type, 1H, 13C, 15N,
etc. matches the I or S nominclature? And how does this apply to the
situation where you have collected C and N relaxation rates for the
same residue (backbone amide N and Ca, or RNA relaxation rates)?
Would these be stored in different saveframes? Also, it's very
important to know the labelling state, i.e. is it double labelled with
15N and 13C, is it deuterated, etc. This would already be within the
NMR-STAR definition, would it not? Oh, also is there a reason for the
brackets in I(+,-)? The + and - are not usually used with brackets,
but are placed as superscript.
As for the saveframe label, could it be something like
'relaxation_data' or 'relaxation_rate'? Could it be extended to
include the R1, R2, and R1rho as possibilities so that the saveframe
covers all standard relaxation rates of a 2 spin system? This would
make the Heteronucl_T*_list frames redundant but might make future
parsing by external programs simpler.
One important part missing from all of this is the relaxation rates
that TROSY, CRIPT, CRINEPT, etc. depend upon. There is no option for
storing cross-correlated relaxation (also know as relaxation
interference). Most rates measured are the cross-correlation between
the CSA relaxation and the dipolar relaxation of a heteronuclear 2
spin system. But you can also have cross-correlation between 2 or
more dipolar relaxation mechanisms, for example in a methyl group. An
important use for this in relaxation analyses is that for big systems,
RNA, etc., the cross-correlated rates eta_z and eta_xy can be used as
replacements for the R1 and R2 rates respectively. This is not yet in
relax, but wouldn't take me very long to add once someone with these
rates would like to perform model-free or another analysis. One
possibility would be to use operators such as I(+,-)Sa, I(+,-)Sb,
IaS(+,-), IbS(+,-). I'm not sure of all the possible options here,
but the eta rates may not be able to be split into these 4 components
in all cases. And then for a full listing of these rates, again I'm
not sure of all the possibilities.
Regards,
Edward
On Sat, Jan 24, 2009 at 6:40 PM, Eldon Ulrich <elu@xxxxxxxxxxxxx> wrote:
Hi,
For the T1(R1), T2 (R2), and T1rho (R1rho) relaxation data a tag has been
available in the NMR-STAR dictionary for defining the 'coherence type' that
was observed in collecting the data. It has been pointed out that the
enumerated values for the coherence type tags were not accurate. The
existing enumerations include atom types (N, H, etc.), information repeated
in some sense in the data tables where the atoms involved in the relaxation
are listed.
In trying to improve how these data are represented, we have consulted with
people in the NMR facility here and have derived the draft proposal shown
below and would like to have feed back from you and those working on the
Relax project.
In this proposal, I and S are used as the general terms for the spins
involved. 'z' and '+' and '-' are used to describe the magnetization. In
addition to the tables for T1, T2, and T1rho, a new saveframe
(general_relaxation) has been added to capture relaxation data that may not
fit in the other categories. If a better term than 'general_relaxation'
would fit these kinds of data, please provide your advice.
Your comments and suggestions would be very helpful.
Thank you,
Eldon
save__Heteronucl_T1_list.T1_coherence_type
loop_
_item_enumeration_value
_item_enumeration_description
Iz 'zero quantum, longitudinal'
Sz 'zero quantum, longitudinal'
stop_
save_
save__Heteronucl_T1rho_list.T1rho_coherence_type
loop_
_item_enumeration_value
_item_enumeration_description
I(+,-) 'single quantum'
S(+,-) 'single quantum'
stop_
save_
save__Heteronucl_T2_list.T2_coherence_type
loop_
_item_enumeration_value
_item_enumeration_description
I(+,-) 'single quantum'
S(+,-) 'single quantum'
stop_
save_
save__General_relaxation_list.Relaxation_coherence_type
loop_
_item_enumeration_value
_item_enumeration_description
I(+,-)S(-,+) 'zero quantum'
IzSz 'zero quantum, longitudinal spin order'
I(+,-)Sz 'single quantum, antiphase'
IzS(+,-) 'single quantum, antiphase'
I(+,-)S(+,-) 'double quantum'
stop_
save_
Re: [task #6438] To relax the BMRB.