On Wed, Jan 28, 2009 at 4:43 PM, Eldon Ulrich <elu@xxxxxxxxxxxxx> wrote:
Hi,
Thank you very much for the comments. There is a lot to be considered. I
will try to provide a more detailed response to your comments later, but
would like to give a quick response now to keep the conversation going.
1. The parentheses are suggested for +,- because within the ASCII 127
character limited of NMR-STAR, subscripts and superscripts are not
available. Would there be a better way to construct the nomenclature that
can be handled with the limited ASCII values available?
I don't know if this violates the NMR-STAR style, but maybe for
example allow S- and S+ as 2 separate options for the R2? Both
operators relax with the same rate and are essentially the same thing.
Or maybe S+,- without the brackets, although that's not as neat.
From my perspective, rather than the BMRB, this doesn't matter too
much.
2. The list of enumeration values provided was not intended to be complete.
Hopefully the style of nomenclature would be flexible enough to accommodate
other coherence types.
Well, essentially this covers the diagonal of the 16x16 element
Redfield kite. This is where you use, for example, Sz and Sz to get
the R1 rate. The relaxation super-operator is between 2 operators,
see for example equation 5.56 of "Protein NMR Spectroscopy, Principles
and Practice" by Cavanagh et al. where the Br and Bs notation is used
for these operators. So for the R1, you look at Sz and Sz operators.
However there are off-diagonal elements such as the steady-state NOE.
All the other off-diagonal elements are equal to zero, unless you have
degenerate transitions. Then you can have relaxation between Iz and
Sz.
None of this is cross-correlated relaxation though. I think most
relaxation interference is also using the operators Sz with Sz (eta_z)
or S+ with S+ (eta_xy). I'm not an expert here so I don't know if you
can have Iz with Sz.
3. The isotopic labeling of the molecules studied is defined in the sample
description. Depositors should provide a full description including
deuteration and any specific site labeling used.
Ok. I might consider this when designing the relax STAR output for
BMRB submission.
4. Saveframes do exist for cross-correlation dipole-dipole and dipole-CSA
relaxation in the dictionary and these kinds of data can be deposited using
the ADIT-NMR interface. Comments on how these saveframes are constructed
would be much appreciated. In each case, the idea is that the atoms involved
are defined for each value reported.
Are these defined in the same way as those for standard relaxation
data? Is there enough flexibility to handle the 16x16 elements for
dipole-CSA and the 16x16 elements for dipole-dipole (well that's
assuming 2 spins)? A lot of these elements will be zero and many will
be impossible to interpret due to spin diffusion, but maybe someone
might be crazy enough to collect the data.
5. The category names could be changed. R1, R2, and R1rho data can be
handled in the current T1, T2, and T1rho saveframes, by providing the
appropriate units for the val_units tag. I know this does not make you
comfortable. I will try to bring this issue up with our Advisory Board to
see if they feel the dictionary needs to be changed.
The suggestion was just to make the definition more compact and
cleaner with a single saveframe for all 16x16 elements of the Redfield
kite. The end result from my perspective doesn't matter, as long as
the data can be stored. I will make sure relax can output the
appropriate saveframe as well as read it in. But if there is one
saveframe for the 16x16 standard relaxation rates, one for the 16x16
dipole-CSA interference rates, and one for the 16x16 dipole-dipole
rates, that should cover most of the data anyone would be insane
enough to collect. Or maybe even one saveframe for all of these
rates. I don't know if anyone would measure the methyl
dipole-dipole-dipole interference rates (although I have a distant,
blurry memory of this being published), but that might require another
saveframe for the 16x16x16 elements (although it might be possible to
measure only one of these 4096 rates). I wonder if you can observe
quadrapolar-dipole or quadrapolar-CSA interference rates? But if all
possible conceivable rates are covered in a concise and clean system,
then these BMRB records should be future proof.
Regards,
Edward
Re: [task #6438] To relax the BMRB.