Spin Dynamics Forum

SpinDynamica support => Bug reports => Topic started by: JBashir on February 28, 2014, 09:28:38 PM

Title: Difficulties simulating ST2PT (Trosy Experiments)
Post by: JBashir on February 28, 2014, 09:28:38 PM
Dear all,
I have tried to simulate the ST2-P-Transfer [Pervushin et al, JBioNMR 1998) using Productoperators in SpinDynamica.
Starting from:

Code: [Select]
opI["I", "\[Beta]"]. opI["S", "+"]
I should end up after the ST2-PT:

Code: [Select]
opI["I", "-"]. opI["S", "\[Beta]"]
to select the most narrow component of the protein amide cross peak in a 15N HSQC . Yet, I end up at:

Code: [Select]
I opI["I", "+"]. opI["S", "\[Alpha]"]
I attached a .nb-File (and the original paper) to demonstrate my problem. Can anyone help me and tell what I am doing wrong?

Thanks in advance,
Title: Re: Difficulties simulating ST2PT (Trosy Experiments)
Post by: MalcolmHLevitt on March 02, 2014, 09:50:04 PM
Dear Dominic,
 I've looked at your notebook and it seems to make sense. As far as I can tell the pulse phases are as specified in the paper as well.
 Since, as far as I can see, your calculation is correct, my suspicion falls on the evolution equation in the paper. Have you followed through in detail the reasoning in the paper? It should be possible to pick the derivation apart and verify it step by step using SpinDynamica. It's conceivable, at least, that there is a mistake in the paper, or possibly two cancelling mistakes. One place to look is the handling of the signs of the interactions and the spectral frequency axis, which are notorious sources of errors and confusion: see my attempts to clear this up in  J. Magn. Reson. 126, 164-182 (1997) and J. Magn. Reson. 142, 190-194 (2000). I do not know whether the paper you cite took the steps necessary to ensure that the signs of the spin interactions are handled correctly when deriving the equations: if they did not, this could easily have caused the discrepancy. Cross-correlation effects, as exploited in TROSY and related experiments,  do require extraordinary care in this regard (there is an example in my 1997 paper).

It will be interesting to see if you manage to understand what's going on. Sorry for not being of more immediate help.

Title: Re: Difficulties simulating ST2PT (Trosy Experiments)
Post by: JBashir on March 03, 2014, 02:35:37 PM
Dear Prof. Levitt,
thank you very much for your quick reply.
I dissected the transfer and compared it with the S3CT-selection (Sorensen et al, 1997, JBioNMR 10, pp 181-186), which - I think - forms the basis of the ST-2PT block.
It turns out, that the only significant difference between both is an inverted phase (-y--> y) of the S-Spin (attached .nb).

Having looked at your papers, I checked the paper from Prof. Pervushin again, but they did not specify, whether pulse phases are 'mashine phases' or 'math rotation phases'. My guess (or hope)  is, that as a consequence of the inverted sign of gamma_N, the specified -y-phase actually is a +y-phase in mathematical terms.
However, I looked at some other Trosy papers: some use the same phases as Prof. Pervushin. In others paper, phases are specified that would result in different semi-trosy transfer.
Can this be a matter of right- and left-handed axis system and their different implementation in Bruker and Varian?

Title: Re: Difficulties simulating ST2PT (Trosy Experiments)
Post by: MalcolmHLevitt on March 03, 2014, 07:47:16 PM
Hi Dominic,
 this is indeed a very confusing topic.

 I have checked manually the SpinDynamica transformations and they seem to be correct.

 I noted in the paper that Pervushin chose to cite experimental pulse phases with the opposite sign (for 1H (positive gamma), but not for 15N (negative gamma)) having seen my paper. SpinDynamica uses the mathematical rotation phases (not the experimental radiofrequency phases) so the sign of one 1H phase needs to be corrected in your notebook. When this is done the correct transformation is generated (see attached) -- although with an extra factor of i.

 However there is yet another complication. The coupling JIS is negative. Hence your notebook should have JIS = -100 and tauJ = Abs[1/JIS]. When this is taken into account the transformations again lose correspondence with the paper (attached).

 I have a suspicion that workers in this area mess around with the phases until they get the expected result on the particular spectrometer in use.

Unfortunately the spectrometer manufacturers have not taken care of correcting the pulse phases for the rf mixing scheme or for the sign of gamma so it is very difficult to predict a priori what a pulse sequence will do.