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Messages - JBashir

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Bug reports / Re: Difficulties simulating ST2PT (Trosy Experiments)
« 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?


Bug reports / Difficulties simulating ST2PT (Trosy Experiments)
« 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,

Bug reports / Symbolic phase fails for RotationSuperoperator
« on: August 04, 2013, 01:41:23 PM »
it appears, that RotationSuperoperator[] with sympbolic phases "-x" & "-y" returns a non-numerical matrix, which cannnot be used for Amplitude calculations:
Code: [Select]
 opI["z"] -> opI["y"],
 {RotationSuperoperator[{\[Pi]/2, "-x"}]}
SpinDynamica returns the erromessage:

NPropagate::nonnumeric: A non-numeric matrix was detected. The requested context does not permit Operators or Superoperators with symbolic coefficients.

Setting the phase numerically (pi) circumvents the problem. I attached a notebook demonstrating the issue.


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