Author Topic: Liquid state NMR  (Read 5176 times)

srbh.sxna

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Liquid state NMR
« on: October 15, 2012, 12:12:36 PM »
Dear Sir,
I am new to this community but I have been using Spinach library since last six months. I am trying out some liquid state pulse sequences, in particular HSQC; and my spin system has CA-CO coupling. Problem is that I can't get rid of the CO coupling from the indirect dimension. I have tried using shaped off resonance pulse in middle of the F1 evolution(to invert CO only), but this seems to affect the "on resonance" CA peak (severe phase distortion). I think I am missing something...

I suspect the evolution "during" the pulse. I tried to compensate it by applying another pulse at the end of the period ..but it didn't help.

am I missing something?...Could you please guide me on this :)
« Last Edit: October 17, 2012, 09:25:23 AM by srbh.sxna »

srbh.sxna

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Re: Liquid state NMR
« Reply #1 on: October 15, 2012, 12:24:04 PM »
Just to mention...pwrf, npoints and B1 are the parameters taken form the generated shape file!

srbh.sxna

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Re: Liquid state NMR
« Reply #2 on: October 15, 2012, 01:06:29 PM »
One more thing...how does Spinach account for the evolution during the pulse(shaped pulse)?

kuprov

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Re: Liquid state NMR
« Reply #3 on: October 15, 2012, 01:59:17 PM »
Looking into it... in principle, the easiest way to run a selective pulse is to specify the spins the operator should act on:

operator(spin_system,{'L+'},{3}) is the L+ on the third spin -- so if you make a pulse operator that only affects your chosen spins, the pulse may well be a hard pulse.

Spinach does include evolution during the shaped pulse -- would you like an option to turn it off?

srbh.sxna

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Re: Liquid state NMR
« Reply #4 on: October 17, 2012, 09:49:18 AM »
It's fixed...I was able to decouple with the same approach mentioned above..but this time I took into account the error in the "shaped_pulse" function(by shifting the chemical shifts of my spin system). It seems that the offset error was responsible for incorrect results
(I believe my error conclusion for shaped_pulse function was wrong..something else seems to be meddling with my spectrum)!

Just two more things...
1). Is it possible to speed up the simulation involving shaped pulses?...it takes really a long time (in minutes on my 4X3.3GHz).
2). I observed when I run Spinach scripts, only one core is used..is there any option in Spinach that forces the threading or parallel computation with multiple cores?

thanks :)
« Last Edit: October 18, 2012, 12:03:19 PM by srbh.sxna »

kuprov

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Re: Liquid state NMR
« Reply #5 on: October 17, 2012, 06:48:39 PM »
I am still puzzled by your offset troubles -- shaped_pulse does take offsets into account, you can see that yourself if you look into the code. Can you send me the simulation where it does not perform as advertized?

Regarding parallelization, many functions in Spinach would run in parallel -- just run the "matlabpool" command before you run a Spinach simulation.

How many points does your shaped pulse have?

srbh.sxna

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Re: Liquid state NMR
« Reply #6 on: October 18, 2012, 11:22:21 AM »
Many thanks :) ...sorry for bothering you with such trivial issues.

Indeed the offset is accounted and I believe that my perception about having some issue in shaped_pulse function was wrong. But now my problem goes back to the CO decoupling issue I started with. I will send you the simulation script to make sure if I haven't made any mistakes.

I will be thankful if you could look at it :)
« Last Edit: October 18, 2012, 11:40:24 AM by srbh.sxna »

kuprov

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Re: Liquid state NMR
« Reply #7 on: October 18, 2012, 07:57:50 PM »
OK, sent you the file -- see if it works as you expect.

srbh.sxna

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Re: Liquid state NMR
« Reply #8 on: October 19, 2012, 11:10:37 AM »
Great..it works as it should :) many thanks :)