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Messages - srbh.sxna

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1
Spinach bug reports / Re: Offset problem for shaped pulse
« on: October 19, 2012, 11:25:25 AM »
Great...it works :) thanks a lot :)

2
Simulations / Re: Liquid state NMR
« on: October 19, 2012, 11:10:37 AM »
Great..it works as it should :) many thanks :)

3
Spinach bug reports / Re: Offset problem for shaped pulse
« on: October 18, 2012, 11:38:07 AM »
thanks for help :) ..

Yes..indeed.. the center of the spectrum changes when we change the offset...so setting the offset is ok(shaped_pulse function seems correct)....but there seems to be some issue related to the effect of the "off resonance pulse" at "on resonance".

yes..The offset was put in Hz (I just wrote in ppm here to avoid cluttering). Also the parameters.offset was given as an input argument to the shaped_pulse function.

I have attached the code for your reference..kindly guide :)

4
Simulations / Re: Liquid state NMR
« 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 :)

5
Simulations / Re: Liquid state NMR
« 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 :)

6
Spinach bug reports / Re: Offset problem for shaped pulse
« on: October 16, 2012, 02:51:54 PM »
thanks.. :)
For your ref.. I have attached two 1D spectra to show the offset error. I have used off resonance sinc pulse (CO 180 of CA) on 62spins(13C).

Pulse sequence= shaped_pulse + step(spin_system,Ly_C,rho,pi/2)-->acquire;

Case1:
inter.zeeman.scalar=num2cell(linspace(0,180,62));
parameters.offset=35 %(in ppm)
result: wrong_offset.eps (attached)

Case2:
inter.zeeman.scalar=num2cell(linspace(-35,145,62)); %[(0-35),(180-35)]
parameters.offset=0 %(in ppm)
result: offset_corrected.eps (attached)

of course..it is not in good CO range..but this offset error can play a big role in 2D exps!

7
Simulations / Re: Liquid state NMR
« on: October 15, 2012, 01:06:29 PM »
One more thing...how does Spinach account for the evolution during the pulse(shaped pulse)?

8
Spinach bug reports / Offset problem for shaped pulse
« on: October 15, 2012, 12:59:04 PM »
Hi..
I am using the Spinach (Version 1.1.1054) and I found that the function "shaped_pulse" does not enforces the offset given by the user. I tried this with varying offsets and pulses ..and surprisingly it assumes the offset to be at 0 every time.

For very simple spin system (60 spins "13C" distributed from 35ppm to 180 ppm )..to observe the effect at any desired offset(say 35 ppm) I had to shift the shift the chemical shift (0-chemical shift=-35ppm))..and then this works perfectly. But this can't be done in practice!!

could it be the bug or i am making any mistake?
thanks..

9
Simulations / Re: Liquid state NMR
« on: October 15, 2012, 12:24:04 PM »
Just to mention...pwrf, npoints and B1 are the parameters taken form the generated shape file!

10
Simulations / 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 :)

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