Mjeppesen: Undo revision 1220 by Mjeppesen (talk)

2022-01-20T05:01:12Z

Undo revision 1220 by Mjeppesen (talk)

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Mjeppesen at 04:59, 20 January 2022

2022-01-20T04:59:18Z

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Mjeppesen: LearningSorting

2021-09-11T04:42:43Z

LearningSorting

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			[[category:Protocols\|Protocols]]
			[[category:Data_Processing_and_Analysis]]

Isintuna: Created page with "This page details how to get started collecting decent-quality nonuniformly sampled (NUS) NMR datasets. = Schedule creation = For two-dimensional (2D) NMR datasets, determini..."

2021-01-21T21:19:20Z

Created page with "This page details how to get started collecting decent-quality nonuniformly sampled (NUS) NMR datasets. = Schedule creation = For two-dimensional (2D) NMR datasets, determini..."

New page

This page details how to get started collecting decent-quality nonuniformly sampled (NUS) NMR datasets.

= Schedule creation =
For two-dimensional (2D) NMR datasets, deterministic Sine-Burst sampling (''a.k.a.'' SB) is recommended, as it has a lower average IST reconstruction error than pseudorandom Poisson-Gap sampling (''a.k.a'' PG).

== Deterministic Sine-Gap ==
There's an easy web interface for ''dgs'', [http://bionmr.unl.edu/dgs.php located here]. Also, the ''dpg'' program is available in the path on our cluster, so you can run it from Linux/PuTTY without issues, like so:

dpg 50 512

Since printing the numbers to the screen is fairly useless, you can write a schedule like so:

dpg 50 512 > sched-10-512

In the ''dpg'' command, the first value is the number of points to sample in the schedule, and the second value is the total number of complex points in the uniform (reconstructed) dataset.

== Pseudorandom Poisson-Gap ==
The Wagner group hosts an online PG schedule generator [http://gwagner.med.harvard.edu/intranet/hmsIST/gensched_new.html here].

= Data collection =
Once you've generated a schedule, you'll need to set up an experiment in Topspin that uses that new schedule file. On the spectrometer PC, copy the schedule file into the directory that contains variable counter lists:

cp -iv /path/to/my/schedule/file /opt/topspin3.2.6/exp/stan/nmr/lists/vc/

Now, open Topspin and create a new experiment. Set '''FnTYPE''' to ''non-uniform sampling'', set '''TD(F1)''' to the number of total complex data points that you used to build your schedule, and set '''NUSLIST''' to the filename of your schedule that you just placed in the '''vc''' directory. (''e.g.'' it would be '''file''' for the above example copy statement)

'''CAUTION!''' NEVER click ''Calculate'' or ''Show table'' once you've set the '''NUSLIST''' parameter. Doing so will blow away your carefully crafted Poisson-Gap schedule file, turning it into a useless uniform-random schedule file.

= Data processing =
This section describes the reconstruction and processing of NUS data using hmsIST and nmrPipe. If you want to use different software packages, you'll have to look elsewhere for documentation.

== Format conversion ==
Converting from the Bruker binary format into the nmrPipe format works exactly as before, with the exception that the number of complex points in any nonuniformly sampled dimension must reflect the number of ''sampled'' points, not the number of ''total'' points. The following script should serve as an example:

#!/bin/bash
# fid.sh: generated as usual from `bruker’

bruk2pipe -in 1/ser \
-bad 0.0 -aswap -DMX -decim 2200 -dspfvs 20 \
-grpdly 67.986083984375 \
-xN 8192 -yN 100 \
-xT 4096 -yT 50 \
-xMODE DQD -yMODE Echo-AntiEcho \
-xSW 9090.909 -ySW 29239.766 \
-xOBS 700.213 -yOBS 176.081 \
-xCAR 4.700 -yCAR 75.000 \
-xLAB 1H -yLAB 13C \
-ndim 2 -aq2D States \
-out 1/hsqc.fid -verb -ov

The above dataset was collected by sampling 50 complex data points from a Nyquist grid having 512 complex points. (''i.e.'' the '''TD''' field in Topspin for 13C was set to 1024)

== Direct-dimension processing ==
Processing the uniformly sampled direct dimension proceeds just like you'd expect, so the '''proc1.sh''' script is basically the top half of the '''proc.sh''' script used to process uniformly sampled data.

#!/bin/bash
# proc1.sh: basically the first half of proc.sh

nmrPipe -in 1/hsqc.fid | \
nmrPipe -fn SOL | \
nmrPipe -fn SP -off 0.45 -end 0.98 -pow 2 | \
nmrPipe -fn ZF -auto | \
nmrPipe -fn FT | \
nmrPipe -fn PS -p0 -43.0 -p1 0.0 -di \
-verb -ov -out 1/hsqc.nus

The output file, ''1/hsqc.nus'' will be processed in the direct dimension only. It's important to open up the ''1/hsqc.nus'' file in nmrDraw to check that the first slice is phased properly before proceeding to the next step.

== Reconstruction ==
Once the direct dimension is processed, the nonuniformly sampled indirect dimension may be reconstructed. The following script shows how to take the ''hsqc.nus'' file generated in the previous step and reconstruct the complete dataset into ''hsqc.ft1'':

#!/bin/bash
# procR.sh: reconstruction of the full Nyquist grid

nmrPipe -in 1/hsqc.nus | \
nmrPipe -fn TP | \
hmsIST \
-ref 0 \
-vlist 1/nuslist \
-xN 512 \
-itr 500 \
-user 1 \
-verb 0 > \
1/hsqc.ft1

The most important options you'll need to edit will be the '''xN''' (number of complex total points) and '''itr''' (number of reconstruction iterations) flags. Just about everything else can always remain the same.

== Indirect-dimension processing ==
Once reconstruction is complete, you can process the indirect dimension in nmrPipe as you normally would. The following script, which should look eerily like the bottom half of the uniform ''proc.sh'', does exactly that:

#!/bin/bash
# proc2.sh: basically the second half of proc.sh

nmrPipe -in 1/hsqc.ft1 | \
nmrPipe -fn SP -off 0.45 -end 0.98 -pow 2 -size 512 -c 0.5 | \
nmrPipe -fn FT | \
nmrPipe -fn PS -p0 -90.0 -p1 0.0 -di | \
nmrPipe -fn TP \
-verb -ov -out 1/hsqc.ft2

Non-Uniform Sampling - Revision history

Mjeppesen: Undo revision 1220 by Mjeppesen (talk)

Mjeppesen at 04:59, 20 January 2022

Mjeppesen: Added to Category

Mjeppesen: LearningSorting

Mjeppesen: Added to Category

Isintuna: Created page with "This page details how to get started collecting decent-quality nonuniformly sampled (NUS) NMR datasets. = Schedule creation = For two-dimensional (2D) NMR datasets, determini..."