As we know, array in VnmrJ can be used to optimize parameters for data
collection and to acquire a series of dataset, which are not limited to 1D
only. For example, for backbone dynamics measurement, 15N R1, R2,
heteronuclear NOE, one can use array to collect all the individual 2D HSQC
type data in an interleaved fashion, rather than to collect one by one.
There are advantages to use array here. First, system conditions such as lock
level, temperature etc, are averaged over entire datasets. Second, the
experiment can be stopped before it is fully completed and the data is still
usable. If without array, system conditions could be a little different from
one delay point to another. Also, one has to wait till the acquisition of the last delay point
finishes in order to process the data. Obviously, it is more
convenient to use array.
To set up such arrayed 2D NMR is not difficult. Below is an example used
to acquire 15N R1 relaxation data. Just 4 more commands and you are ready
to go.
/* setup a regular HSQC, choose N15T1 */
relaxT=0.02,0.05,0.1,0.2,0.4,0.6,0.9,1.3 /*8 delays in relaxT array */
array=’relaxT,phase’ /* keep phase the innermost loop */
bs=1 /* block size */
il=’y’ /* interleave on for dynamics experiment */
go /* collect data */
Below is an example to monitor HD exchange using HSQC. ‘pad’ is arrayed.
In the example, 4 hsqc is acquired with 10 min delay in between.
/* for a series of HSQC, eg. to monitor HD exchange, try array ‘pad’ */
il=’n’ /* no interleave for HD exchange HSQC*/
pad=0.5,600,600,600 /*pre-acquisition delay in sec, 4 HSQC */
/* the following array will collect 99 HSQC continuously */
array(‘pad’,99,1.0,0.0)
array=’pad,phase’ /* keep phase the innermost loop */
The arrayed data has a single fid file and can’t be processed within VnmrJ.
The attached nmrPipe scripts can process the data.
######### Beginning of fid.com #########
#!/bin/csh
var2pipe -in ./fid \
-noaswap \
-xN 1024 -yN 8 -zN 128 \
-xT 512 -yT 8 -zT 64 \
-xMODE Complex -yMODE Real -zMODE Rance-Kay \
-xSW 7225.434 -ySW 0 -zSW 1823.306 \
-xOBS 599.801 -yOBS 0 -zOBS 60.784 \
-xCAR 4.773 -yCAR 0 -zCAR 120.134 \
-xLAB HN -yLAB ID -zLAB N15 \
-ndim 3 -aq2D States \
| nmrPipe -fn TP \
| nmrPipe -fn ZTP \
| nmrPipe -fn TP -hyper \
| pipe2xyz -out ./data/test%03d.fid -verb -ov
sleep 5
######### End of fid.com #########
######### Beginning of nmrproc.com #########
#!/bin/csh
xyz2pipe -in data/test%03d.fid -x \
# SOL and POLY similar result \
| nmrPipe -fn SOL \
| nmrPipe -fn GM -g1 5.0 -g2 10.0 -g3 0.0 -c 0.5 \
| nmrPipe -fn ZF -size 2048 \
| nmrPipe -fn FT -auto \
| nmrPipe -fn PS -p0 136.00 -p1 0.00 -di -verb \
| nmrPipe -fn EXT -x1 6.5ppm -xn 10.5ppm -sw \
| nmrPipe -fn TP \
| nmrPipe -fn LP -ps90-180 -ord 8 \
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
| nmrPipe -fn ZF -size 256 \
| nmrPipe -fn FT -auto \
| nmrPipe -fn PS -p0 0.00 -p1 0.00 -di -verb \
| nmrPipe -fn TP \
| pipe2xyz -out ft/test%03d.ft2 -x
######### End of nmrproc.com #########
