Processing NUS Data Examples of 2D in addition to 3D spectra 4D to be appended soon. Assume

Processing NUS Data Examples of 2D in addition to 3D spectra 4D to be appended soon. Assume www.phwiki.com

Processing NUS Data Examples of 2D in addition to 3D spectra 4D to be appended soon. Assume

Mendenhall, Laurie, Contributing Editor has reference to this Academic Journal, PHwiki organized this Journal Processing NUS Data Examples of 2D in addition to 3D spectra 4D to be appended soon. Assumed knowledge: NMRPipe in addition to NMRDraw : Unix Environment 2D Processing 1D Reconstruction 15N, 13C HSQC in addition to Homonuclear Spectra Single indirect dimension acquired non-uni as long as mly We convert data from Bruker/Varian like normal Processing starts by doing FT on directly acquired data first Data is then transposed ready as long as reconstruction 2D Spectra Conversion fid.com !/bin/sh -f bruk2pipe -in ser -DMX -swap -decim 24 -dspfvs 12 -xN 2048 -yN 80 -xT 1024 -yT 40 -xMODE DQD -yMODE Echo-AntiEcho -xSW 7002.801 -ySW 1824.568 -xOBS 500.130 -yOBS 50.678 -xCAR 4.697 -yCAR 118.000 -xLAB 1H -yLAB 15N -ndim 2 -aq2D States -out data.fid -ov -verb Nothing Special as long as 2D Spectra Conversion!

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Direct Dimension Trans as long as m ft1.com nmrPipe -in data.fid nmrPipe -fn SOL nmrPipe -fn SP -off 0.3 -end 0.98 -pow 2 nmrPipe -fn ZF -auto nmrPipe -fn FT nmrPipe -fn PS -p0 46 -p1 0.0 -di nmrPipe -fn EXT -left -sw -verb nmrPipe -fn TP -verb -ov -out test.ft1 Viewing this output in NMRPipe allows you to phase direct dimension. Direct Dimension Processing Only Let’s fill in the blanks ist.com !/bin/csh istHMS -in $1 -out $2 -zero 1 -vlist sched.1d -xN 440 -over 0 -ref 0 -itr 400 -verb 1 If this script is called ist.com then you would run it as: ist.com test.ft1 test.ft2

Direct Dimension Processing Only Let’s FT indirect dimension! ft2.com nmrPipe -in test.ft2 nmrPipe -fn SP -off 0.3 -end 0.98 -pow 1 -size 512 -c 0.5 nmrPipe -fn ZF -size 1024 nmrPipe -fn FT nmrPipe -fn PS -p0 90 -p1 0.0 -di nmrPipe -fn POLY -ord 0 -auto nmrPipe -fn TP nmrPipe -fn POLY -ord 0 -auto -verb -ov -out test.ft3 pipe2ucsf test.ft3 HSQC.ucsf 2D Processing Done

Simplified 2D Reconstruction ft12.com nmrPipe -in data.fid nmrPipe -fn SOL nmrPipe -fn SP -off 0.5 -end 0.98 -size 512 -c 1.0 nmrPipe -fn ZF -size 1024 nmrPipe -fn FT -auto nmrPipe -fn PS -p0 -120.0 -p1 0.0 -di nmrPipe -fn EXT -left -sw -verb nmrPipe -fn TP istHMS -xN 512 -sched ./sched.1d -itr 400 nmrPipe -fn SP -off 0.5 -end 0.98 -c 0.5 -size 512 nmrPipe -fn ZF -auto nmrPipe -fn FT -auto nmrPipe -fn PS -p0 -90.0 -p1 0.0 -di -verb nmrPipe -fn POLY -ord 0 -auto nmrPipe -fn TP nmrPipe -fn POLY -ord 0 -auto -ov -out test.ft12 Looks great! 3D Processing 2D Reconstruction Triple Rez, 3D NOESY, HC(C)H, XX(CO)NH etc Two indirect dimensions acquired non-uni as long as mly We convert data from Bruker/Varian differently in addition to cautiously Processing starts by doing FT on directly acquired data first – just like 2D Data is then transposed ready as long as reconstruction Reconstruction followed by FT in 2nd in addition to 3rd dimension.

3D Spectra Conversion fid.com !/bin/csh bruk2pipe -in ./ser -bad 0.0 -noaswap -DMX -decim 24 -dspfvs 12 -grpdly 0 -xN 2048 -yN 4 -zN 818 -xT 1024 -yT 2 -zT 409 -xMODE DQD -yMODE Real -zMODE Real -xSW 7002.801 -ySW 1824.818 -zSW 2777.778 -xOBS 500.132 -yOBS 50.684 -zOBS 125.780 -xCAR 4.772 -yCAR 119.571 -zCAR 176.054 -xLAB HN -yLAB 15N -zLAB 13C -ndim 3 -aq2D States nmrPipe -fn MAC -macro $NMRTXT/ranceY.M -noRd -noWr pipe2xyz -out ./fid/test%03d.fid -verb -ov -to 0 What is going on here What is going on here Data no longer collected as a series of planes. Instead, treat data as string of points acquired according to the schedule. In 3D spectrum there are 4 FIDs per indirect point. -yN = 4 2 FIDs as long as each indirect dimension. E.g. 2 FIDs as long as Nitrogen (a complex point) 2 FIDs as long as Carbon (a complex point) This is how the Pulse Program Acquires the data Then there are 818 points acquired. -zN = 818 We treat each FID is real as long as conversion Each FID is put into a complex line of data by the reconstruction program Any dimension with non-complex acquisition (read Echo-AntiEcho) needs to be labeled as such. nmrPipe -fn MAC -macro $NMRTXT/ranceY.M -noRd -noWr Here the Y dimension (Nitrogen) is labeled as Rance-Kay (Echo-AntiEcho). Direct Dimension Trans as long as m ft1xyz.com xyz2pipe -in fid/test%03d.fid -x nmrPipe -fn SOL nmrPipe -fn SP -off 0.3 -end 0.98 -pow 2 -c 1.0 -size 512 nmrPipe -fn ZF -size 512 nmrPipe -fn FT -verb nmrPipe -fn PS -p0 -34.4 -p1 0.0 -di nmrPipe -fn EXT -x1 11.0ppm -xn 5.5ppm -sw pipe2xyz -ov -out xyz/test%03d.ft1 -x Read in x dimension, write out to x dimension This allows phasing of direct dimension in NMRPipe.

Direct Dimension Processing Only Phase, Transpose as long as Reconstruction ft1.com xyz2pipe -in fid/test%03d.fid -x nmrPipe -fn SOL nmrPipe -fn SP -off 0.3 -end 0.98 -pow 2 -c 1.0 -size 512 nmrPipe -fn ZF -size 512 nmrPipe -fn FT -verb nmrPipe -fn PS -p0 -34.4 -p1 0.0 -di nmrPipe -fn EXT -x1 11.0ppm -xn 5.5ppm -sw pipe2xyz -ov -out xyz/test%03d.ft1 -z Read in x dimension, write out to z dimension This places indirect data in the x in addition to y dimensions. This is necessary as long as istHMS reconstruction. Fill in with Blanks, Reconstruct ist.csh !/bin/csh -xv set F = $1 set in = $F:t set out = $F:t:r.phf set ft1 = $F:t:r.ft1 echo $in $out $ft1 istHMS -dim 2 -incr 1 -xN 64 -yN 128 -user 1 -itr 400 -verb 1 -ref 0 -vlist ./sched.2d < ./yzx/${in} >! ./yzx-ist/${out} -xN in addition to -yN can be replaced with -autoN which gets the limits of reconstruction from the schedule file Each file in ‘yzx’ directory needs to be processed this way. Opportunity as long as parallelization of this process.

Cluster Submission E.g. as long as each F (yzx/test.ft1) qsub -cwd ./ist.csh $F end Many other methods. Consult your sys/cluster admin. Multicore Laptop/Desktop Processing Use a perl program that will run multiple jobs as long as you at once, but never more than one job per possible thread. My Macbook pro: 4 cores, 8 threads. 8 processes at once. Not too shabby. parallel -j 100% ‘csh ist.csh {} 2> /dev/null; echo {}’ ::: yzx/test.ft1 Running at 100% will make things toasty. You can run at 50% etc etc. This will take 15-30 minutes as long as typical spectra . coffee time! Reordering FIDs phf2pipe.com !/bin/csh xyz2pipe -in yzx-ist/test%03d.phf phf2pipe -user 1 -xproj xz.ft1 -yproj yz.ft1 pipe2xyz -out rec/test%03d.ft1 FIDs are fully reconstructed from last step FIDs are now in conventional order (planes) xproj in addition to yproj give the first plane in each indirect dimension – as long as phasing. Lets look at yz.ft1

Projection Phasing Final Processing ft23.com !/bin/csh -f xyz2pipe -in rec/test%03d.ft1 -x nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 nmrPipe -fn ZF -size 64 nmrPipe -fn FT -verb nmrPipe -fn PS -p0 0.0 -p1 0.0 -di nmrPipe -fn REV -verb nmrPipe -fn TP nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 nmrPipe -fn ZF -size 128 nmrPipe -fn FT -alt -verb nmrPipe -fn PS -p0 0.0 -p1 0.0 -di nmrPipe -fn ZTP > rec/data.pipe pipe2xyz -in rec/data.pipe -out rec/test%03d.ft3 -y pipe2ucsf rec/data.pipe GB1-NUS-HNCO.ucsf Nice Spectrum!

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