NUS and hmsist Tutorial

Transcription

1 NUS and hmsist Tutorial How to setup NUS experiments on Bruker Spectrometer with PGS? (Topspin 3 and above) How to process NUS experiments on Bruker using hmsist How to think about coding NUS pulse sequences for Topspin 2 and 1 How to generate PGS schedules How to obtain NUS sofware and install it How to process NUS spectra using nmrpipe and hmsist How to extract NUS data from linear dataset and play with it

2 How to get hmsist (stand alone) and the Bruker (on spectrometer) NIH Grants Help us push new version of the software Stand Alone Version for 2D/3D/4D Linux 64b Darwin 64b Bruker 2D/3D Clemens Anklin (Bruker) No license needed Linux Windows?

3 How to get PSG scheduler to work on the spectrometer. Two files 1) C program scheduler; should be placed in the /opt/.. prog/bin directory 2) au program /opt/..au/src/user That is it

4 NUS and hmsist Tutorial How to install hmsist on Linux/Darwin (Mac) Place these files in the same directory you have the nmrpipe files (Done)

5 NUS and hmsist Tutorial Comes with example data sets and instructions.

6 NUS and hmsist Tutorial How to setup NUS experiments on Bruker Spectrometer with PGS? (Topspin 3 and above)

7 Steps Involved in the Reconstruction of 3D- NUS spectra by hmsist 1) Convert the Bruker/Varian data into nmrpipe format (fid.com) 2) Fourier Transform the direct dimension that was linearly acquired ; Adjust the phase in the direct dimension (ft1xyz.com) ; Fourier Transform the data in the direct dimension and rearrange the data for hmsist (ft1.com) 3) Reconstruct the two indirect dimensions using hmsist. (using script ist.csh; this is run using all the processors available by calling ist.csh from run.local) 4) Rearrange the data to nmrpipe format, making it suitable for nmrpipe based Fourier Transform of the two indirect dimensions. (phf.com) 5) Fourier Transform the two indirect dimensions which are now reconstructed. (ft23.com) The name of the scripts are shown in red bold

8 Detail Explanation of Each Step

9 #!/bin/csh 1) Convert the Bruker/Varian data into nmrpipe format (fid.com) This could be setup using the bruker/varian command from nmrpipe bruk2pipe -in./ser \ -bad 0.0 -aswap -DMX -decim dspfvs 20 -grpdly \ -xn yn 4 -zn 1280 \ -xt yt 2 -zt 640 \ -xmode DQD -ymode Real -zmode Real \ -xsw ysw zsw \ -xobs yobs zobs \ -xcar ycar zcar \ -xlab HN -ylab 13C -zlab 1H \ -ndim 3 -aq2d States \ nmrpipe -fn MAC -macro $NMRTXT/ranceY.M -nord -nowr \ pipe2xyz -out./data/test%03d.fid -verb -ov

10 #!/bin/csh 1) Convert the Bruker/Varian data into nmrpipe format (fid.com) This could be setup using the bruker/varian command from nmrpipe bruk2pipe -in./ser \ -bad 0.0 -aswap -DMX -decim dspfvs 20 -grpdly \ -xn yn 4 -zn 1280 \ -xt yt 2 -zt 640 \ -xmode DQD -ymode Real -zmode Real \ -xsw ysw zsw \ -xobs yobs zobs \ -xcar ycar zcar \ -xlab HN -ylab 13C -zlab 1H \ -ndim 3 -aq2d States \ nmrpipe -fn MAC -macro $NMRTXT/ranceY.M -nord -nowr \ pipe2xyz -out./data/test%03d.fid -verb -ov Number of lines in your schedule

11 #!/bin/csh 1) Convert the Bruker/Varian data into nmrpipe format (fid.com) This could be setup using the bruker/varian command from nmrpipe bruk2pipe -in./ser \ -bad 0.0 -aswap -DMX -decim dspfvs 20 -grpdly \ -xn yn 4 -zn 1280 \ -xt yt 2 -zt 640 \ -xmode DQD -ymode Real -zmode Real \ -xsw ysw zsw \ -xobs yobs zobs \ -xcar ycar zcar \ -xlab HN -ylab 13C -zlab 1H \ -ndim 3 -aq2d States \ nmrpipe -fn MAC -macro $NMRTXT/ranceY.M -nord -nowr \ pipe2xyz -out./data/test%03d.fid -verb -ov

12 1) Convert the Bruker/Varian data into nmrpipe format (fid.com) This could be setup using the bruker/varian command from nmrpipe #!/bin/csh bruk2pipe -in./ser \ Always have to 4 and 2 to denote the 4 phases, two for each dimension -bad 0.0 -aswap -DMX -decim dspfvs 20 -grpdly \ -xn yn 4 -zn 1280 \ -xt yt 2 -zt 640 \ -xmode DQD -ymode Real -zmode Real \ -xsw ysw zsw \ -xobs yobs zobs \ -xcar ycar zcar \ -xlab HN -ylab 13C -zlab 1H \ -ndim 3 -aq2d States \ nmrpipe -fn MAC -macro $NMRTXT/ranceY.M -nord -nowr \ pipe2xyz -out./data/test%03d.fid -verb -ov

13 1) Convert the Bruker/Varian data into nmrpipe format (fid.com) This could be setup using the bruker/varian command from nmrpipe #!/bin/csh Number of points in the direct dimension bruk2pipe -in./ser \ -bad 0.0 -aswap -DMX -decim dspfvs 20 -grpdly \ -xn yn 4 -zn 1280 \ -xt yt 2 -zt 640 \ -xmode DQD -ymode Real -zmode Real \ -xsw ysw zsw \ -xobs yobs zobs \ -xcar ycar zcar \ -xlab HN -ylab 13C -zlab 1H \ -ndim 3 -aq2d States \ nmrpipe -fn MAC -macro $NMRTXT/ranceY.M -nord -nowr \ pipe2xyz -out./data/test%03d.fid -verb -ov

14 #!/bin/csh 1) Convert the Bruker/Varian data into nmrpipe format (fid.com) This could be setup using the bruker/varian command from nmrpipe bruk2pipe -in./ser \ -bad 0.0 -aswap -DMX -decim dspfvs 20 -grpdly \ -xn yn 4 -zn 1280 \ -xt yt 2 -zt 640 \ -xmode DQD -ymode Real -zmode Real \ -xsw ysw zsw \ -xobs yobs zobs \ -xcar ycar zcar \ -xlab HN -ylab 13C -zlab 1H \ -ndim 3 -aq2d States \ nmrpipe -fn MAC -macro $NMRTXT/ranceY.M -nord -nowr \ pipe2xyz -out./data/test%03d.fid -verb -ov Keep this Real always, we will correct later

15 #!/bin/csh 1) Convert the Bruker/Varian data into nmrpipe format (fid.com) This could be setup using the bruker/varian command from nmrpipe bruk2pipe -in./ser \ -bad 0.0 -aswap -DMX -decim dspfvs 20 -grpdly \ -xn yn 4 -zn 1280 \ -xt yt 2 -zt 640 \ -xmode DQD -ymode Real -zmode Real \ -xsw ysw zsw \ -xobs yobs zobs \ -xcar ycar zcar \ -xlab HN -ylab 13C -zlab 1H \ -ndim 3 -aq2d States \ nmrpipe -fn MAC -macro $NMRTXT/ranceY.M -nord -nowr \ pipe2xyz -out./data/test%03d.fid -verb -ov These are SW, Frequency, and carrier Frequency, can be obtained from eda in Bruker. There is nothing special here.

16 #!/bin/csh 1) Convert the Bruker/Varian data into nmrpipe format (fid.com) This could be setup using the bruker/varian command from nmrpipe bruk2pipe -in./ser \ -bad 0.0 -aswap -DMX -decim dspfvs 20 -grpdly \ -xn yn 4 -zn 1280 \ -xt yt 2 -zt 640 \ -xmode DQD -ymode Real -zmode Real \ -xsw ysw zsw \ -xobs yobs zobs \ -xcar ycar zcar \ -xlab HN -ylab 13C -zlab 1H \ -ndim 3 -aq2d States \ nmrpipe -fn MAC -macro $NMRTXT/ranceY.M -nord -nowr \ pipe2xyz -out./data/test%03d.fid -verb -ov Add this line if one of the dimension if acquired in an Echo-AntiEcho fashion.

17 1) Convert the Bruker/Varian data into nmrpipe format (fid.com) This could be setup using the bruker/varian command from nmrpipe nmrpipe -fn MAC -macro $NMRTXT/ranceY.M -nord -nowr \ If the Y dimension is Echo-AntiEcho nmrpipe -fn MAC -macro $NMRTXT/ranceZ.M -nord -nowr \ If the Z dimension is Echo-AntiEcho

18 #!/bin/csh 1) Convert the Bruker/Varian data into nmrpipe format (fid.com) This could be setup using the bruker/varian command from nmrpipe bruk2pipe -in./ser \ -bad 0.0 -aswap -DMX -decim dspfvs 20 -grpdly \ -xn yn 4 -zn 1280 \ -xt yt 2 -zt 640 \ -xmode DQD -ymode Real -zmode Real \ -xsw ysw zsw \ -xobs yobs zobs \ -xcar ycar zcar \ -xlab HN -ylab 13C -zlab 1H \ -ndim 3 -aq2d States \ pipe2xyz -out./data/test%03d.fid -verb -ov fid.com will look like this if both indirect dimensions are collected in STATES-TPPI/STATES/TPPI

19 STEP 2 Fourier Transform the direct dimension and phase correct the direct dimension. #!/bin/csh -f # # 3D States-Mode HN-Detected Processing. xyz2pipe -in data/test%03d.fid -x \ nmrpipe -fn SOL \ ; Solvent Supression nmrpipe -fn SP -off 0.5 -end pow 1 -c 1.0 -size 400 \ nmrpipe -fn ZF -size 1024 \ nmrpipe -fn FT -verb \ nmrpipe -fn PS -p p1 0 -di \ nmrpipe -fn EXT -x1 11.0ppm -xn -1.0ppm -sw \ pipe2xyz -ov -out xyz/test%03d.ft1 -x

20 STEP 2 Fourier Transform the direct dimension and phase correct the direct dimension. #!/bin/csh -f # # 3D States-Mode HN-Detected Processing. xyz2pipe -in data/test%03d.fid -x \ nmrpipe -fn SOL \ nmrpipe -fn SP -off 0.5 -end pow 1 -c 1.0 -size 400 \ ;Apodization nmrpipe -fn ZF -size 1024 \ nmrpipe -fn FT -verb \ nmrpipe -fn PS -p p1 0 -di \ nmrpipe -fn EXT -x1 11.0ppm -xn -1.0ppm -sw \ pipe2xyz -ov -out xyz/test%03d.ft1 -x

21 STEP 2 Fourier Transform the direct dimension and phase correct the direct dimension. #!/bin/csh -f # # 3D States-Mode HN-Detected Processing. xyz2pipe -in data/test%03d.fid -x \ nmrpipe -fn SOL \ nmrpipe -fn SP -off 0.5 -end pow 1 -c 1.0 -size 400 \ ;Apodization nmrpipe -fn ZF -size 1024 \ ; Zerofill to the 1024 or nearest power of 2 nmrpipe -fn FT -verb \ nmrpipe -fn PS -p p1 0 -di \ nmrpipe -fn EXT -x1 11.0ppm -xn -1.0ppm -sw \ pipe2xyz -ov -out xyz/test%03d.ft1 -x

22 STEP 2 Fourier Transform the direct dimension and phase correct the direct dimension. #!/bin/csh -f # # 3D States-Mode HN-Detected Processing. xyz2pipe -in data/test%03d.fid -x \ nmrpipe -fn SOL \ nmrpipe -fn SP -off 0.5 -end pow 1 -c 1.0 -size 400 \ ;Apodization nmrpipe -fn ZF -size 1024 \ ; Zerofill to the 1024 or nearest power of 2 nmrpipe -fn FT -verb \ ; Fourier Transform nmrpipe -fn PS -p p1 0 -di \ nmrpipe -fn EXT -x1 11.0ppm -xn -1.0ppm -sw \ pipe2xyz -ov -out xyz/test%03d.ft1 -x

23 STEP 2 Fourier Transform the direct dimension and phase correct the direct dimension. #!/bin/csh -f # # 3D States-Mode HN-Detected Processing. xyz2pipe -in data/test%03d.fid -x \ nmrpipe -fn SOL \ nmrpipe -fn SP -off 0.5 -end pow 1 -c 1.0 -size 400 \ ;Apodization nmrpipe -fn ZF -size 1024 \ ; Zerofill to the 1024 or nearest power of 2 nmrpipe -fn FT -verb \ ; Fourier Transform nmrpipe -fn PS -p p1 0 -di \ ;Phase the data (start with 0 phase initially) nmrpipe -fn EXT -x1 11.0ppm -xn -1.0ppm -sw \ pipe2xyz -ov -out xyz/test%03d.ft1 -x

24 STEP 2 Fourier Transform the direct dimension and phase correct the direct dimension. #!/bin/csh -f # # 3D States-Mode HN-Detected Processing. xyz2pipe -in data/test%03d.fid -x \ nmrpipe -fn SOL \ nmrpipe -fn SP -off 0.5 -end pow 1 -c 1.0 -size 400 \ ;Apodization nmrpipe -fn ZF -size 1024 \ ; Zerofill to the 1024 or nearest power of 2 nmrpipe -fn FT -verb \ ; Fourier Transform nmrpipe -fn PS -p p1 0 -di \ ;Phase the data (start with 0 phase initially) nmrpipe -fn EXT -x1 11.0ppm -xn -1.0ppm -sw \ ; Extract the spectral space in the direct dimension where we have signal pipe2xyz -ov -out xyz/test%03d.ft1 -x

25 STEP 2 Fourier Transform the direct dimension and phase correct the direct dimension. #!/bin/csh -f # # 3D States-Mode HN-Detected Processing. xyz2pipe -in data/test%03d.fid -x \ nmrpipe -fn SOL \ nmrpipe -fn SP -off 0.5 -end pow 1 -c 1.0 -size 400 \ ;Apodization nmrpipe -fn ZF -size 1024 \ ; Zerofill to the 1024 or nearest power of 2 nmrpipe -fn FT -verb \ ; Fourier Transform nmrpipe -fn PS -p p1 0 -di \ ;Phase the data (start with 0 phase initially) nmrpipe -fn EXT -x1 11.0ppm -xn -1.0ppm -sw \ pipe2xyz -ov -out xyz/test%03d.ft1 -x Write out the data into the directr xyz

26 STEP 2 Fourier Transform the direct dimension and phase correct the direct dimension. Phasing the data in the direct dimension. Open the spectrum in nmrdraw, go to xyz directory and open test%03d.ft1 and phase the first (or sometimes the second) fid in nmrdraw. Note the phase and incoporate the phase in the next script ft1.com

27 STEP 2 Fourier Transform the direct dimension and rewrite the data ready for hmsist (ft1.com) #!/bin/csh -f # # 3D States-Mode HN-Detected Processing. rm -rf yzx xyz2pipe -in data/test%03d.fid -x \ nmrpipe -fn SOL \ nmrpipe -fn SP -off 0.5 -end pow 1 -c 1.0 -size 400 \ nmrpipe -fn ZF -size 1024 \ nmrpipe -fn FT -verb \ nmrpipe -fn PS -p0 87 -p1 0 -di \ ; put the phase that was determined from the previous effort nmrpipe -fn EXT -x1 12.0ppm -xn -1.0ppm -sw \ pipe2xyz -ov -out yzx/test%03d.ft1 -z

28 STEP 2 Fourier Transform the direct dimension and rewrite the data ready for hmsist (ft1.com) #!/bin/csh -f # # 3D States-Mode HN-Detected Processing. rm -rf yzx xyz2pipe -in data/test%03d.fid -x \ nmrpipe -fn SOL \ nmrpipe -fn SP -off 0.5 -end pow 1 -c 1.0 -size 400 \ nmrpipe -fn ZF -size 1024 \ nmrpipe -fn FT -verb \ nmrpipe -fn PS -p0 87 -p1 0 -di \ ; put the phase that was determined from the previous effort nmrpipe -fn EXT -x1 12.0ppm -xn -1.0ppm -sw \ pipe2xyz -ov -out yzx/test%03d.ft1 z ;Note we rearrange the data along z compared to x in the previous script (ft1xyz.com). Now the data is ready in the directory yzx Note the rest of the script is the same as ft1xyz.com.

29 Step 3 Reconstruct the two indirect dimensions using hmsist. (using script ist.csh; this is run using all the processors available by calling ist.csh from run.local) First let us look at ist.csh #!/bin/csh -xv setenv FM_PROG /Users/hari/Applications/nmrPipe/nmrbin.mac set F = $1 set in = $F:t set out = $F:t:r.phf set ft1 = $F:t:r.ft1 echo $in $out $ft1 ${FM_PROG}/hmsIST -dim 2 -incr 1 -auton 1 -user 1 \ -itr 400 -verb 1 -ref 0 -vlist./nuslist \ <./yzx/${in} >!./yzx_ist/${out}

30 Step 3 Reconstruct the two indirect dimensions using hmsist. (using script ist.csh; this is run using all the processors available by calling ist.csh from run.local) First let us look at ist.csh #!/bin/csh -xv setenv FM_PROG /Users/hari/Applications/nmrPipe/nmrbin.mac ; this is normally the directory in which the program hmsist is located, which is typically where the nmrpipe excecutables are. set F = $1 set in = $F:t set out = $F:t:r.phf set ft1 = $F:t:r.ft1 echo $in $out $ft1 ${FM_PROG}/hmsIST -dim 2 -incr 1 -auton 1 -user 1 \ -itr 400 -verb 1 -ref 0 -vlist./nuslist \ <./yzx/${in} >!./yzx_ist/${out}

31 Step 3 Reconstruct the two indirect dimensions using hmsist. (using script ist.csh; this is run using all the processors available by calling ist.csh from run.local) First let us look at ist.csh #!/bin/csh -xv setenv FM_PROG /Users/hari/Applications/nmrPipe/nmrbin.mac ; this is normally the directory in which the program hmsist is located, which is typically where the nmrpipe excecutables are. set F = $1 set in = $F:t set out = $F:t:r.phf set ft1 = $F:t:r.ft1 Keep these the way they are, setting inputs and output holders echo $in $out $ft1 ${FM_PROG}/hmsIST -dim 2 -incr 1 -auton 1 -user 1 \ -itr 400 -verb 1 -ref 0 -vlist./nuslist \ <./yzx/${in} >!./yzx_ist/${out}

32 Step 3 Reconstruct the two indirect dimensions using hmsist. (using script ist.csh; this is run using all the processors available by calling ist.csh from run.local) First let us look at ist.csh #!/bin/csh -xv setenv FM_PROG /Users/hari/Applications/nmrPipe/nmrbin.mac ; this is normally the directory in which the program hmsist is located, which is typically where the nmrpipe excecutables are. set F = $1 set in = $F:t set out = $F:t:r.phf set ft1 = $F:t:r.ft1 echo $in $out $ft1 Defines that there are two indirect dimensions that are NUS ${FM_PROG}/hmsIST -dim 2 -incr 1 -auton 1 -user 1 \ -itr 400 -verb 1 -ref 0 -vlist./nuslist \ <./yzx/${in} >!./yzx_ist/${out}

33 Step 3 Reconstruct the two indirect dimensions using hmsist. (using script ist.csh; this is run using all the processors available by calling ist.csh from run.local) First let us look at ist.csh #!/bin/csh -xv setenv FM_PROG /Users/hari/Applications/nmrPipe/nmrbin.mac rm rf yzx_ist mkdir yzx_ist set F = $1 set in = $F:t set out = $F:t:r.phf set ft1 = $F:t:r.ft1 echo $in $out $ft1 Automatically takes the maximum increment from the schedule ${FM_PROG}/hmsIST -dim 2 -incr 1 -auton 1 -user 1 \ -itr 400 -verb 1 -ref 0 -vlist./nuslist \ <./yzx/${in} >!./yzx_ist/${out}

34 Step 3 Reconstruct the two indirect dimensions using hmsist. (using script ist.csh; this is run using all the processors available by calling ist.csh from run.local) First let us look at ist.csh #!/bin/csh -xv setenv FM_PROG /Users/hari/Applications/nmrPipe/nmrbin.mac ; this is normally the directory in which the program hmsist is located, which is typically where the nmrpipe excecutables are. rm -rf yzx_ist mkdir yzx_ist set F = $1 set in = $F:t set out = $F:t:r.phf set ft1 = $F:t:r.ft1 This creates the directory for placing the reconstructed spectrum Tells that the schedule starts with the first point echo $in $out $ft1 ${FM_PROG}/hmsIST -dim 2 -incr 1 auton 1 --user 1 \ -itr 400 -verb 1 -ref 0 -vlist./nuslist \ <./yzx/${in} >!./yzx_ist/${out}

35 Step 3 Reconstruct the two indirect dimensions using hmsist. (using script ist.csh; this is run using all the processors available by calling ist.csh from run.local) First let us look at ist.csh #!/bin/csh -xv setenv FM_PROG /Users/hari/Applications/nmrPipe/nmrbin.mac ; this is normally the directory in which the program hmsist is located, which is typically where the nmrpipe excecutables are. rm rf yzx_ist mkdir yzx_ist set F = $1 set in = $F:t set out = $F:t:r.phf set ft1 = $F:t:r.ft1 echo $in $out $ft1 Tells that NUS schedule file is named nuslist, if you have a different name please change this. ${FM_PROG}/hmsIST -dim 2 -incr 1 auton 1 --user 1 \ -itr 400 -verb 1 -ref 0 -vlist./nuslist \ <./yzx/${in} >!./yzx_ist/${out}

36 Step 3 Reconstruct the two indirect dimensions using hmsist. (using script ist.csh; this is run using all the processors available by calling ist.csh from run.local) First let us look at ist.csh #!/bin/csh -xv setenv FM_PROG /Users/hari/Applications/nmrPipe/nmrbin.mac ; this is normally the directory in which the program hmsist is located, which is typically where the nmrpipe excecutables are. rm rf yzx_ist mkdir yzx_ist set F = $1 set in = $F:t set out = $F:t:r.phf set ft1 = $F:t:r.ft1 echo $in $out $ft1 Tells that NUS schedule file is named nuslist, if you have a different name please change this. ${FM_PROG}/hmsIST -dim 2 -incr 1 auton 1 --user 1 \ -itr 400 -verb 1 -ref 0 -vlist./nuslist \ <./yzx/${in} >!./yzx_ist/${out}

37 Step 3 Reconstruct the two indirect dimensions using hmsist. (using script ist.csh; this is run using all the processors available by calling ist.csh from run.local) First let us look at ist.csh #!/bin/csh -xv setenv FM_PROG /Users/hari/Applications/nmrPipe/nmrbin.mac ; this is normally the directory in which the program hmsist is located, which is typically where the nmrpipe excecutables are. rm rf yzx_ist mkdir yzx_ist set F = $1 set in = $F:t set out = $F:t:r.phf set ft1 = $F:t:r.ft1 echo $in $out $ft1 400 iterations or until it converges for reconstruction ${FM_PROG}/hmsIST -dim 2 -incr 1 auton 1 --user 1 \ -itr 400 -verb 1 -ref 0 -vlist./nuslist \ <./yzx/${in} >!./yzx_ist/${out}

38 Step 3 Reconstruct the two indirect dimensions using hmsist. (using script ist.csh; this is run using all the processors available by calling ist.csh from run.local) First let us look at ist.csh #!/bin/csh -xv setenv FM_PROG /Users/hari/Applications/nmrPipe/nmrbin.mac ; this is normally the directory in which the program hmsist is located, which is typically where the nmrpipe excecutables are. rm rf yzx_ist mkdir yzx_ist set F = $1 set in = $F:t set out = $F:t:r.phf set ft1 = $F:t:r.ft1 echo $in $out $ft1 Input and output directories ${FM_PROG}/hmsIST -dim 2 -incr 1 auton 1 --user 1 \ -itr 400 -verb 1 -ref 0 -vlist./nuslist \ <./yzx/${in} >!./yzx_ist/${out}

39 Step 3 Reconstruct the two indirect dimensions using hmsist. (using script ist.csh; this is run using all the processors available by calling ist.csh from run.local) First let us look at ist.csh #!/bin/csh -xv setenv FM_PROG /Users/hari/Applications/nmrPipe/nmrbin.mac ; this is normally the directory in which the program hmsist is located, which is typically where the nmrpipe excecutables are. rm rf yzx_ist mkdir yzx_ist set F = $1 set in = $F:t set out = $F:t:r.phf set ft1 = $F:t:r.ft1 echo $in $out $ft1 ${FM_PROG}/hmsIST -dim 2 -incr 1 auton 1 --user 1 \ -itr 400 -verb 1 -ref 0 -vlist./nuslist \ <./yzx/${in} >!./yzx_ist/${out} Normally one does not need to change anything in this script.

40 Step 3 Reconstruct the two indirect dimensions using hmsist. (using script ist.csh; this is run using all the processors available by calling ist.csh from run.local) Let us look at run.local parallel -j 100% './ist.csh {} > /dev/null; echo {}' ::: yzx/test*.ft1 Uses the program parallel (provided in the directory) to run the script ist.csh on all the processors and using 100% of all the available processors.

41 STEP 4 Rearrange the data to nmrpipe format, making it suitable for nmrpipe based Fourier Transform of the two indirect dimensions. (phf.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 This script takes the reconstructed data from the yzx_ist directory and uses the program phf2pipe (supplied along with hmsist) and rearranges the data for nmrpipe and writes to a directory rec. Normally nothing needs to be changed in this script. Make sure the program phf2pipe is in the nmrpipe executable directory.

42 STEP 5 Fourier Transform the two indirect dimensions which are now reconstructed. (ft23.com) #!/bin/csh -f # # 3D States-Mode HN-Detected Processing. xyz2pipe -in rec/test%03d.ft1 -x \ # nmrpipe -fn LP -fb -ord 64\ nmrpipe -fn SP -off 0.4 -end pow 1 -c 0.5 \ nmrpipe -fn ZF -auto \ nmrpipe -fn FT -verb \ nmrpipe -fn PS -p0 0 -p1 0 -di \ # nmrpipe -fn REV -verb \ nmrpipe -fn TP \ # nmrpipe -fn LP -fb -ord 64 \ nmrpipe -fn SP -off 0.4 -end pow 1 -c 0.5 \ nmrpipe -fn ZF -auto \ nmrpipe -fn FT -alt -verb \ nmrpipe -fn PS -p0 0 -p1 0 -di \ # nmrpipe -fn PS -p p di \ # nmrpipe -fn REV -verb \ nmrpipe -fn TP -verb\ nmrpipe -fn ZTP \ pipe2xyz -ov -out rec2/test%03d.ft3 -x

43 STEP 5 Fourier Transform the two indirect dimensions which are now reconstructed. (ft23.com) #!/bin/csh -f # # 3D States-Mode HN-Detected Processing. xyz2pipe -in rec/test%03d.ft1 -x \ # nmrpipe -fn LP -fb -ord 64\ nmrpipe -fn SP -off 0.4 -end pow 1 -c 0.5 \ nmrpipe -fn ZF -auto \ nmrpipe -fn FT -verb \ nmrpipe -fn PS -p0 0 -p1 0 -di \ # nmrpipe -fn REV -verb \ nmrpipe -fn TP \ # nmrpipe -fn LP -fb -ord 64 \ nmrpipe -fn SP -off 0.4 -end pow 1 -c 0.5 \ nmrpipe -fn ZF -auto \ nmrpipe -fn FT -alt -verb \ nmrpipe -fn PS -p0 0 -p1 0 -di \ # nmrpipe -fn PS -p p di \ # nmrpipe -fn REV -verb \ nmrpipe -fn TP -verb\ nmrpipe -fn ZTP \ pipe2xyz -ov -out rec2/test%03d.ft3 -x Optional Linear Prediction Apodization of the first Indirect Dim Zerofill of the first Indirect Dim Fourier Transform of the first Indirect Dim Phase correction of the first Indirect Dim Optional Reverse of the first Indirect Dim Optional Linear Prediction of the second ind dim Apodization of the second Indirect Dim Zerofill of the second Indirect Dim Fourier Transform of the second Indirect Dim Phase correction of the second Indirect Dim Optional Reverse of the second Indirect Dim

44 STEP 5 Fourier Transform the two indirect dimensions which are now reconstructed. (ft23.com) #!/bin/csh -f # # 3D States-Mode HN-Detected Processing. xyz2pipe -in rec/test%03d.ft1 -x \ # nmrpipe -fn LP -fb -ord 64\ nmrpipe -fn SP -off 0.4 -end pow 1 -c 0.5 \ nmrpipe -fn ZF -auto \ nmrpipe -fn FT -verb \ nmrpipe -fn PS -p0 0 -p1 0 -di \ # nmrpipe -fn REV -verb \ nmrpipe -fn TP \ # nmrpipe -fn LP -fb -ord 64 \ nmrpipe -fn SP -off 0.4 -end pow 1 -c 0.5 \ nmrpipe -fn ZF -auto \ nmrpipe -fn FT -alt -verb \ nmrpipe -fn PS -p0 0 -p1 0 -di \ # nmrpipe -fn PS -p p di \ # nmrpipe -fn REV -verb \ nmrpipe -fn TP -verb\ nmrpipe -fn ZTP \ pipe2xyz -ov -out rec2/test%03d.ft3 -x Note the difference in the FT statement. Where there is a Echo-AntiEcho dim we have nmrpipe -fn FT -verb Note the difference in the FT statement. Where there is a States-TPPI dim we have nmrpipe -fn FT -alt -verb We need to have the -alt flag

45 STEP 5 Fourier Transform the two indirect dimensions which are now reconstructed. (ft23.com) #!/bin/csh -f # # 3D States-Mode HN-Detected Processing. xyz2pipe -in rec/test%03d.ft1 -x \ # nmrpipe -fn LP -fb -ord 64\ nmrpipe -fn SP -off 0.4 -end pow 1 -c 0.5 \ nmrpipe -fn ZF -auto \ nmrpipe -fn FT -verb \ nmrpipe -fn PS -p0 0 -p1 0 -di \ # nmrpipe -fn REV -verb \ nmrpipe -fn TP \ # nmrpipe -fn LP -fb -ord 64 \ nmrpipe -fn SP -off 0.4 -end pow 1 -c 0.5 \ nmrpipe -fn ZF -auto \ nmrpipe -fn FT -alt -verb \ nmrpipe -fn PS -p0 0 -p1 0 -di \ # nmrpipe -fn PS -p p di \ # nmrpipe -fn REV -verb \ nmrpipe -fn TP -verb\ nmrpipe -fn ZTP \ pipe2xyz -ov -out rec2/test%03d.ft3 -x The Fourier Transformed Spectra is written into the rec2 directory. We can write to Sparky format using pipe2ucsf

46 NUS-Pulse Programming in Bruker

47 15 N 13 C DW 13 C 2,1 1,1 1,2 1,4 1,3 X 1,7 DW 15 N

48 Schedule 1,1 1, 2 1, 4 1, 7 1, 9 1, 11 2, 1 2, 2 2, t1 list t2 list

49 prosol relations=<triple> #include <Avance.incl> #include <Grad.incl> #include <Delay.incl> define list<loopcounter> t1list=<$vclist> define list<loopcounter> t2list=<$vplist> 20u "cnst29=(t1list%2)*180" 20u "cnst30=(t2list%2)*180" 20u "cnst31=cnst29+cnst30" 3m ip4+cnst29 3m ip5+cnst30 3m ip31+cnst31 20u "d0=in0*t1list+3u" 20u "d10=tau1+in10*t2list" 20u "d29=tau2+in10*t2list" 20u "d30=tau1-in10*t2list" ; d11 do:f3 mc #0 to 2 ; F1PH(rd10 & rd29 & rd30 & rp5 & ip4, id0) ; F2PH(dp5, id10 & id29 & dd30) d11 do:f3 wr #0 if #0 zd 3m dp5 lo to 3 times 2 3m ip5*2 3m ip4 lo to 4 times 2 3m rp4 3m rp5 3m t1list.inc 3m t2list.inc 20u "cnst29=(t1list%2)*180" 20u "cnst30=(t2list%2)*180" 20u "cnst31=cnst29+cnst30" 3m ip4+cnst29 3m ip5+cnst30 3m ip31+cnst31 lo to 5 times COUNTER

50 #include <Avance.incl> #include <Grad.incl> #include <Delay.incl> #include<sysconf_nmrc.incl> define list<loopcounter> t1list=<$vclist> define list<loopcounter> t2list=<$vplist> define loopcounter MAX15N "p2=p1*2" "p22=p21*2" "p4=p3*2" "d0=3u" "d11=30m" "d13=4u" "d21=5.5m" "d23=12.4m" "d26=2.3m" "d28=3.6m" "in0=inf1/2" "in10=inf2/4 # ifdef CB_ONLY "d28=6.8m" # else "d28=3.6m" # endif /*CB_ONLY*/ "TAU=d28-p16-d16" "in29=in10" "in30=in10" "d10=d23/2-p14/2" "d29=d23/2-p14/2-p26-d21-4u" "d30=d23/2-p14/2" "DELTA1=d23-d21-p26" "DELTA2=d0*2+larger(p14,p22)-p14" "DELTA3=d26-p16-d16-p11-12u" "spoff2=0" "spoff3=0" "spoff5=bf2*(cnst21/ )-o2" "spoff8=0" "TAU1=d23/2-p14/2" "TAU2=d23/2-p14/2-p26-d21-4u" "TAU3=d23/2-p14/2" "MAX15N=d30*2/in30" "l29=max15n" "cnst31=l31" aqseq 321 "COUNTER=l3*l13/4" 1 ze ;if (l31==1) ;{ ;"d28=6.8m" ;"TAU=d28-p16-d16" ;} d11 pl16:f3 20u "cnst29=(t1list%2)*180" 20u "cnst30=(t2list%2)*180" 20u "cnst31=cnst29+cnst30" 3m ip9+cnst29 3m ip10+cnst29 3m ip5+cnst30 3m ip31+cnst3

51 2 d11 do:f3 3m 3 9m m ; d1 20u "d0=in0*t1list+3u" 20u "d10=tau1+in10*t2list" 20u "d29=tau2+in10*t2list" 20u "d30=tau3-in10*t2list" d11 pl1:f1 (p1 ph1) d26 pl3:f3 (center (p2 ph1) (p22 ph1):f3 ) d26 UNBLKGRAD (p1 ph2):f1 4u pl0:f1 (p11:sp1 ph1:r):f1 4u p16:gp1 d16 (p21 ph3):f3 d21 pl19:f1 (p26 ph2):f1 DELTA1 cpds1:f1 ph1 (center (p14:sp3 ph1):f2 (p22 ph1):f3 ) d23 (p21 ph1):f3 4u do:f1 (p26 ph7):f1 4u p16:gp6 d16 (p26 ph2):f1 20u cpds1:f1 ph1 (p13:sp2 ph10):f2 d28 (p13:sp8 ph9):f2 d0 (center (p14:sp5 ph1):f2 (p22 ph1):f3 ) d0 4u (p14:sp3 ph8):f2 DELTA2 (p14:sp5 ph1):f2 4u

52 go=2 ph31 cpd3:f3 ; d11 do:f3 mc #0 to 2 ; F1PH(rd10 & rd29 & rd30 & ip9 & ip10, id0 & dp9*2) ; F2PH(ip5, id10 & id29 & dd30) d11 do:f3 wr #0 if #0 zd 3m dp5 lo to 3 times 2 3m ip5*2 3m ip9 3m ip10 lo to 4 times 2 20u "cnst29=(t1list%2)*180" 20u "cnst30=(t2list%2)*180" 20u "cnst31=cnst29+cnst30" 3m ip9+cnst29 3m ip10+cnst29 3m ip5+cnst30 3m ip31+cnst31 lo to 5 times COUNTER 3m rp5 3m rp9 3m rp10 ; 3m dp9*2 3m t1list.inc 3m t2list.inc