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<fs large>[[http://www.ibbr.umd.edu/nmrpipe |New NMRPipe Site]]</fs>

====== Qukck Reference ======
  * [[https://spin.niddk.nih.gov/NMRPipe/doc1/ | NMRPipe Introductory Tutorial]]
  * [[https://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/ | NMRPipe Processing Functions]]

====== Installation ======
===== where to download =====
  * https://www.ibbr.umd.edu/nmrpipe/install.html

===== Install on Linux =====
  * suppose you downloaded all files to /home/yxue/build/nmrpipe (I only downloaded NMRPipeX.tZ, install.com, binval.com)
  * execute the following command
<code>
mkdir /home/usr/share/nmrpipe
cd /home/usr/share/nmrpipe
ln -s /home/yxue/build/nmrpipe/*.tZ .
cp -R /home/yxue/build/nmrpipe/*.com .
csh ./install.com
</code>
  * install.com will create a proper .cshrc under your home folder finally. I modified it a little bit and rename it to .cshrc.nmr because I'd like to source it manual. If you remain it as .cshrc, running movie maker plugin in VMD would give some troubles. This is my version of .cshrc.nmr
<code>
if (-e /home/usr/share/nmrpipe/com/nmrInit.linux212_64.com) then
   source /home/usr/share/nmrpipe/com/nmrInit.linux212_64.com
endif

if (-e /home/usr/share/nmrpipe/dynamo/com/dynInit.com) then
   source /home/usr/share/nmrpipe/dynamo/com/dynInit.com
endif

alias nmrDraw  "nmrDraw &"
</code>

===== Tweak Color Scheme =====
  * Edit /home/usr/share/nmrpipe/nmrbin.linux212_64/nmrDraw
<code>
...
nmrdraw.exe \
   -default scrollbar.repeatDelay 999 -position 0 0 -Wfsdb               \
#  -fg black -bg gray30 -scale small                                     \
   -fg black -bg purple -scale medium                                    \
    $argv                                                                \
   -xAdj 3 -yAdj 30                                                      \
   -frp 1 -peak -nozfht -text $NMRTXT -func proc.tab -nosvri -XOR always \
   -lw1d 1 -labMode overlay -file "*.fid *.ft* *.lp *.dat *.DAT"         \
   -useTitle -nogrid -read -draw -zero -cursor -vert -clear $INARG
...
</code>

===== Install on WSL =====
The prequisite is that Ubuntu-WSL2 has already been installed on your computer. If not, [[linux:wsl|this page]] may be helpful.
The file **README_NMRPIPE_USERS** tells a lot, but you have a brand new Ubuntu-wsl2, so there are many packages to be installed. 

  * Enable i386 for some lib installed later, otherwise comes the error **E: Unable to locate package libx11-6:i386**
<code>
sudo dpkg --add-architecture i386
sudo apt update
sudo apt upgrade
</code>
  * Install the lib needed by nmrpipe, according to **README_NMRPIPE_USERS**
<code>
sudo apt-get install tcsh xterm lib32z1 libx11-6:i386 libxext6:i386 xfonts-75dpi msttcorefonts default-jre default-jdk
</code>
If a window just comes out, the button TAB can be used to select yes or no.
  * The shell tcsh is a must, so one needs to change the deault shell from bash to tcsh
<code>
sudo vi /etc/passwd
</code>
change the line 'zhangyk:x:1000:1000:,,,:/home/zhangyk:/bin/bash' to 'zhangyk:x:1000:1000:,,,:/home/zhangyk:/bin/tcsh'
  * Other packages
<code>
sudo apt install xserver-xorg x11-xserver-utils xfonts-base
</code>
x11-xserver-utils for 'Command 'xset' not found'

xserver-xorg for problems about xserver

xfonts-base for problems about font
  * Install nmrpipe following the instruction above!

====== workflow ======
===== format conversion =====
  * run "varian" or "bruker"; specify raw fid data file ("fid" <varian> or "ser" <bruker>) in "spectrometer input" or leave it blank if you are under the data directory; click button "read parameters"(the programs search acquisition parameters contained in file named “procpar” <Varian> or “acq” <Bruker>, therefore these file should be present in the same directory as the raw spectral data file); The parameters that need user inspection and eventual re-selection or manual input are highlighted in yellow.
  * check temperature. The program tried to read it from parameter file. Modify it if needed, but the parameters should be re-read (with another mouse click on “Read Parameters”). The conversion program utilizes a standard referencing for the water signal relative to TSP according to the temperature. User can also specify if an offset relative to the water signal was used in the experimental setup by manually entering it in the 1H dimension. Re-reading the parameters with this offset correction (and the right sample temperature!) will still provide a correct referencing in all other dimensions.

====== FAQ ======
===== if NMRPipe version expired =====
You can override NMRPipe expiration by setting the following environment variable (you can put this in your com/nmrInit.*.com file):
<code>
setenv NMR_CONT CORRECT
</code>


======Update NMRDraw 20180330======
====Notice====
  * Test the stability of new nmrDraw For three days
  * Any problems,please report to PY
  * Thanks for your coorperation

====Please update your ~/.cshrc Files====
<code>
if (-e /home/usr/share/nmrpipe/com/nmrInit.linux212_64.com) then
   source /home/usr/share/nmrpipe/com/nmrInit.linux212_64.com
endif

if (-e /home/usr/share/nmrpipe/dynamo/com/dynInit.com) then
   source /home/usr/share/nmrpipe/dynamo/com/dynInit.com
endif
</code>

====Please Remember to Source the ~/.cshrc ====
====Test====
<code>
nmrDraw &
</code>
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