My software notes

January 22, 2006

automatically process you NMR FIDs

Filed under: NMRPipe and NMRview — kpwu @ 3:20 am

Descriptions:
Once  you have lots of dynamics experiments, such as T1, T2 , or  diffusion data, you  won’t want to process all FIDs one by one and convert to nmrivew format one by one again.

If you acquire all FIDs in same parameters (ex:TD1,TD2 for Bruker, np, ni for Varian) , then just set the file location “base” and the file name you want those files to be (“name”), and the destination you want to move (“location”).

Make sure your fid.com, ft2.com is executable, and ft2.com has done phase corrections. 

————————————————————————————

#!/bin/sh

#process FIDs in a script, quickly and easily
base=”/disk1/data/kpwu/nmr/T1″   # file location
name=”t1″                                    # file name
location=”/disk1/data/kpwu/nv/T1″  # where you want to collect

i=21                                            # initial number of the FID
while [ “$i” -lt 37 ]                         # last FID number +1 ( ex: 36+1)
do
cp *.com $base/$i
cd $base/$i
./fid.com
./ft2.com
pipe2xyz -in test.ft2 -nv -out $name-$i.nv
mv $name-$i.nv $location
i=`expr $i + 1`
done

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