Varian CRINEPT FID

Read from NMRPipe mailing list at Yahoo groups. A guy said the varian version crinept type TROSY has to be process into two files after process, like IPAP type experiment. Although I had processed a CRINEPT type TROSY obtained from Bruker 800MHz, I never know to do such seperation. Moreover, there are some special tips to know for processing such FID, I paste the scripts provided by the poster who said Frank Degladio gave him the script.

———– script starts at next line————

#!/bin/csh

var2pipe -in ./fid -noaswap  \
-xN              2050  -yN               128  \
-xT              1025  -yT                64  \
-xMODE        Complex  -yMODE      Rance-Kay  \
-xSW        13008.130  -ySW         3000.000  \
-xOBS         899.804  -yOBS          91.187  \
-xCAR           4.815  -yCAR         118.438  \
-xLAB              HN  -yLAB             N15  \
-ndim               2  -aq2D          States  \
-out ./test.fid -verb -ov

nmrPipe -in test.fid \
| nmrPipe -fn COADD -cList 1 0 -axis Y -time \
| nmrPipe  -fn SOL                                    \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5    \
| nmrPipe  -fn ZF -auto                               \
| nmrPipe  -fn FT                                     \
| nmrPipe  -fn PS -p0 120  -p1 0.0 -di                \
| nmrPipe  -fn EXT -left -sw -verb                    \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5    \
| nmrPipe  -fn ZF -auto                               \
| nmrPipe  -fn FT -neg                                     \
| nmrPipe  -fn PS -p0 90 -p1 0 -di                     \
-verb -ov -out A.ft2

nmrPipe -in test.fid \
| nmrPipe -fn COADD -cList 0 1 -axis Y -time \
| nmrPipe  -fn SOL                                    \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5    \
| nmrPipe  -fn ZF -auto                               \
| nmrPipe  -fn FT                                     \
| nmrPipe  -fn PS -p0 120  -p1 0.0 -di                \
| nmrPipe  -fn EXT -left -sw -verb                    \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5    \
| nmrPipe  -fn ZF -auto                               \
| nmrPipe  -fn FT -neg                                     \
| nmrPipe  -fn PS -p0 0 -p1 0 -di                     \
-verb -ov -out B.ft2

addNMR -in1 A.ft2 -in2 B.ft2 -out A+B.ft2 -add -c1 1.0 -c2 1.0
addNMR -in1 A.ft2 -in2 B.ft2 -out A-B.ft2 -sub -c1 1.0 -c2 1.0

——————– end ———————————————-

NMRView startup file

You could generate a startup file for NMRView,especially when you are going to analyze lots of dynamic data. The startup file can load many spectra in seconds, also including the sequence file, the peak list and PDB coordinate files.

Usage: save the following lines in a file and run “source your_file”

—————- file content ——————————–

##### read in spectra #############
nv_dataset dir /disk1/nv/mouse/gftnmr
nv_dataset open /disk1/nv/mouse/gftnmr/masyn-15c-hsqc-1216.nv
nv_dataset open /disk1/nv/mouse/gftnmr/hacacocanh-dp1.nv
nv_dataset open /disk1/nv/mouse/gftnmr/hacacocanh-dp2.nv
#nv_dataset open /disk1/nv/mouse/gftnmr/hacacocanh-dp3.nv
nv_dataset open /disk1/nv/mouse/gftnmr/hacacocanh-dp4.nv
##### read in molecule sequence file
nv_sread seq /disk1/nv/mouse/gftnmr/mouse.seq
##### read in assignment peaklist ##
readpks /disk1/nv/mouse/gftnmr/masyn-15c-1216-hsqc.xpk
##### read in ppm file
#readppm /disk1/nv/mouse/gftnmr/nv/ppm.out

convert all *.ps to PNG format by a script

1. ONLY convert the files in the directory where this script is.
2. “-density 150″ is the resolution, in this case 150 dpi
3. -geometry 100% is the scale you want to resize by %
4. also, you can convert lots of JPEG to smaller resolution, just change .ps to .jpg, and change the output to another directory, either using .jpg or .png

———— following lines are the content of the script ———

#!/bin/sh

########################
## using “convert” from ImageMagick to do ps convert into PNG
#########################

echo PS convert to PNG, please wait the process
for INP in *.ps
do
newname=`basename $INP .ps`
convert -density 150 -geometry 100% $INP $newname%02d.png
echo ” convert $INP to $newname.png completely”
done
echo ” process ended, please check your graphical files”