Tuesday, September 09, 2008

Help me Please

For the first time after almost 2 years, you have the oppurtunity to give me something.
There is an apparently nice collection of 3D spectra on the web:
but I can't process them because they are Varian spectra. If you are able to process at least one of them with any software, would you please explain me what's happening? Or, in other words, what you see?


At 5:39 PM, Blogger dan said...

Hey Old Swan,

Unfortunately the UCL server seems to be down so I can't look at the files for you. But if you have a copy of the files then CCPN analysis can display Varian (and other widely used spectrometers) spectra from NMRPipe processed files and most other places.

At 5:41 PM, Blogger dan said...

Whoops - sorry I misread your post. Azara can process Varian data but we will have to write a new script - this should be easy if the NMRPipe files are included.

At 7:21 PM, Blogger old swan said...

Dear Dan, I have uploaded one of the 3 archives here:


It's a 86 MB download. I am tackling the spectrum called cnoesqc, but eventually I want to process them all. I have no problem with the 2D spectra, but I am still far from understanding the 3D data-sets.

Each spectrum comes with the corresponding NMRPipe script. For example, the one I have chosen contains this script:

# nmrpipe script for processing 3D 13C NOESY-HSQC
set MAKECUBE = y
set PIPE2AZARA = y
set PIPE = /nmr/data1/pipe/nmrtxt
# 1. data conversion
if ($CONVERSION == 'y') then
var2pipe -verb -in fid \
-xN 512 -yN 192 -zN 96 \
-xT 512 -yT 96 -zT 48 \
-xMODE Complex -yMODE Complex -zMODE Complex \
-xSW 3250 -ySW 5400 -zSW 5200 \
-xOBS 499.8352598 -yOBS 499.8363349 -zOBS 125.6864733 \
-xCAR 2.61 -yCAR 4.75 -zCAR 27.5 \
-xLAB H -yLAB H -zLAB C \
-ndim 3 -aq2D States -aqORD 1 \
| nmrPipe -fn MAC -macro $PIPE/ranceZ.M -noRd -noWr \
| pipe2xyz -ov -out plane%03d_con.pip -x
# 2. processing
if ($PROCESSING == 'y') then
xyz2pipe -in plane%03d_con.pip -x \
| nmrPipe -fn ZF -size 1024 \
| nmrPipe -fn GMB -c 0.5 -lb -4.0 -gb 0.01 \
| nmrPipe -fn FT \
| nmrPipe -fn PS -p0 -70.0 -p1 29.0 -di \
| nmrPipe -fn POLY -auto -ord 1 \
| nmrPipe -fn TP \
| nmrPipe -fn ZF -size 512 \
| nmrPipe -fn SP -off 0.60 \
| nmrPipe -fn FT \
| nmrPipe -fn PS -p0 0.0 -p1 10.0 -di \
| nmrPipe -fn POLY -auto -ord 1 \
| pipe2xyz -ov -verb -out plane%03d.ft12 -x
xyz2pipe -in plane%03d.ft12 -z \
| nmrPipe -fn ZF -size 256 \
| nmrPipe -fn SP -off 0.6 \
| nmrPipe -fn FT \
| nmrPipe -fn PS -p0 -90.0 -p1 180.0 -di \
| nmrPipe -fn POLY -auto -ord 1 \
| nmrPipe -fn REV \
| pipe2xyz -ov -verb -out plane%03d.spec -z -inPlace
# 3. stuff all planes in a cube for p2x conversion
if ($MAKECUBE == 'y') then
xyz2pipe -verb -in plane%03d.spec -y \
| nmrPipe -ov -out cube3d.spec
# 4. conversion to AZARA format
if ($PIPE2AZARA == 'y') then
p2a -ov -verb -in cube3d.spec -out cnoesqc
process make_smx.script
rm tmp_ub.aza tmp_ub.aza.par
rm make_smx.script

As you can see Azara is mentioned explicitly. If you prefer to explain me how to install AZARA and use it, instead of processing the spectra directly, for me it's the same. I suspect, however, that it will be very though to explain such a thing to me. To start with: can AZARA be installed on my iMac G5 computer (OS 10.4)?


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