Processing of 2D spectrum collected in QF mode

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Ewen Lescop

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Jul 15, 2017, 12:36:34 PM7/15/17
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Dear all,
I'm trying to process 2D spectra collected in QF mode on Bruker instruments such as cosygpppqf or hmbcgpndqf pulseprograms. Topspin is able to do it properly, however I'm stuck with qMDD. To fix the idea, I used 30% NUS points with TD=256, corresponding to 76 real points collected.
I started by using the default parameters generated by qMDD. qMDD is trying first to recognize complex points instead of real points. So I modified the various files to account for real vs complex points (see below). Doing this allowed progressively to remove error messages. With the current settings, I obtain the ./XYZA/ft4sp.xyza.2D that seems to be correct with 76 real points in the indirect dimension. However, I still have this error message "Error ReadInFidData: unexpected end of data in ./XYZA/ft4sp.xyza.2D 244264 of 488528
  For Bruker data try to ZF to a defined size with -fn ZF -size ... ". Changing ZF from -auto to -size does not change the error.
Below are the current settings. I highlighted by arrows (->) the changes I made compared to the automatically generated files.
This thread is related to another thread regarding TPPI but I did not find conclusive information there.
I would appreciate any help that would allow me to go the end of the processing.
All the best
Ewen

########## fidSP.com
bruk2pipe -in ./ser -bad 0.0 -noswap -DMX -decim 2376 -dspfvs 20 -grpdly 67.9872589111328 \
-xN             4096            -yN             76               \
-xT             2048            -yT             38 (->76)              \
-xMODE          Complex         -yMODE          QF (->Real)               \
-xSW            8417.508        -ySW            6002.401         \
-xOBS           600.330         -yOBS           600.330          \
-xCAR           4.265           -yCAR           4.265            \
-xP0              0.0           -yP0              0.0            \
-xP1              0.0           -yP1              0.0            \
-xLAB           1H              -yLAB           H                \
-ndim 2 -aq2D States (->Real) \
| nmrPipe -fn POLY -time                               \
| nmrPipe -fn SP -off 0.48 -end 0.95 -pow 2 -c 0.5     \
| nmrPipe -fn ZF -auto                                 \
| nmrPipe -fn FT -auto                                 \
| nmrPipe -fn PS -hdr                                  \
| nmrPipe -fn PS -p0 0 -p1 0 -di                       \
| nmrPipe -fn POLY -auto -xn 5.0ppm -ord 1              \
| nmrPipe -fn EXT -sw                                  \
| pipe2xyz -z -out ft/data%03d.DAT -ov -nofs -verb

############ nls.in
NDIM 2
sptype over
NHOLES -1
NIMAX 128 (->256) 1
NI 38 (->76) 1
SPARSE y
f180
SW 14.0214090835534 9.99845977866832
CT_SP nn
CEXP nn
T2 1 1
Jsp 0 0


############# proc.sh
#!/bin/tcsh
setenv FID ../16
setenv fidSP fidSP.com
setenv REC2FT recFT.com
setenv in_file nls.in
setenv selection_file nuslist
setenv FST_PNT_PPM 11
setenv ROISW 11
setenv proc_out test.dat
setenv SPARSE               y
setenv NUS_TABLE_ORDER      '1'
setenv NUS_TABLE_OFFSET     0
setenv NUS_POINTS           38 (->76)
setenv NI                   '38 (->76) 1 '
setenv NIMAX                '128 (->256) 1 '
setenv NDIM                 2
setenv MDDTHREADS           10
setenv METHOD               CS
setenv CS_alg               IRLS
setenv CS_norm              0
setenv CS_lambda            1.0
setenv CS_niter             10
setenv CS_VE                n
setenv SRSIZE               0.1

mddnmr4pipeN.sh  1 2 3 4 5
set ecode=$? ;if ( $ecode ) exit($ecode)

--
-------------------------------
Ewen LESCOP, PhD
Laboratoire de Biologie et Chimie Structurales
Institut de Chimie des Substances Naturelles - CNRS
1, avenue de la Terrasse
91190 Gif-sur-Yvette
France
Tél: 33-1-69-82-37-64
Fax: 33-1-69-82-37-84
http://www.icsn.cnrs-gif.fr/lescop
------------------------------- 
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