You could do this with the NMRPipe adjustable sine-bell window "SP",
but NMRPipe has a related "window" function called JMOD, with parameters
specifically for coupling.  So, multiplying by a 35 Hz cosine modulation
would be:

| nmrPipe -fn JMOD -j 35 -cos \

Add the "-inv" flag to divide by the coupling modulation instead.
This will only work if the coupling is small enough that its
modulation does not cross zero.  Removing a coupling in this
way will also likely increase the noise level.

For general purpose application of j deconvolution, some have
have proposed using maximum entropy reconstruction.  NMRPipe's
MEM can be used for this, but I've only done so with synthetic
test cases.

JMOD: Options for J-Modulation Profile:
   -off off  [0.0]  Modulation Start*PI.     (Q1)
   -j   jHz  [0.0]  J-Modulation, Hz.        (Q2)
   -lb  lbHz [0.0]  Line Broadening, Hz.     (Q3)
   -sin             Sine Modulation.   (Q1 = 0.0)
   -cos             Cosine Modulation. (Q1 = 0.5)
General Options:
   -size  aSize  [APOD] Apodize Length.
   -start aStart [1]    Apodize Start.
   -c     fScale [1]    Point 1 Scale.
   -one                 Outside = 1.
   -hdr                 Use Q Values from Header.
   -inv                 Invert Window.

Quoting "Kelly, Mark" <Mark.Kelly@...>:

>
> Dear nmrPipe group,
>
> I'm trying process the CaCb dimension of an HNCACB and would like to
> multiplying the t1 time domain with an inverse cosine tuned to 35 Hz
> to remove the JCa-Cb coupling (ref below). Can you tell me what this
> would look like in a pipe script?
>
> Many thanks, Mark
>
>
> Wittekind, M. & Mueller, L. (1993). "HNCACB, a High-Sensitivy 3D NMR
> Experiment to Correlate Amide-Proton and Nitrogen Resonances with
> the Alpha- and Beta-Carbon Resonances in Proteins". J. Magn. Reson.,
> Series B. B101: 201-205.
>

Hello all,

Iam trying to project the diagonal peaks of a 2D TOCSY spectra to a 1D spectra
so as to compare it with a 1D reference spectra collected at different time
point. I can see that proj.tcl can do projection of a rectangular region, but is
it possible to perform the same projection for a diagonal strip (45 degrees
angle) of region? . I would like to use this feature if available in NMRPipe.
Thank you,

hi,

why
| nmrPipe  -fn PS -p0 152.0 -p1 62.8 -di -verb                \
| nmrPipe  -fn EXT -x1 6.0ppm -xn 10.5ppm -sw -verb           \

produces different result as

| nmrPipe  -fn EXT -x1 6.0ppm -xn 10.5ppm -sw -verb           \
| nmrPipe  -fn PS -p0 152.0 -p1 62.8 -di -verb                \

I'm trying to develop 'ideal phase finder'. I want to apply PS as late as
possible. Currently only EXT and POLY are blocking my way to the end.

I would appreciate link to source codes for POLY and EXT functions too. I can't
find them.

thank you,
Jure

First order phase correction is a phase correction which changes linearly
from the first point in the spectrum to the last point. A code example is
below.

The nmrPipe phase correction function PS is set via two values,
P0 (-p0 argument) and P1 (-p1 argument).

In the nmrPipe PS function, the phase applied at the first point of the
given data is PO, and the phase applied at the last point is P0 + P1.

So, if you change the the range of points via EXT, you change the meaning
of first-order phase correction. For  example, lets say that the full
spectral window of your data is 12ppm to -1.0ppm.  In this example, the
phase applied at 12ppm would be 152.0 and the phase applied at
-1.0ppm would be (152.0 + 62.8):

| nmrPipe  -fn PS -p0 152.0 -p1 62.8 -di -verb                \
| nmrPipe  -fn EXT -x1 10.5ppm -xn 6.0ppm -sw -verb           \

but in this example, the phase applied at 10.5ppm would be 152.0
and the phase applied at 6.0ppm would be (152.0 + 62.8):

| nmrPipe  -fn EXT -x1 10.5ppm -xn 6.0ppm -sw -verb           \
| nmrPipe  -fn PS -p0 152.0 -p1 62.8 -di -verb                \

As to baseline correction: a brief description of the auto-correction
mechanism of the POLY function is given in the NMRPipe paper.
Those who build auto-phasing schemes often find that baseline
correction steps need to be combined with phase correction,
because statistics used to judge good phasing are usually
sensitive to baseline distortion.

Correspondingly, auto baseline correction will usually required
well-phased data in order to work well. So, one strategy for
automated phase correction is to include more than one round of
auto phase correction and auto baseline correction.  Here's an example
which uses multiple rounds of zero-order auto phase, baseline correction,
and combined zero and first order auto phase:

nmrPipe -in test.fid \
| nmrPipe -fn EM -lb 1.0 -c 1.0 \
| nmrPipe -fn ZF -zf 1 -auto \
| nmrPipe -fn FT \
| nmrPipe  -fn MAC -macro $NMRTXT/aph1D.M -all \
             -reg -str psX1 9.0ppm psX2 6.0ppm -var xP1 0 \
| nmrPipe -fn POLY -auto \
| nmrPipe  -fn MAC -macro $NMRTXT/aph1D.M -all \
             -reg -str psX1 9.0ppm psX2 6.0ppm -var xP1 0 \
| nmrPipe  -fn MAC -macro $NMRTXT/aphP1_1D.M -all -str \
             p0X1 9.0ppm p0X2 6.0ppm  p1X1 3.0ppm p1X2 -0.1ppm \
| nmrPipe -fn POLY -auto \
| nmrPipe  -fn MAC -macro $NMRTXT/aph1D.M -all \
             -reg -str psX1 9.0ppm psX2 6.0ppm -var xP1 0 \
| nmrPipe -fn POLY -auto \
| nmrPipe  -fn MAC -macro $NMRTXT/aphP1_1D.M -all -str \
             p0X1 9.0ppm p0X2 6.0ppm  p1X1 3.0ppm p1X2 -0.1ppm \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di \
    -out test.ft1 -ov

/***/
/* phaseRI: Phase a range ix1 to ix3 of separated real/imaginary data.
/*          Only points within the range are adjusted.
/*
/*          Phase is specified according to first and last points of
/*          the full data vectors rdata/idata:
/*
/*          phase at rdata[0] is p0
/*          phase at rdata[length-1] is p0 + p1
/***/

int phaseRI( rdata, idata,  /* Real and imaginary parts to phase. */
               ix1, ix3,      /* Region limits, first point = 1.    */
               length,        /* Size of rdata and idata.           */
               p0, p1 )       /* Effective phase values, degrees.   */

     int       ix1, ix3, length;
     float     *rdata, *idata, p0, p1;
{
      float phi, tR, tI, tCOS, tSIN;
      int i;

      if (p0 == 0.0 && p1 == 0.0) return( 0 );

      ix1--;
      ix3--;

      rdata += ix1;
      idata += ix1;

      p0 = 2.0*PI*p0/360.0;
      p1 = 2.0*PI*p1/360.0;

      for( i = ix1; i < ix3; i++ )
         {
          phi   = p0 + p1*i/length;

          tCOS  = cos( (double) phi );
          tSIN  = sin( (double) phi );

          tR    = *rdata;
          tI    = *idata;

          *rdata++ = tCOS*tR - tSIN*tI;
          *idata++ = tCOS*tI + tSIN*tR;
         }

      return( 0 );
}

Quoting "s.jure9" <s.jure9@...>:

> hi,
>
> why
> | nmrPipe  -fn PS -p0 152.0 -p1 62.8 -di -verb                \
> | nmrPipe  -fn EXT -x1 6.0ppm -xn 10.5ppm -sw -verb           \
>
> produces different result as
>
> | nmrPipe  -fn EXT -x1 6.0ppm -xn 10.5ppm -sw -verb           \
> | nmrPipe  -fn PS -p0 152.0 -p1 62.8 -di -verb                \
>
> I'm trying to develop 'ideal phase finder'. I want to apply PS as
> late as possible. Currently only EXT and POLY are blocking my way to
> the end.
>
> I would appreciate link to source codes for POLY and EXT functions
> too. I can't find them.
>
> thank you,
> Jure
>
>

Oh I have completely forgotten the pivot. Thanks for reminder.

To share my further experience:

multiple POLY functions blur my data, so I just use one POLY to get 'reference
data' which I use for acquiring p0 and p1 parameters. Then those are applied to
data before POLY (and then it can be repeated).
For p0 the ideal parameter is straight forward:
p0=arctan(-sum(idata)/sum(rdata))
Before that I filter out points with absolute value lower than threshold.
For P1 parameter 'for' loop is necessary.

I have trouble finding right evaluating function.
so, What do you think is good criteria for determination ideal phase parameters?

Hi,

I'm currently using Dynamo to evaluate molecular structure according to noe
restraints. I've modified some of the scripts provided (pdb2dyn.tcl,
dynEval.tcl) so that I can evaluate several pdb structures (different conformers
of a molecule from molecular modeling) according to noe restraints in one single
operation. Things work great, but I would like to modify the contents of the
output file since there several useless informations. This output file is
directly produce by the dynWrite command which is built in nmrWish, and I've no
idea of how this function reads the information contain in the noe restraint
file I provide and then writes everything in the output file. If someone could
provide the source code of the dynWrite function, I think I could use it to had
a process in the script that will write only the information I need in the
output file.

Thanks

 

Hi,

I'm currently using Dynamo to evaluate molecular structure according to noe restraints. I've modified some of the scripts provided (pdb2dyn.tcl, dynEval.tcl) so that I can evaluate several pdb structures (different conformers of a molecule from molecular modeling) according to noe restraints in one single operation. Things work great, but I would like to modify the contents of the output file since there several useless informations. This output file is directly produce by the dynWrite command which is built in nmrWish, and I've no idea of how this function reads the information contain in the noe restraint file I provide and then writes everything in the output file. If someone could provide the source code of the dynWrite function, I think I could use it to had a process in the script that will write only the information I need in the output file.

Thanks

Hi,

I am using peak volumes from "fully relaxed" 2D correlation spectra to quantify
populations in a slowly exchanging system. Is there a way to get an error in the
calculated volume to propagate?  I feel it should be a function of the
uncertainty in the height and line widths, which is all related to the noise,
when I fit the peaks.

I also noticed from the website that in the peak detection function of nmrDraw
the VOL is "estimated as the sum of intensities in the neighborhood of the peak
maximum." How is this neighborhood defined?  I guess I could propagate the error
over the sum of intensities to get the error in volume.

Finally, on an unrelated note, we have noticed that after fitting using
autoFit.tcl the DHEIGHT is not updated in nlin.tab.

Cheers,
Mike

Dear nmrPIPE comunity

I would like to ask you for help with my problem. I'm trying to replace
defective points in 3D spectrum. I can not use LP because spectrum was acquired
in NUS mode, however I have the correct points in different spectrum.

I have split 3D spectrum into 2D slices. Now I need to split 2D slices into 1D
fids. I'm using readROI script.

The problem that I have is that read ROI extracts either real or imaginary point
in y axis (x axis is already after FT) and I need both.

My question is: is there a way how to force readROI script to extract both real
and imaginary part?

Or alternatively, how can I add real and imaginary point so that complex point
will be formed? I have already tried addNMR in interleaved mode, but it adds the
second point as if it would be x-axis imaginary point but it is y axis imaginary
point.

Thank you

P.S. Im attaching the 2 two fids

real part: http://depositfiles.com/files/fg6l5hs23
imaginary part: http://depositfiles.com/files/n5z1h4fgq

Probably lots of ways to do this, even ways without splitting up
the data.  For similar NUS tasks, I usually work with an NMRPipe-format
mask file of ones and zeros, and do things by multiplication and
addition.

In order to combine real and imaginary data into a single complex
data set, we make two intermediate complex data sets (nmrPipe -ac ...)
One output has the real data with zeros in the imaginaries.
The other output has zeros in the real part, and the imaginary data
in the imaginary part (SHUF -swap).  Then we add these together
using addNMR.

Below is an example, which takes an ordinary 2D scheme,
splits the interferogram into real and imaginary parts,
and rejoins the parts before the second FT.

#!/bin/csh

nmrPipe -in fid/test001.fid \
| 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 -207  -p1 0.0 -di               \
| nmrPipe  -fn EXT -x1 10.5ppm -xn 6.0ppm -sw -verb   \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn NULL -di -out real.ft1 -ov

nmrPipe -in fid/test001.fid \
| 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 -207  -p1 0.0 -di               \
| nmrPipe  -fn EXT -x1 10.5ppm -xn 6.0ppm -sw -verb   \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn SHUF -swap -di -out imag.ft1 -ov

nmrPipe -in real.ft1 -fn NULL       -ac -out real_zero.ft1 -ov
nmrPipe -in imag.ft1 -fn SHUF -swap -ac -out zero_imag.ft1 -ov

addNMR -in1 real_zero.ft1 -in2 zero_imag.ft1 -out test.ft1

nmrPipe -in test.ft1 \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5    \
| nmrPipe  -fn ZF -auto                               \
| nmrPipe  -fn FT                                     \
| nmrPipe  -fn PS -p0 22 -p1 0 -di                    \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn POLY -auto                             \
     -verb -ov -out test.ft2





Quoting tomas5122 <sikorsky.tomas@...>:

> Dear nmrPIPE comunity
>
> I would like to ask you for help with my problem. I'm trying to
> replace defective points in 3D spectrum. I can not use LP because
> spectrum was acquired in NUS mode, however I have the correct points
> in different spectrum.
>
> I have split 3D spectrum into 2D slices. Now I need to split 2D
> slices into 1D fids. I'm using readROI script.
>
> The problem that I have is that read ROI extracts either real or
> imaginary point in y axis (x axis is already after FT) and I need
> both.
>
> My question is: is there a way how to force readROI script to
> extract both real and imaginary part?
>
> Or alternatively, how can I add real and imaginary point so that
> complex point will be formed? I have already tried addNMR in
> interleaved mode, but it adds the second point as if it would be
> x-axis imaginary point but it is y axis imaginary point.
>
> Thank you
>
> P.S. Im attaching the 2 two fids
>
> real part: http://depositfiles.com/files/fg6l5hs23
> imaginary part: http://depositfiles.com/files/n5z1h4fgq
>
>

Thank you

It helped

--- In nmrpipe@yahoogroups.com, delaglio@... wrote:
>
>
>
> Probably lots of ways to do this, even ways without splitting up
> the data.  For similar NUS tasks, I usually work with an NMRPipe-format
> mask file of ones and zeros, and do things by multiplication and
> addition.
>
> In order to combine real and imaginary data into a single complex
> data set, we make two intermediate complex data sets (nmrPipe -ac ...)
> One output has the real data with zeros in the imaginaries.
> The other output has zeros in the real part, and the imaginary data
> in the imaginary part (SHUF -swap).  Then we add these together
> using addNMR.
>
> Below is an example, which takes an ordinary 2D scheme,
> splits the interferogram into real and imaginary parts,
> and rejoins the parts before the second FT.
>
> #!/bin/csh
>
> nmrPipe -in fid/test001.fid \
> | 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 -207  -p1 0.0 -di               \
> | nmrPipe  -fn EXT -x1 10.5ppm -xn 6.0ppm -sw -verb   \
> | nmrPipe  -fn TP                                     \
> | nmrPipe  -fn NULL -di -out real.ft1 -ov
>
> nmrPipe -in fid/test001.fid \
> | 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 -207  -p1 0.0 -di               \
> | nmrPipe  -fn EXT -x1 10.5ppm -xn 6.0ppm -sw -verb   \
> | nmrPipe  -fn TP                                     \
> | nmrPipe  -fn SHUF -swap -di -out imag.ft1 -ov
>
> nmrPipe -in real.ft1 -fn NULL       -ac -out real_zero.ft1 -ov
> nmrPipe -in imag.ft1 -fn SHUF -swap -ac -out zero_imag.ft1 -ov
>
> addNMR -in1 real_zero.ft1 -in2 zero_imag.ft1 -out test.ft1
>
> nmrPipe -in test.ft1 \
> | nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5    \
> | nmrPipe  -fn ZF -auto                               \
> | nmrPipe  -fn FT                                     \
> | nmrPipe  -fn PS -p0 22 -p1 0 -di                    \
> | nmrPipe  -fn TP                                     \
> | nmrPipe  -fn POLY -auto                             \
>     -verb -ov -out test.ft2
>
>
>
>
>
> Quoting tomas5122 <sikorsky.tomas@...>:
>
> > Dear nmrPIPE comunity
> >
> > I would like to ask you for help with my problem. I'm trying to
> > replace defective points in 3D spectrum. I can not use LP because
> > spectrum was acquired in NUS mode, however I have the correct points
> > in different spectrum.
> >
> > I have split 3D spectrum into 2D slices. Now I need to split 2D
> > slices into 1D fids. I'm using readROI script.
> >
> > The problem that I have is that read ROI extracts either real or
> > imaginary point in y axis (x axis is already after FT) and I need
> > both.
> >
> > My question is: is there a way how to force readROI script to
> > extract both real and imaginary part?
> >
> > Or alternatively, how can I add real and imaginary point so that
> > complex point will be formed? I have already tried addNMR in
> > interleaved mode, but it adds the second point as if it would be
> > x-axis imaginary point but it is y axis imaginary point.
> >
> > Thank you
> >
> > P.S. Im attaching the 2 two fids
> >
> > real part: http://depositfiles.com/files/fg6l5hs23
> > imaginary part: http://depositfiles.com/files/n5z1h4fgq
> >
> >
>

Dear Pipe users,
I have the same problem as Kate: heavy baseline distortions in the acquisition
dimension in the methyl region of some of my 2D and 3D noesys.
"POLY -auto" does not do a good job recognizing and correcting the baseline in
these regions resulting in a rolling baseline around the strongest signals after
correction.
The MED function is too harsh and I tried every combination of POLY orders to
solve this problem without success.
On the other hand, the automatic baseline correction function of Topspin seems
to be able to deal with these heavy distortions just fine.
Any advice on what else to try would be appreciated as I would really like to
keep on using Pipe with all its other nice features that work better than
Topspin :)
Maybe someone could enlighten me on the difference between the Pipe and Topspin
automatic baseline correction procedures?
Many thanks in advance,
Malgosia

Hello all,
I added some identical 3D data using addNMR.
In order to be sure, that the data has been added, after adding, i checked the
max and min of the first 2D plane using Scale2D
eg: my data are data1/test%03d.fid, data2/test%03d.fid and  data2/test%03d.fid
and added

data1/test%03d.fid + data2/...=data12/...
Similarly,
data12+data3=data123


When i get the max&min of data12/test001.fid it is roughly the sum of
data1+data2. However the max and min of data123 is not the sum of
data1+data2+data3 but much less.


Infact, it is always the case when i add data3 to anything and the sum is
always:
data3x < data3+datax


Is this due to some destructive intereference due to different phases of the
time domain signal? if yes, is it detrimental or somehow although the displayed
intensity goes down, the SNR would have actually increased.

Hoping for helpful answer.

regards
Santhosh

Dear nmrPipe users,

I used a pulse program called "hsqcetgpiasp" on a 700MHz Bruker NMR spectrometer
to colloect HACA RDCs. When I'm processing the data, I used the QMIX command to
separate IP and AP spectra. The Fn Mode is echo-antiecho, so I set C= ( 1 0 \ 0
1 \ 0 0 \ 0 0 ) and C= ( 0 0 \ 0 0 \ 1 0 \ 0 1 ).  But it does not work. I also
tried the COADD command following the instructions on message #389. It does not
work either.

Could anyone help me with the processing of IPAP data in echo-antiecho mode? How
should I set my C matrix and combine my fids to get the right IP and AP spectra?

Thanks in advance.

Yang

Department of Biochemistry
Duke University

********************************************************************************\
**********

My processing script is:
#!/bin/csh

set C = ( 1 0 \ 0 1 \ 0 0 \ 0 0 )

bruk2pipe -in ./ser \
   -bad 0.0 -aswap -DMX -decim 1792 -dspfvs 20 -grpdly 67.9841766357422  \
   -xN              2048  -yN              1024  \
   -xT              1024  -yT               512  \
   -xMODE            DQD  -yMODE  Echo-AntiEcho  \
   -xSW        11160.714  -ySW         5279.831  \
   -xOBS         700.133  -yOBS         176.057  \
   -xCAR           4.657  -yCAR          55.619  \
   -xLAB              HN  -yLAB             13C  \
   -ndim               2  -aq2D          States  \
| nmrPipe  -fn QMIX -ic 4 -oc 2 -cList $C -time         \
| nmrPipe  -fn SOL -mode 1 -fl 32                       \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 1        \
| nmrPipe  -fn ZF -auto                                 \
| nmrPipe  -fn FT                                       \
| nmrPipe  -fn PS -p0 0.0 -p1 0.0  -di   -ov         \
| nmrPipe  -fn TP                                       \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5      \
| nmrPipe  -fn ZF -auto                                 \
| nmrPipe  -fn FT                                  \
| nmrPipe  -fn CS -rs 50%                               \
| nmrPipe  -fn TP                                       \
| nmrPipe  -fn POLY -auto                               \
   -out ./isotropic_CH_IPAP.ft2 -verb -ov

The pulse program is "hsqcetgpiasp":
;hsqcetgpiasp
;avance-version (10/02/12)
;HSQC - IPAP
;2D H-1/X correlation via double inept transfer
;phase sensitive using Echo/Antiecho-TPPI gradient selection
;with decoupling during acquisition
;using shaped pulses for inversion on f2 - channel
;
;$CLASS=HighRes
;$DIM=2D
;$TYPE=
;$SUBTYPE=
;$COMMENT=


prosol relations=


#include
#include
#include


"p2=p1*2"
"p4=p3*2"
"p22=p21*2"
"d4=1s/(cnst2*4)"
"d11=30m"
"d24=1s/(cnst2*cnst11)"


"d0=3u"

"in0=inf1/2"


"DELTA=p16+d16+p22+d0*2-p3*4/3.1316"
"DELTA1=d4-p16-larger(p2,p8)/2-8u"
"DELTA2=d4-larger(p2,p8)/2"
"DELTA3=d24-p19-d16"
"DELTA4=d24-p19-d16-p1"


"l0=1"


1 ze
d11 pl12:f2
2 d1 do:f2
3 (p1 ph1)
DELTA2 pl0:f2
4u
(center (p2 ph1) (p8:sp13 ph7):f2 )
4u
DELTA2 pl2:f2 UNBLKGRAD
(p1 ph2)

p16:gp3
d16

if "l0 %2 == 1"
{
(p2 ph1)
(p3 ph3):f2
p19:gp4
d16
DELTA3
(p4 ph5):f2
DELTA3
p19:gp4
d16
}
else
{
(p3 ph4):f2
p19:gp4
d16
DELTA3
(center (p2 ph1) (p4 ph5):f2 )
DELTA4
p19:gp4
d16
(p1 ph6)
}

d0
(p22 ph1):f3
d0
p16:gp1*EA
d16
(p4 ph1):f2
DELTA
(p3 ph1):f2

(p1 ph1)
DELTA2 pl0:f2
(center (p2 ph1) (p8:sp13 ph1):f2 )
4u
p16:gp2
DELTA1 pl12:f2
4u BLKGRAD

if "l0 %2 == 1"
{
go=2 ph30 cpd2:f2
}
else
{
go=2 ph31 cpd2:f2
}

d1 do:f2 mc #0 to 2
F1I(iu0, 2)
F1EA(calgrad(EA), caldel(d0, +in0) & calph(ph3, +180) & calph(ph4, +180) &
calph(ph7, +180) & calph(ph30, +180) & calph(ph31, +180))
exit


ph1=0
ph2=3 1
ph3=0 0 2 2
ph4=3 3 1 1
ph5=0 0 0 0 1 1 1 1 2 2 2 2 3 3 3 3
ph6=0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 2
ph7=0
ph30=0 2 2 0
ph31=0 2 2 0 2 0 0 2


;pl0 : 0W
;pl1 : f1 channel - power level for pulse (default)
;pl2 : f2 channel - power level for pulse (default)
;pl3 : f3 channel - power level for pulse (default)
;pl12: f2 channel - power level for CPD/BB decoupling
;sp13: f2 channel - shaped pulse 180 degree (adiabatic)
;p1 : f1 channel - 90 degree high power pulse
;p2 : f1 channel - 180 degree high power pulse
;p3 : f2 channel - 90 degree high power pulse
;p4 : f2 channel - 180 degree high power pulse
;p8 : f2 channel - 180 degree shaped pulse for inversion (adiabatic)
;p16: homospoil/gradient pulse
;p19: gradient pulse 2 [500 usec]
;p21: f3 channel - 90 degree high power pulse
;p22: f3 channel - 180 degree high power pulse
;p28: f1 channel - trim pulse
;d0 : incremented delay (2D) [3 usec]
;d1 : relaxation delay; 1-5 * T1
;d4 : 1/(4J)CH
;d11: delay for disk I/O [30 msec]
;d16: delay for homospoil/gradient recovery
;d24: 1/(4J)CH for CH
; 1/(8J)CH for all multiplicities
;cnst2: = J(CH)
;cnst11: for multiplicity selection = 4 for CH,
; 8 for all multiplicities
;inf1: 1/SW(C) = 2 * DW(C)
;in0: 1/(2 * SW(C)) = DW(C)
;nd0: 2
;NS: 4 * n
;DS: >= 32
;td1: number of experiments
;FnMODE: echo-antiecho
;cpd2: decoupling according to sequence defined by cpdprg2
;pcpd2: f2 channel - 90 degree pulse for decoupling sequence


;use gradient ratio: gp 1 : gp 2 : gp 3 : gp 4
; 80 : 20.1 : 50 : 5

;for z-only gradients:
;gpz1: 80%
;gpz2: 20.1%
;gpz3: 50%
;gpz4: 5%

;use gradient files:
;gpnam1: SMSQ10.100
;gpnam2: SMSQ10.100
;gpnam3: SMSQ10.100
;gpnam4: SMSQ10.100

The processing to use depends on whether the IP/AP interleaving loop
is the innermost one in the pulse sequence.  If it is, we have to
separate the IP and AP parts before accounting for gradient
shuffling.

Normally, in NMRPipe, gradient enhanced 2D data is converted with
"-yMODE Echo-AntiEcho". This actually runs an NMRPipe macro to perform
gradient shuffling of pairs of adjacent 1D vectors during the
conversion, but it is run "in background", and you don't see it
explicitly. In the case of bruker data,
it is:

| nmrPipe -fn MAC -macro $NMRTXT/bruk_ranceY.M -noRd -noWr \

In an interleaved version of the gradient-enhanced data, there are two
possible formats. In one case, the innermost acquisition loop is the
IP/AP phase encoding. So, adjacent pairs of vectors are Echo-AntiEcho
pairs, and you can convert this data with "-yMODE Echo-AntiEcho".
Then, later processing steps can use COADD to select or combine
channels.

However, in the other case, IP/AP alternation is in the innermost
acquisition loop. This means that manipulation with COADD must happen
before gradient shuffling. In these cases, we convert with "-yMODE
Complex", and then explicitly include gradient shuffling just
afterwards, for example:

nmrPipe -in test.fid \
| nmrPipe -fn COADD -cList 1 -1 -time -axis Y \
| nmrPipe -fn MAC -macro $NMRTXT/bruk_ranceY.M -noRd -noWr \
| nmrPipe -fn SOL \
| nmrPipe -fn SP -off 0.5   ... etc ....  -out dif.ft2

Also, one more tip:

When dealing with this kind of data, it can be handy to extract the IP
and AP channels separately ("COADD -cList 1 0" and "COADD -cList 0 1")
so that they can be inspected first to find the optimum coefficient
for cancelation of IP and AP signals. Then, use the stand-alone
program "addNMR" to combine the two channels to form scaled sum and
difference, for example:

addNMR -in1 A.dat -in2 B.dat -c1 1.0 -c2 1.2 -out sum.dat -add
addNMR -in1 A.dat -in2 B.dat -c2 1.0 -c2 1.2 -out dif.dat -sub

Quoting "yangqi@..." <yangqi.duke@...>:

> Dear nmrPipe users,
>
> I used a pulse program called "hsqcetgpiasp" on a 700MHz Bruker NMR
> spectrometer to colloect HACA RDCs. When I'm processing the data, I
> used the QMIX command to separate IP and AP spectra. The Fn Mode is
> echo-antiecho, so I set C= ( 1 0 \ 0 1 \ 0 0 \ 0 0 ) and C= ( 0 0 \
> 0 0 \ 1 0 \ 0 1 ).  But it does not work. I also tried the COADD
> command following the instructions on message #389. It does not work
> either.
>
> Could anyone help me with the processing of IPAP data in
> echo-antiecho mode? How should I set my C matrix and combine my fids
> to get the right IP and AP spectra?
>
> Thanks in advance.
>
> Yang
>
> Department of Biochemistry
> Duke University
>
>
********************************************************************************\
**********
>
> My processing script is:
> #!/bin/csh
>
> set C = ( 1 0 \ 0 1 \ 0 0 \ 0 0 )
>
> bruk2pipe -in ./ser \
>   -bad 0.0 -aswap -DMX -decim 1792 -dspfvs 20 -grpdly 67.9841766357422  \
>   -xN              2048  -yN              1024  \
>   -xT              1024  -yT               512  \
>   -xMODE            DQD  -yMODE  Echo-AntiEcho  \
>   -xSW        11160.714  -ySW         5279.831  \
>   -xOBS         700.133  -yOBS         176.057  \
>   -xCAR           4.657  -yCAR          55.619  \
>   -xLAB              HN  -yLAB             13C  \
>   -ndim               2  -aq2D          States  \
> | nmrPipe  -fn QMIX -ic 4 -oc 2 -cList $C -time         \
> | nmrPipe  -fn SOL -mode 1 -fl 32                       \
> | nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 1        \
> | nmrPipe  -fn ZF -auto                                 \
> | nmrPipe  -fn FT                                       \
> | nmrPipe  -fn PS -p0 0.0 -p1 0.0  -di   -ov         \
> | nmrPipe  -fn TP                                       \
> | nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5      \
> | nmrPipe  -fn ZF -auto                                 \
> | nmrPipe  -fn FT                                  \
> | nmrPipe  -fn CS -rs 50%                               \
> | nmrPipe  -fn TP                                       \
> | nmrPipe  -fn POLY -auto                               \
>   -out ./isotropic_CH_IPAP.ft2 -verb -ov
>
> The pulse program is "hsqcetgpiasp":
> ;hsqcetgpiasp
> ;avance-version (10/02/12)
> ;HSQC - IPAP
> ;2D H-1/X correlation via double inept transfer
> ;phase sensitive using Echo/Antiecho-TPPI gradient selection
> ;with decoupling during acquisition
> ;using shaped pulses for inversion on f2 - channel
> ;
> ;$CLASS=HighRes
> ;$DIM=2D
> ;$TYPE=
> ;$SUBTYPE=
> ;$COMMENT=
>
>
> prosol relations=
>
>
> #include
> #include
> #include
>
>
> "p2=p1*2"
> "p4=p3*2"
> "p22=p21*2"
> "d4=1s/(cnst2*4)"
> "d11=30m"
> "d24=1s/(cnst2*cnst11)"
>
>
> "d0=3u"
>
> "in0=inf1/2"
>
>
> "DELTA=p16+d16+p22+d0*2-p3*4/3.1316"
> "DELTA1=d4-p16-larger(p2,p8)/2-8u"
> "DELTA2=d4-larger(p2,p8)/2"
> "DELTA3=d24-p19-d16"
> "DELTA4=d24-p19-d16-p1"
>
>
> "l0=1"
>
>
> 1 ze
> d11 pl12:f2
> 2 d1 do:f2
> 3 (p1 ph1)
> DELTA2 pl0:f2
> 4u
> (center (p2 ph1) (p8:sp13 ph7):f2 )
> 4u
> DELTA2 pl2:f2 UNBLKGRAD
> (p1 ph2)
>
> p16:gp3
> d16
>
> if "l0 %2 == 1"
> {
> (p2 ph1)
> (p3 ph3):f2
> p19:gp4
> d16
> DELTA3
> (p4 ph5):f2
> DELTA3
> p19:gp4
> d16
> }
> else
> {
> (p3 ph4):f2
> p19:gp4
> d16
> DELTA3
> (center (p2 ph1) (p4 ph5):f2 )
> DELTA4
> p19:gp4
> d16
> (p1 ph6)
> }
>
> d0
> (p22 ph1):f3
> d0
> p16:gp1*EA
> d16
> (p4 ph1):f2
> DELTA
> (p3 ph1):f2
>
> (p1 ph1)
> DELTA2 pl0:f2
> (center (p2 ph1) (p8:sp13 ph1):f2 )
> 4u
> p16:gp2
> DELTA1 pl12:f2
> 4u BLKGRAD
>
> if "l0 %2 == 1"
> {
> go=2 ph30 cpd2:f2
> }
> else
> {
> go=2 ph31 cpd2:f2
> }
>
> d1 do:f2 mc #0 to 2
> F1I(iu0, 2)
> F1EA(calgrad(EA), caldel(d0, +in0) & calph(ph3, +180) & calph(ph4,
> +180) & calph(ph7, +180) & calph(ph30, +180) & calph(ph31, +180))
> exit
>
>
> ph1=0
> ph2=3 1
> ph3=0 0 2 2
> ph4=3 3 1 1
> ph5=0 0 0 0 1 1 1 1 2 2 2 2 3 3 3 3
> ph6=0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 2
> ph7=0
> ph30=0 2 2 0
> ph31=0 2 2 0 2 0 0 2
>
>
> ;pl0 : 0W
> ;pl1 : f1 channel - power level for pulse (default)
> ;pl2 : f2 channel - power level for pulse (default)
> ;pl3 : f3 channel - power level for pulse (default)
> ;pl12: f2 channel - power level for CPD/BB decoupling
> ;sp13: f2 channel - shaped pulse 180 degree (adiabatic)
> ;p1 : f1 channel - 90 degree high power pulse
> ;p2 : f1 channel - 180 degree high power pulse
> ;p3 : f2 channel - 90 degree high power pulse
> ;p4 : f2 channel - 180 degree high power pulse
> ;p8 : f2 channel - 180 degree shaped pulse for inversion (adiabatic)
> ;p16: homospoil/gradient pulse
> ;p19: gradient pulse 2 [500 usec]
> ;p21: f3 channel - 90 degree high power pulse
> ;p22: f3 channel - 180 degree high power pulse
> ;p28: f1 channel - trim pulse
> ;d0 : incremented delay (2D) [3 usec]
> ;d1 : relaxation delay; 1-5 * T1
> ;d4 : 1/(4J)CH
> ;d11: delay for disk I/O [30 msec]
> ;d16: delay for homospoil/gradient recovery
> ;d24: 1/(4J)CH for CH
> ; 1/(8J)CH for all multiplicities
> ;cnst2: = J(CH)
> ;cnst11: for multiplicity selection = 4 for CH,
> ; 8 for all multiplicities
> ;inf1: 1/SW(C) = 2 * DW(C)
> ;in0: 1/(2 * SW(C)) = DW(C)
> ;nd0: 2
> ;NS: 4 * n
> ;DS: >= 32
> ;td1: number of experiments
> ;FnMODE: echo-antiecho
> ;cpd2: decoupling according to sequence defined by cpdprg2
> ;pcpd2: f2 channel - 90 degree pulse for decoupling sequence
>
>
> ;use gradient ratio: gp 1 : gp 2 : gp 3 : gp 4
> ; 80 : 20.1 : 50 : 5
>
> ;for z-only gradients:
> ;gpz1: 80%
> ;gpz2: 20.1%
> ;gpz3: 50%
> ;gpz4: 5%
>
> ;use gradient files:
> ;gpnam1: SMSQ10.100
> ;gpnam2: SMSQ10.100
> ;gpnam3: SMSQ10.100
> ;gpnam4: SMSQ10.100
>
>

If the phases of the data are not the same, signals will partially
or completely cancel if you add the data directly in the time domain
without any other processing.  So, usually the best approach
is to process, phase, and baseline correct each spectrum
separately, and add them in the frequency domain.

If there is some reason that you need to have time-domain data:
if the time-domain data is different by only zero-order phase,
you could apply phase correction directly to the FIDs before
adding.


Quoting santhosh_karunakaran <santhosh.ayalur@...>:

> Hello all,
> I added some identical 3D data using addNMR.
> In order to be sure, that the data has been added, after adding, i
> checked the max and min of the first 2D plane using Scale2D
> eg: my data are data1/test%03d.fid, data2/test%03d.fid and
> data2/test%03d.fid and added
>
> data1/test%03d.fid + data2/...=data12/...
> Similarly,
> data12+data3=data123
>
>
> When i get the max&min of data12/test001.fid it is roughly the sum
> of data1+data2. However the max and min of data123 is not the sum of
> data1+data2+data3 but much less.
>
>
> Infact, it is always the case when i add data3 to anything and the
> sum is always:
> data3x < data3+datax
>
>
> Is this due to some destructive intereference due to different
> phases of the time domain signal? if yes, is it detrimental or
> somehow although the displayed intensity goes down, the SNR would
> have actually increased.
>
> Hoping for helpful answer.
>
> regards
> Santhosh
>
>

Bruker needs to have good baseline correction facilities in their
software because their acquistion methods result in such badly
distorted baselines.

That being said, there are a couple of ways to get slightly better
baseline behavior when using NMRPipe.

1. When converting data via the "bruker" command, select the
     checkbox for "Digital Oversampling Correction:" to
     "During Processing" ... this will often give better results
     for 1D 1H data and 2D homo data.

2. In the case of data with a strong solvent signal, perform two
     separate baseline corrections above and below the solvent,
     for example:

     | nmrPipe -fn POLY -auto -xn 7.4ppm \
     | nmrPipe -fn POLY -auto -xn 7.4ppm \

3. The POLY function can also be used with a series of specific
     baseline positions specified manually, for example:

     | nmrPipe -fn POLY -nl 10.5ppm 10.0ppm 6.2ppm 5.8ppm 1.2ppm -0.5ppm -nw 2 \



Quoting Malgosia <malgosia@...>:

> Dear Pipe users,
> I have the same problem as Kate: heavy baseline distortions in the
> acquisition dimension in the methyl region of some of my 2D and 3D
> noesys.
> "POLY -auto" does not do a good job recognizing and correcting the
> baseline in these regions resulting in a rolling baseline around the
> strongest signals after correction.
> The MED function is too harsh and I tried every combination of POLY
> orders to solve this problem without success.
> On the other hand, the automatic baseline correction function of
> Topspin seems to be able to deal with these heavy distortions just
> fine.
> Any advice on what else to try would be appreciated as I would
> really like to keep on using Pipe with all its other nice features
> that work better than Topspin :)
> Maybe someone could enlighten me on the difference between the Pipe
> and Topspin automatic baseline correction procedures?
> Many thanks in advance,
> Malgosia
>
>

 

Bruker needs to have good baseline correction facilities in their
software because their acquistion methods result in such badly
distorted baselines.

That being said, there are a couple of ways to get slightly better
baseline behavior when using NMRPipe.

1. When converting data via the "bruker" command, select the
checkbox for "Digital Oversampling Correction:" to
"During Processing" ... this will often give better results
for 1D 1H data and 2D homo data.

2. In the case of data with a strong solvent signal, perform two
separate baseline corrections above and below the solvent,
for example:

| nmrPipe -fn POLY -auto -xn 7.4ppm \
| nmrPipe -fn POLY -auto -xn 7.4ppm \

3. The POLY function can also be used with a series of specific
baseline positions specified manually, for example:

| nmrPipe -fn POLY -nl 10.5ppm 10.0ppm 6.2ppm 5.8ppm 1.2ppm -0.5ppm -nw 2 \

Quoting Malgosia malgosia@...>:

> Dear Pipe users,
> I have the same problem as Kate: heavy baseline distortions in the
> acquisition dimension in the methyl region of some of my 2D and 3D
> noesys.
> "POLY -auto" does not do a good job recognizing and correcting the
> baseline in these regions resulting in a rolling baseline around the
> strongest signals after correction.
> The MED function is too harsh and I tried every combination of POLY
> orders to solve this problem without success.
> On the other hand, the automatic baseline correction function of
> Topspin seems to be able to deal with these heavy distortions just
> fine.
> Any advice on what else to try would be appreciated as I would
> really like to keep on using Pipe with all its other nice features
> that work better than Topspin :)
> Maybe someone could enlighten me on the difference between the Pipe
> and Topspin automatic baseline correction procedures?
> Many thanks in advance,
> Malgosia
>
>

-- Dr. Malgorzata Duszczyk
Group Allain
Institute for Molecular Biology and Biophysics
Schaffmattstr. 30
ETH Hoenggerberg, HPP L13
CH-8093 Zuerich
Switzerland
tel. +41 44 633 0707

Ok, one more trick, hope it helps!

For a given vector-based nmrPipe processing function, you can select which
vectors from the data are passed to it, and which parts are skipped.
For example, to only correct the vectors between 5ppm and 4ppm:

| nmrPipe -select 5ppm 4ppm -fn POLY -auto \

--- from "nmrPipe -help":

Processing or Pass-Through of a Selected Region:
   -select  Y1 YN ...  Specification of Region Limits.
   -outside            Process vectors outside region.
   -inside             Process vectors inside region;
                       (Default).

Quoting Malgosia Duszczyk <malgosia@...>:

> Thanks Frank!
>
> On 10.01.2013 06:02, delaglio@... wrote:
>>
>>
>> Bruker needs to have good baseline correction facilities in their
>> software because their acquistion methods result in such badly
>> distorted baselines.
>>
> Not much to do about that then as bruker machines are the only ones
> at my disposal :)
>>
>> That being said, there are a couple of ways to get slightly better
>> baseline behavior when using NMRPipe.
>>
>> 1. When converting data via the "bruker" command, select the
>> checkbox for "Digital Oversampling Correction:" to
>> "During Processing" ... this will often give better results
>> for 1D 1H data and 2D homo data.
>>
> This actually does improve the distortions (but not enough in my
> case unfortunately...).
>>
>> 2. In the case of data with a strong solvent signal, perform two
>> separate baseline corrections above and below the solvent,
>> for example:
>>
>> | nmrPipe -fn POLY -auto -xn 7.4ppm \
>> | nmrPipe -fn POLY -auto -xn 7.4ppm \
>>
>> 3. The POLY function can also be used with a series of specific
>> baseline positions specified manually, for example:
>>
>> | nmrPipe -fn POLY -nl 10.5ppm 10.0ppm 6.2ppm 5.8ppm 1.2ppm -0.5ppm -nw 2 \
>>
> As there is no possibility to do this only for some y ppm regions,
> while it solves problems in some, it creates others elsewhere
> unfortunately (as in complex crowded spectra there is no combination
> of baseline positions where there is no signal at all y ppm values).
>
> My solution for the moment is converting the topspin processed
> spectra to pipe using the *xyza2pipe *conversion program if I want
> to use any of the pipe programs on my data
>
> http://fermi.pharm.hokudai.ac.jp/olivia/api/index.php/Xyza2pipe_src
>
> BTW this also solves the problem that it is not possible to
> transpose axes while preparing spectra for sparky using bruk2ucsf
> (while it is possible to do it with pipe2ucsf).
>
> Malgosia
>
>>
>> Quoting Malgosia malgosia@...
>> <mailto:malgosia%40mol.biol.ethz.ch>>:
>>
>>> Dear Pipe users,
>>> I have the same problem as Kate: heavy baseline distortions in the
>>> acquisition dimension in the methyl region of some of my 2D and 3D
>>> noesys.
>>> "POLY -auto" does not do a good job recognizing and correcting the
>>> baseline in these regions resulting in a rolling baseline around the
>>> strongest signals after correction.
>>> The MED function is too harsh and I tried every combination of POLY
>>> orders to solve this problem without success.
>>> On the other hand, the automatic baseline correction function of
>>> Topspin seems to be able to deal with these heavy distortions just
>>> fine.
>>> Any advice on what else to try would be appreciated as I would
>>> really like to keep on using Pipe with all its other nice features
>>> that work better than Topspin :)
>>> Maybe someone could enlighten me on the difference between the Pipe
>>> and Topspin automatic baseline correction procedures?
>>> Many thanks in advance,
>>> Malgosia
>>>
>>>
>>
>>
>
>
> --
> Dr. Malgorzata Duszczyk
> Group Allain
> Institute for Molecular Biology and Biophysics
> Schaffmattstr. 30
> ETH Hoenggerberg, HPP L13
> CH-8093 Zuerich
> Switzerland
> tel. +41 44 633 0707
>
>

The IP/AP interleaving loop is the innermost one and the script works. Thank you
so much!

Yang

--- In nmrpipe@yahoogroups.com, delaglio@... wrote:
>
>
> The processing to use depends on whether the IP/AP interleaving loop
> is the innermost one in the pulse sequence.  If it is, we have to
> separate the IP and AP parts before accounting for gradient
> shuffling.
>
> Normally, in NMRPipe, gradient enhanced 2D data is converted with
> "-yMODE Echo-AntiEcho". This actually runs an NMRPipe macro to perform
> gradient shuffling of pairs of adjacent 1D vectors during the
> conversion, but it is run "in background", and you don't see it
> explicitly. In the case of bruker data,
> it is:
>
> | nmrPipe -fn MAC -macro $NMRTXT/bruk_ranceY.M -noRd -noWr \
>
> In an interleaved version of the gradient-enhanced data, there are two
> possible formats. In one case, the innermost acquisition loop is the
> IP/AP phase encoding. So, adjacent pairs of vectors are Echo-AntiEcho
> pairs, and you can convert this data with "-yMODE Echo-AntiEcho".
> Then, later processing steps can use COADD to select or combine
> channels.
>
> However, in the other case, IP/AP alternation is in the innermost
> acquisition loop. This means that manipulation with COADD must happen
> before gradient shuffling. In these cases, we convert with "-yMODE
> Complex", and then explicitly include gradient shuffling just
> afterwards, for example:
>
> nmrPipe -in test.fid \
> | nmrPipe -fn COADD -cList 1 -1 -time -axis Y \
> | nmrPipe -fn MAC -macro $NMRTXT/bruk_ranceY.M -noRd -noWr \
> | nmrPipe -fn SOL \
> | nmrPipe -fn SP -off 0.5   ... etc ....  -out dif.ft2
>
> Also, one more tip:
>
> When dealing with this kind of data, it can be handy to extract the IP
> and AP channels separately ("COADD -cList 1 0" and "COADD -cList 0 1")
> so that they can be inspected first to find the optimum coefficient
> for cancelation of IP and AP signals. Then, use the stand-alone
> program "addNMR" to combine the two channels to form scaled sum and
> difference, for example:
>
> addNMR -in1 A.dat -in2 B.dat -c1 1.0 -c2 1.2 -out sum.dat -add
> addNMR -in1 A.dat -in2 B.dat -c2 1.0 -c2 1.2 -out dif.dat -sub
>
> Quoting "yangqi@..." :
>
> > Dear nmrPipe users,
> >
> > I used a pulse program called "hsqcetgpiasp" on a 700MHz Bruker NMR
> > spectrometer to colloect HACA RDCs. When I'm processing the data, I
> > used the QMIX command to separate IP and AP spectra. The Fn Mode is
> > echo-antiecho, so I set C= ( 1 0 \ 0 1 \ 0 0 \ 0 0 ) and C= ( 0 0 \
> > 0 0 \ 1 0 \ 0 1 ).  But it does not work. I also tried the COADD
> > command following the instructions on message #389. It does not work
> > either.
> >
> > Could anyone help me with the processing of IPAP data in
> > echo-antiecho mode? How should I set my C matrix and combine my fids
> > to get the right IP and AP spectra?
> >
> > Thanks in advance.
> >
> > Yang
> >
> > Department of Biochemistry
> > Duke University
> >
> >
********************************************************************************\
**********
> >
> > My processing script is:
> > #!/bin/csh
> >
> > set C = ( 1 0 \ 0 1 \ 0 0 \ 0 0 )
> >
> > bruk2pipe -in ./ser \
> >   -bad 0.0 -aswap -DMX -decim 1792 -dspfvs 20 -grpdly 67.9841766357422  \
> >   -xN              2048  -yN              1024  \
> >   -xT              1024  -yT               512  \
> >   -xMODE            DQD  -yMODE  Echo-AntiEcho  \
> >   -xSW        11160.714  -ySW         5279.831  \
> >   -xOBS         700.133  -yOBS         176.057  \
> >   -xCAR           4.657  -yCAR          55.619  \
> >   -xLAB              HN  -yLAB             13C  \
> >   -ndim               2  -aq2D          States  \
> > | nmrPipe  -fn QMIX -ic 4 -oc 2 -cList $C -time         \
> > | nmrPipe  -fn SOL -mode 1 -fl 32                       \
> > | nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 1        \
> > | nmrPipe  -fn ZF -auto                                 \
> > | nmrPipe  -fn FT                                       \
> > | nmrPipe  -fn PS -p0 0.0 -p1 0.0  -di   -ov         \
> > | nmrPipe  -fn TP                                       \
> > | nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5      \
> > | nmrPipe  -fn ZF -auto                                 \
> > | nmrPipe  -fn FT                                  \
> > | nmrPipe  -fn CS -rs 50%                               \
> > | nmrPipe  -fn TP                                       \
> > | nmrPipe  -fn POLY -auto                               \
> >   -out ./isotropic_CH_IPAP.ft2 -verb -ov
> >
> > The pulse program is "hsqcetgpiasp":
> > ;hsqcetgpiasp
> > ;avance-version (10/02/12)
> > ;HSQC - IPAP
> > ;2D H-1/X correlation via double inept transfer
> > ;phase sensitive using Echo/Antiecho-TPPI gradient selection
> > ;with decoupling during acquisition
> > ;using shaped pulses for inversion on f2 - channel
> > ;
> > ;$CLASS=HighRes
> > ;$DIM=2D
> > ;$TYPE=
> > ;$SUBTYPE=
> > ;$COMMENT=
> >
> >
> > prosol relations=
> >
> >
> > #include
> > #include
> > #include
> >
> >
> > "p2=p1*2"
> > "p4=p3*2"
> > "p22=p21*2"
> > "d4=1s/(cnst2*4)"
> > "d11=30m"
> > "d24=1s/(cnst2*cnst11)"
> >
> >
> > "d0=3u"
> >
> > "in0=inf1/2"
> >
> >
> > "DELTA=p16+d16+p22+d0*2-p3*4/3.1316"
> > "DELTA1=d4-p16-larger(p2,p8)/2-8u"
> > "DELTA2=d4-larger(p2,p8)/2"
> > "DELTA3=d24-p19-d16"
> > "DELTA4=d24-p19-d16-p1"
> >
> >
> > "l0=1"
> >
> >
> > 1 ze
> > d11 pl12:f2
> > 2 d1 do:f2
> > 3 (p1 ph1)
> > DELTA2 pl0:f2
> > 4u
> > (center (p2 ph1) (p8:sp13 ph7):f2 )
> > 4u
> > DELTA2 pl2:f2 UNBLKGRAD
> > (p1 ph2)
> >
> > p16:gp3
> > d16
> >
> > if "l0 %2 == 1"
> > {
> > (p2 ph1)
> > (p3 ph3):f2
> > p19:gp4
> > d16
> > DELTA3
> > (p4 ph5):f2
> > DELTA3
> > p19:gp4
> > d16
> > }
> > else
> > {
> > (p3 ph4):f2
> > p19:gp4
> > d16
> > DELTA3
> > (center (p2 ph1) (p4 ph5):f2 )
> > DELTA4
> > p19:gp4
> > d16
> > (p1 ph6)
> > }
> >
> > d0
> > (p22 ph1):f3
> > d0
> > p16:gp1*EA
> > d16
> > (p4 ph1):f2
> > DELTA
> > (p3 ph1):f2
> >
> > (p1 ph1)
> > DELTA2 pl0:f2
> > (center (p2 ph1) (p8:sp13 ph1):f2 )
> > 4u
> > p16:gp2
> > DELTA1 pl12:f2
> > 4u BLKGRAD
> >
> > if "l0 %2 == 1"
> > {
> > go=2 ph30 cpd2:f2
> > }
> > else
> > {
> > go=2 ph31 cpd2:f2
> > }
> >
> > d1 do:f2 mc #0 to 2
> > F1I(iu0, 2)
> > F1EA(calgrad(EA), caldel(d0, +in0) & calph(ph3, +180) & calph(ph4,
> > +180) & calph(ph7, +180) & calph(ph30, +180) & calph(ph31, +180))
> > exit
> >
> >
> > ph1=0
> > ph2=3 1
> > ph3=0 0 2 2
> > ph4=3 3 1 1
> > ph5=0 0 0 0 1 1 1 1 2 2 2 2 3 3 3 3
> > ph6=0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 2
> > ph7=0
> > ph30=0 2 2 0
> > ph31=0 2 2 0 2 0 0 2
> >
> >
> > ;pl0 : 0W
> > ;pl1 : f1 channel - power level for pulse (default)
> > ;pl2 : f2 channel - power level for pulse (default)
> > ;pl3 : f3 channel - power level for pulse (default)
> > ;pl12: f2 channel - power level for CPD/BB decoupling
> > ;sp13: f2 channel - shaped pulse 180 degree (adiabatic)
> > ;p1 : f1 channel - 90 degree high power pulse
> > ;p2 : f1 channel - 180 degree high power pulse
> > ;p3 : f2 channel - 90 degree high power pulse
> > ;p4 : f2 channel - 180 degree high power pulse
> > ;p8 : f2 channel - 180 degree shaped pulse for inversion (adiabatic)
> > ;p16: homospoil/gradient pulse
> > ;p19: gradient pulse 2 [500 usec]
> > ;p21: f3 channel - 90 degree high power pulse
> > ;p22: f3 channel - 180 degree high power pulse
> > ;p28: f1 channel - trim pulse
> > ;d0 : incremented delay (2D) [3 usec]
> > ;d1 : relaxation delay; 1-5 * T1
> > ;d4 : 1/(4J)CH
> > ;d11: delay for disk I/O [30 msec]
> > ;d16: delay for homospoil/gradient recovery
> > ;d24: 1/(4J)CH for CH
> > ; 1/(8J)CH for all multiplicities
> > ;cnst2: = J(CH)
> > ;cnst11: for multiplicity selection = 4 for CH,
> > ; 8 for all multiplicities
> > ;inf1: 1/SW(C) = 2 * DW(C)
> > ;in0: 1/(2 * SW(C)) = DW(C)
> > ;nd0: 2
> > ;NS: 4 * n
> > ;DS: >= 32
> > ;td1: number of experiments
> > ;FnMODE: echo-antiecho
> > ;cpd2: decoupling according to sequence defined by cpdprg2
> > ;pcpd2: f2 channel - 90 degree pulse for decoupling sequence
> >
> >
> > ;use gradient ratio: gp 1 : gp 2 : gp 3 : gp 4
> > ; 80 : 20.1 : 50 : 5
> >
> > ;for z-only gradients:
> > ;gpz1: 80%
> > ;gpz2: 20.1%
> > ;gpz3: 50%
> > ;gpz4: 5%
> >
> > ;use gradient files:
> > ;gpnam1: SMSQ10.100
> > ;gpnam2: SMSQ10.100
> > ;gpnam3: SMSQ10.100
> > ;gpnam4: SMSQ10.100
> >
> >
>

--- In nmrpipe@yahoogroups.com, sette@... wrote:
>
>
>
> Dear all,
>
> after moving to Ubuntu 12.04 I'm experiencing this problem with NMRDraw
>
> (NMRDraw) XView error: Cannot open connection to window server: :0.0
> (Server package).
>
> I then reinstalled the software,
> then sudo apt-get install msttcorefonts
> then restart
>
> But I still have the same error :(
>
> Bruker, and processing files works well but would be nice to see the
> results...
>
> Any suggestion?
>
> Thanks,
> Marco
>
>
> Dr.Marco Sette, Ph.D.
>
> Department of Chemical Sciences and Technology
> University of Rome, "Tor Vergata"
> via della Ricerca Scientifica, 00133, Rome, Italy
> e-mail:        sette@...
> e-mail:        m77it@...
> Tel.:          +39-0672594424
> Fax:           +39-0672594328
>
> www.rete29aprile.it
>
>
> ----------------------------------------------------------------
> Invito da parte dell'Ateneo:
> Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del
> tuo aiuto. Dona il  5 x mille all'Universita' di Roma Tor Vergata
> codice fiscale: 80213750583 http://5x1000.uniroma2.it
>

Hello,

following execution of install.com, I receive an error message: failed to find
software directory nmrbin.linux9

I specifiy the base directory as suggested in the original instillation
instructions: /home/kozlova/nmr; and change write permission.

Also, changing permissions to all the installation files.

Can you advise me please what should be checked next?

Hi Weidong,

nmrPipe does not have MDD functionality to my knowledge, but it does have the
capability of reconstructing spectra from non-uniformly sampled NMR data using a
maximum entropy algorithm, which is just a different approach compared to MDD. 
The nmrPipe function is called MEM, and you can read all about it by searching
MEM using Google or by reading the MEM man page.

Alternatively, you can just download the MDD software directly and process the
data offline from the spectrometer.  I believe the current version of the mddnmr
software is 2.2.  There is also a web portal where you can submit data for
spectral reconstruction by MDD:
http://www.enmr.eu/webportal/mdd.html


Hope this helps.

Matthew


--- In nmrpipe@yahoogroups.com, Weidong Hu <lakesu@...> wrote:
>
> Dear nmrPipe users,
>  
> We just installed a new Bruker 700 with NUS package. A user collected a 3D
data set, but could not process the data since the MDD processing package coming
with Topspin 3.1 was a trial version, and expired after new year (Jan. 1st,
2013). I am wondering could we process the NUS 2D to 4D with nmrPipe, if so,
could someone share the procedure how to do it?
>  
> Thank you very much.
>  
> Weidong
>  
>  
>

Hi all,

I have a 3D acquired with Topspin 3.1 using 64 x 64 points for N15 and
C13 reduced both to 25% with NUS.
The strange thing happens with bruk2pipe that says it's a 2D with 1024
C13 points in F1. But in Bruker 3 dimensions appear in acquisition
window.
Is there a reason for this?

Thanks,
Marco



Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail:        sette@...
e-mail:        m77it@...
Tel.:          +39-0672594424
Fax:           +39-0672594328

www.rete29aprile.it


----------------------------------------------------------------
Invito da parte dell'Ateneo:
Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del
tuo aiuto. Dona il  5 x mille all'Universita' di Roma Tor Vergata
codice fiscale: 80213750583 http://5x1000.uniroma2.it

Hi Marco,

I too was confused at first that the bruker-->pipe conversion macro wasn't
getting the details of the acquired data correct when the data is acquired in
NUS mode in TopSpin 3.1.

I believe this is happening because Bruker has changed the name of certain
parameters in the newest version of TopSpin and in the newest versions of its
standard pulse programs, and so NMRPipe doesn't know the correct parameters to
look for.

Whatever the cause, I have found that everything works fine when I manually
changing the bruker-->pipe conversion script to correspond to what I know to be
correct about the acquired data.
For example, even though bruk2pipe thinks your data is 2D, you can change it
manually to 3D processing by changing the "Dimension Count" (upper right column
in the NMRPipe Conversion Utility window) to 3D and then updating the spectral
widths, observed frequencies, centers, etc. to the proper values.

Your particular results occurred because you have a grid of 64 x 64 = 4096 total
pairs of indirect points, 25% of which makes 1024.

Hope this helps, and good luck!

Matthew

Hi All,

Just as an added note, the latest NMRPipe schemes for 3D NUS data start
by converting the FID as a 2D file, but with parameters filled in for
all three dimensions. Then, a subsequent expansion script converts that
result into a full 3D FID, with zeros for all the "missing" values.

Cheerful Regards,

f

Quoting "Matthew J. Whitley" <matthew.j.whitley@...>:

> Hi Marco,
>
> I too was confused at first that the bruker-->pipe conversion macro
> wasn't getting the details of the acquired data correct when the
> data is acquired in NUS mode in TopSpin 3.1.
>
> I believe this is happening because Bruker has changed the name of
> certain parameters in the newest version of TopSpin and in the
> newest versions of its standard pulse programs, and so NMRPipe
> doesn't know the correct parameters to look for.
>
> Whatever the cause, I have found that everything works fine when I
> manually changing the bruker-->pipe conversion script to correspond
> to what I know to be correct about the acquired data.
> For example, even though bruk2pipe thinks your data is 2D, you can
> change it manually to 3D processing by changing the "Dimension
> Count" (upper right column in the NMRPipe Conversion Utility window)
> to 3D and then updating the spectral widths, observed frequencies,
> centers, etc. to the proper values.
>
> Your particular results occurred because you have a grid of 64 x 64
> = 4096 total pairs of indirect points, 25% of which makes 1024.
>
> Hope this helps, and good luck!
>
> Matthew
>
>
>

Hi Matthew,

thanks for your explanation.
I used my own script to convert the 2D conversion file in a 3D
conversion file but now is much more clear to me what happens,
especially the stranges 1024 points in F1.
Thanks a lot !!!

Frank, one question, everything on NUS is into the nusdemo2d and
nusdemo3d directories or there are extra files, readme, tutorial on
the web site?

Cheers,
Marco


delaglio@... ha scritto:

>
> Hi All,
>
> Just as an added note, the latest NMRPipe schemes for 3D NUS data start
> by converting the FID as a 2D file, but with parameters filled in for
> all three dimensions. Then, a subsequent expansion script converts that
> result into a full 3D FID, with zeros for all the "missing" values.
>
> Cheerful Regards,
>
> f
>
> Quoting "Matthew J. Whitley" <matthew.j.whitley@...>:
>
>> Hi Marco,
>>
>> I too was confused at first that the bruker-->pipe conversion macro
>> wasn't getting the details of the acquired data correct when the
>> data is acquired in NUS mode in TopSpin 3.1.
>>
>> I believe this is happening because Bruker has changed the name of
>> certain parameters in the newest version of TopSpin and in the
>> newest versions of its standard pulse programs, and so NMRPipe
>> doesn't know the correct parameters to look for.
>>
>> Whatever the cause, I have found that everything works fine when I
>> manually changing the bruker-->pipe conversion script to correspond
>> to what I know to be correct about the acquired data.
>> For example, even though bruk2pipe thinks your data is 2D, you can
>> change it manually to 3D processing by changing the "Dimension
>> Count" (upper right column in the NMRPipe Conversion Utility window)
>> to 3D and then updating the spectral widths, observed frequencies,
>> centers, etc. to the proper values.
>>
>> Your particular results occurred because you have a grid of 64 x 64
>> = 4096 total pairs of indirect points, 25% of which makes 1024.
>>
>> Hope this helps, and good luck!
>>
>> Matthew
>>
>>
>>
>
>
>
>



Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail:        sette@...
e-mail:        m77it@...
Tel.:          +39-0672594424
Fax:           +39-0672594328

www.rete29aprile.it


----------------------------------------------------------------
Invito da parte dell'Ateneo:
Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del
tuo aiuto. Dona il  5 x mille all'Universita' di Roma Tor Vergata
codice fiscale: 80213750583 http://5x1000.uniroma2.it

Dear Colleagues,

I have an opening for a 2-year post-doctoral position in the area of
development and application of NMR spectroscopy to proteins. Please
find the announcement below my signature. More information and the
application procedure are found at
http://www.au.dk/en/job/nat/academicpositions/.

I would appreciate if you could pass this message on to qualified individuals.

Kind regards,

Frans

ps. I apologize if you receive this message multiple times.
===========================================================

Dr. Frans A.A. Mulder
Associate Professor of Biological NMR
Interdisciplinary Nanoscience Center (iNANO) and
Department of Chemistry, Aarhus University

Phone  +45 87 15 58 89
Cell  +45 51 44 73 44
Email  fmulder@...<mailto:fmulder@...>
www.protein-nmr.org<http://www.protein-nmr.org/>, inano.au.dk
bionmr.chem.au.dk, www.inspin.dk<http://www.inspin.dk/>

============================================================


Postdoc position in Protein NMR Spectroscopy





A post-doctoral position for one year with the possibility of
extension for another year is available immediately at the Department
of Chemistry and Interdisciplinary Nanoscience Center (iNANO) at
Aarhus University, Denmark in the group of Associate Professor Dr.
Frans A.A. Mulder.

http://www.protein-nmr.org<http://www.protein-nmr.org/>
http://inano.au.dk/organization/research-groups/laboratory-for-biomolecular-nmr-\
spectroscopy/

Project and Tasks
Our group develops NMR spectroscopy methods for the study of proteins,
with an emphasis on the integrative analysis of their structure,
dynamics and electrostatics in relation to function. We focus on
enzymes, protein-protein interactions and studies of intrinsically
disordered proteins in relation to cellular function and disease. To
overcome the challenges that these systems pose we are looking for a
knowledgeable and creative person. It is expected that the successful
candidate will independently manage the development, implementation of
NMR experiments and data analysis, as well as collaborate with other
groups in local and international collaborations.

Scientific Surroundings
The Protein NMR Laboratory offers a stimulating research environment,
covering complementary research activities in the area of liquid state
NMR, oriented and MAS solid state NMR, pulse sequence development,
low-field NMR and imaging. The lab is currently equipped with three
highly flexible instruments for liquid and solid-state applications
operating at 700 MHz, 500 MHz, and 400 MHz. In 2013 a new
state-of-the-art 950 MHz spectrometer will be installed, which will be
the highest field NMR magnet in Scandinavia. The BioNMR research is
embedded within the Center for Insoluble Protein Structures (inSPIN;
http://www.inspin.dk<http://www.inspin.dk/>), the Department of
Chemistry (http://chem.au.dk<http://chem.au.dk/>) and the
Interdisciplinary Nanoscience Center (iNANO;
http://inano.au.dk<http://inano.au.dk/>). These laboratories provide
abundant complementary and state-of-the-art techniques in structural
and molecular biology, nanoscience and technology.

Aarhus University further provides a strong international research and
training environment with excellent professional and private
conditions. Foreign employees can get help and information from the AU
International Center (http://www.au.dk/en/internationalcentre/) and
Work in Denmark (https://workindenmark.dk/).

Qualifications and Conditions of Employment
? The candidate must have a PhD in Chemistry, Physics or in closely
related fields, with demonstrated experience in NMR spectroscopy.
? The candidate must understand advanced NMR theory and experiments
and be able to apply advanced NMR techniques.
? The candidate should be able to work independently and participate
creatively in refining project directions.
? The candidate must have good oral and written communication skills.

Applicants should provide two letters of reference to
natcharlotte@...<mailto:natcharlotte@...>.

For further information please contact:

Associate Professor Dr. Frans Mulder
email: fmulder@...<mailto:fmulder@...>
tel: +45 8715 5889 / +45 51 44 73 44



Formalities and salary range

The Faculty of Science refers to the Ministerial Order on the
Appointment of Academic Staff at Danish Universities under the Danish
Ministry of Science, Technology and
Innovation<http://www.au.dk/en/rules/2008/bek284>.

Further information on qualification requirements and job content may
be found in the Memorandum on Job Structure for Academic Staff at
Danish Universities<http://www.au.dk/en/rules/2006/vtu1>.

The application must be in English and include a curriculum vitae,
degree certificate, a complete list of publications, a statement of
future research plans and information about research activities,
teaching portfolio and verified information on previous teaching
experience (if any). The recommended level of
detail<http://science.au.dk/en/positions-and-fellowships/academic-positions/rule\
s-and-instructions/curriculum-vitae-for-applications-for-scientific-positions/>.

Salary depends on seniority as agreed between the Danish Ministry of
Finance and the Confederation of Professional Unions.




Deadline

All applications must be made online and received by:


08/04/2013



Please apply online
here<https://ssl1.peoplexs.com/Peoplexs22/CandidatesPortalNoLogin/ApplicationFor\
m.cfm?CFID=1423085&CFTOKEN=cdd3108e6bdfd51-058DEE49-9990-C8C0-9C11BECA5BCE3D21&j\
sessionid=1a30f4148bb23fde43968019613d476b4e3cTR&PortalID=1407&VacatureID=564308\
>