Probably, you can craft your own macro that will work the way you like.

In NMRipe-format data, the "zero frequency" point is at N/2 + 1 of 1 to N.
So, I expect that your tilt formula might more appropriately be written
here as:

    n = tiltfactor*( 1 + nscol/2 - col )

So, you could have a macro, lets say "mytilt.M":

    shift = tiltfactor*( 1 + ySize/2 - yLoc );

    p0 = 0.0;
    p1 = -360.0*shift;

    (void) hilbert( rdata, idata, size );
    (void) ift( rdata, idata, size );
    (void) phase( rdata, idata, size, p0, p1 );
    (void) fft( rdata, idata, size );

So, if your "tiltfactor"  is -4.4, macro would be applied in the
indirect dimension like this:

    | nmrPipe -fn MAC -macro mytilt.M -var tiltfactor -4.4 \


Quoting Steve Bai <bais@...>:

> Hi
>
> I need to do a tilting to a 2D dataset (SUPER CSA 2D spectrum) along
>  the columns.  Bruker command 'ptilt1' that works for this purpose.
>  It tilts the 2D spectrum about a user defined angle, by shifting
> the  data points in the F1 direction.  The tilt factor is determined
> by  the F1 processing parameter alpha {-2,2}.  Each column of the 2D
>  matrix is shifted by n points where n is defined as n=tiltfactor *
> (nscol/2-col) , where tiltfactor=alpha * SI1/SI2, nscol=total number
>  of columns, and col is the column numbers.
>
> I have looked the group message database and found scripts such as
> 'shear.M' and the related .com scripts.  These scripts did not do
> exactly what I need to do as described above.  Maybe I just do not
> know how to adjust the offset and slope. Any suggestions is
> appreciated.
>
> Steve

There is some useful documentation on the NIH NMRPipe web page:

     http://spin.niddk.nih.gov/NMRPipe

A comprehensive list of all the programs, commands, and functions of
NMRPipe is here:

     http://spin.niddk.nih.gov/NMRPipe/ref

Another example on the web:

     http://www.cs.cmu.edu/~pittMB3/data/NMRinstructions.doc


Quoting srinivasaprabhu <prabhubiograd@...>:

> Hello all,�� � � I am a beginner in nmrpipe and nmrviewj. I need a
> beginner's tutorial to get hands-on experience. Can someone suggest
> me one? I got one over the internet but I could only go till the
> midway with it.
> Thanks in advance.Prabhu
>
>
>

Hi

I need to do a tilting to a 2D dataset (SUPER CSA 2D spectrum) along the
columns.  Bruker command 'ptilt1' that works for this purpose.  It tilts the 2D
spectrum about a user defined angle, by shifting the data points in the F1
direction.  The tilt factor is determined by the F1 processing parameter alpha
{-2,2}.  Each column of the 2D matrix is shifted by n points where n is defined
as n=tiltfactor * (nscol/2-col) , where tiltfactor=alpha * SI1/SI2, nscol=total
number of columns, and col is the column numbers.

I have looked the group message database and found scripts such as 'shear.M' and
the related .com scripts.  These scripts did not do exactly what I need to do as
described above.  Maybe I just do not know how to adjust the offset and slope.
Any suggestions is  appreciated.

Steve

Greetings ...

The script used by nmrDraw for "Auto Process 1D" is the script
$NMRTXT/proc1d.com ... you can find a hint of this obscure fact
via "nmrDraw -help"  in the argument listing for option "-proc" ...

In the current version of this script, if the dimension label is "HN"
or "HNx", the script will process the data as if it is typical
amide-detected protein data ... it will apply an SOL solvent filter,
usual FT processing, and then extract a typical amide region,
in this case 11ppm to 5ppm.

So, you can either convert your data using an axis name other than
HN or HNx, or you can use the nmrDraw "Proc/NMRPipe Command" command-line
to exexcute processing functions one-at-a-time.

A RELATED ITEM ...

An interesting note for those who haven't used it this way: when used
on a frequency-domain vector from a spectrum, the nmrDraw "Proc/Auto Proc 1D"
command will attempt to perform complete inverse-processing, including
removal of any window function which was previously applied.  This is
handy for
examining an indirect dimension for its
degree of decay, or to look for possible evidence of bad data points, etc.

Note that this kind of inverse processing, which must divide data by the
original window function, will only work well if the window function used
to process the data does not have values which are equal or too close
to zero.  Most example nmrPipe schemes use cosine functions which
are adjusted so that they don't go all the way down to zero.







Quoting "luke.hillary" <luke.hillary@...>:

> Hi all,
>
> I'm having issues displaying my data using a freshly installed copy
> of NmrPipe/ NmrDraw. I can import my data from the Bruker ser file
> however when I try to phase the direct dimension and use the
> 'auto-process 1D' function, the x axis will only display the amide
> region of the 1D spectrum. I have also tried this with 3D
> experiments where the x axis will only display the region of the
> spectrum containing the residual water signal. This does not occur
> on other lab members' computers when using the same data set however
>  they are at a loss as to why this is happening on my machine
> (Fedora  8). I get the same issue when using my laptop (Ubuntu
> 9.10). I don't  get any error messages during the installation
> procedure and have  followed the instructions to the letter. Am I
> missing something  obvious or could there be some more complicated
> issue I am not aware  of?
>
> Any help would be greatly appreciated.
>
> Luke
>
>
>
>

Hi all,

I'm having issues displaying my data using a freshly installed copy of NmrPipe/
NmrDraw. I can import my data from the Bruker ser file however when I try to
phase the direct dimension and use the 'auto-process 1D' function, the x axis
will only display the amide region of the 1D spectrum. I have also tried this
with 3D experiments where the x axis will only display the region of the
spectrum containing the residual water signal. This does not occur on other lab
members' computers when using the same data set however they are at a loss as to
why this is happening on my machine (Fedora 8). I get the same issue when using
my laptop (Ubuntu 9.10). I don't get any error messages during the installation
procedure and have followed the instructions to the letter. Am I missing
something obvious or could there be some more complicated issue I am not aware
of?

Any help would be greatly appreciated.

Luke

Thanks... I should have thought a little more about what pipe2xyz, and
xyz2pipe actualy stand for!

On Wed, 9 Dec 2009, Frank Delaglio wrote:

> From: Frank Delaglio <delaglio@...>
> To: "nmrpipe@yahoogroups.com" <nmrpipe@yahoogroups.com>
> Subject: Re: [nmrpipe] 3d .ft3 file to planes conversion
>
>
>
>
> maybe this would do it:
>
> pipe2xyz -in test.ft3 -out ft/test%03d.ft3
> pipe2xyz -in test.ft2 -out test.nv -nv
>
> Quoting Tara Sprules <tara.sprules@...>:
>
> > Hi,
> >
> > I have a 3D dataset as a single file in nmrPipe format (test.ft3). I can
> > read it with nmrDraw, and go through all the planes to look at the data,
> > but I can't figure out how to either
> >
> > a) convert that file directly into a nmrview file.
> >
> > or b) write it out as a series of 2D planes, so that I can use the usual
> > conversion
> >
> > xyz2pipe -in ft/test%03d.ft3 -x -verb | pipe2xyz -nv -out test.nv to make
> > an NMRView file, or so that I can create nmrPipe format projections from
> > it.
> >
> > Thanks,
> >
> > Tara
> >
> > *********************************************
> > Dr. Tara Sprules
> > Quebec/Eastern Canada High Field NMR Facility
> >
> > www.nmrlab.mcgill.ca
> >
> > phone: (514) 398-1721
> > fax: (514) 398-8254
> >
> > 3420 University St., Rm 023
> > McGill University
> > Montreal, QC, H3A 2A7
> > *********************************************
> >
>
>
>
>

*********************************************
Dr. Tara Sprules
Quebec/Eastern Canada High Field NMR Facility

www.nmrlab.mcgill.ca

phone: (514) 398-1721
fax: (514) 398-8254

3420 University St., Rm 023
McGill University
Montreal, QC, H3A 2A7
*********************************************

maybe this would do it:

     pipe2xyz -in test.ft3 -out ft/test%03d.ft3
     pipe2xyz -in test.ft2 -out test.nv -nv


Quoting Tara Sprules <tara.sprules@...>:

> Hi,
>
> I have a 3D dataset as a single file in nmrPipe format (test.ft3). I can
> read it with nmrDraw, and go through all the planes to look at the data,
> but I can't figure out how to either
>
> a) convert that file directly into a nmrview file.
>
> or b) write it out as a series of 2D planes, so that I can use the usual
> conversion
>
> xyz2pipe -in ft/test%03d.ft3 -x -verb | pipe2xyz -nv -out test.nv to make
> an NMRView file, or so that I can create nmrPipe format projections from
> it.
>
> Thanks,
>
> Tara
>
> *********************************************
> Dr. Tara Sprules
> Quebec/Eastern Canada High Field NMR Facility
>
> www.nmrlab.mcgill.ca
>
> phone: (514) 398-1721
> fax: (514) 398-8254
>
> 3420 University St., Rm 023
> McGill University
> Montreal, QC, H3A 2A7
> *********************************************
>

Hi,

I have a 3D dataset as a single file in nmrPipe format (test.ft3). I can
read it with nmrDraw, and go through all the planes to look at the data,
but I can't figure out how to either

a) convert that file directly into a nmrview file.

or b) write it out as a series of 2D planes, so that I can use the usual
conversion

xyz2pipe -in ft/test%03d.ft3 -x -verb | pipe2xyz -nv -out test.nv to make
an NMRView file, or so that I can create nmrPipe format projections from
it.

Thanks,

Tara

*********************************************
Dr. Tara Sprules
Quebec/Eastern Canada High Field NMR Facility

www.nmrlab.mcgill.ca

phone: (514) 398-1721
fax: (514) 398-8254

3420 University St., Rm 023
McGill University
Montreal, QC, H3A 2A7
*********************************************

Try "addNMR -help" ... here is the long version ...

Program "addNMR" works with NMRPipe format 1D-4D data.

In the case below, it was probably a mistake to save the NMRPipe-format
3D data as a single file.  Just convert the data as usual.  For example,
the case below might start with the converted data:

     fid32/test%03d.fid
     fid64/test%03d.fid
     fid96/test%03d.fid

Program "addNMR" allows in-place processing. So, to add the above 3 sets:

     addNMR -in1 fid32/test%03d.fid -in2 fid64/test%03d.fid -out
sum/test%03d.fid
     addNMR -in2 fid96/test%03d.fid -in2 sum/test%03d.fid   -out
sum/test%03d.fid

To test the results, you can use the program "scale2D", which
reports the max and min values in one or more NMRPipe format files,
for example:

     scale2D fid32/*.fid
     scale2D sum/*.fid





Quoting hoa_ibt <Quynh.Do@...>:

>
>
>
>
>
> Dear xiaohuxj83 and NMR users,
>
> I also have questions regarding to addition of number of scans from
> the individual 3D solid state NMR experiments which have the same
> size of time domain data and I really need your help :)
>
> Xiaohuxj83, did you get answers for your questions? Could you tell
> more detail about the process which you used addNMR to do that?
>
> And the following part is my questions...
>
> I recorded 3 separated sets of 3D NCOCX time domain data with the
> different number of scans, let say 32scans, 64scans and 96scans. And
>  then adding these time domain data together in order to get a new
> set of time domain data which contains 32scans + 64scans + 96 scans
> = 192 scans.
> Could somebody suggest me some ways to do that? Which programs,
> scripts or functions from NMRPipe software shall I use? Afterward,
> is there any way to check whether the numbers of scans are added or
> not?
> Thank your very much in advance.
>
> I tried to do that with addNMR program but it seems it does not help.
> The following is process which I did:
>
> * Step 1: all time domain data recorded from Varian spectrometer
> (800MHz) were converted to NMRPipe format without the template of
> output name such as test%03d.fid but changed into 32scans.fid,
> 64scans.fid and so on.
>
> * Step 2: addNMR was used as following:
>
> - Option 1:
>  addNMR � in1 32scans.fid �in2 64scans.fid �out test32_64.fid
>  addNMR � in1 test32_64.fid �in2 96scans.fid �out 3DNCOCX.fid
>
> - Option 2:
>  addNMR �add � in1 32scans.fid �in2 64scans.fid �out test32_64.fid
>  addNMR �add � in1 test32_64.fid �in2 96scans.fid �out 3DNCOCX.fid
>
> In the 3D NCOCX experiments, the 1st dimension is N15 and the 2nd is
>  CO, which correspond to Z axis and Y axis in NMRPipe file,
> respectively.
> When inspecting the first FID on Y or Z axis in 3DNCOCX.fid, I don't
>  see any significant differences from 32scans.fid, 64scans.fid,
> 96scans.fid. Trying to do "auto process 1D" for the first FID, it
> gives me mainly noise spectrum.
> Before recording 3D NCOCX experiments, I did 2D NCOCX experiment,
> 128 scans and used the same pulse sequence and phase cycle, I got
> quite nice spectrum and see all expected peaks on 1D projection.
>
> Question for addNMR:
> - Did I use the wrong program to add time domain data or the wrong
> way of using addNMR?
> - If addNMR is correct program to use, how can I check whether or
> not the numbers of scans from different fid files were added?
>
> Thank you very much for your help.
> Best wishes,
>
> Hoa
> ---------
> Hoa Quynh Do, PhD student
> Heinrich Heine University D�sseldorf
> Germany
>
>
> --- In nmrpipe@yahoogroups.com, "xiaohuxj83" <xpeng@...> wrote:
>>
>> I have two identical 3D solid state NMR spectra with 8 and 4 scans
>> respectively and tried to add fids. After processing the added data,
>> the spectrum looked completely different from the processed 8/4-scan
>> spectrum.
>> Does anyone have the experience of adding fids of solid state data?
>> Thank you.
>>
>
>
>

Dear xiaohuxj83 and NMR users,

I also have questions regarding to addition of number of scans from the
individual 3D solid state NMR experiments which have the same size of time
domain data and I really need your help :)

Xiaohuxj83, did you get answers for your questions? Could you tell more detail
about the process which you used addNMR to do that?

And the following part is my questions...

I recorded 3 separated sets of 3D NCOCX time domain data with the different
number of scans, let say 32scans, 64scans and 96scans. And then adding these
time domain data together in order to get a new set of time domain data which
contains 32scans + 64scans + 96 scans = 192 scans.
Could somebody suggest me some ways to do that? Which programs, scripts or
functions from NMRPipe software shall I use? Afterward, is there any way to
check whether the numbers of scans are added or not?
Thank your very much in advance.

I tried to do that with addNMR program but it seems it does not help.
The following is process which I did:

* Step 1: all time domain data recorded from Varian spectrometer (800MHz) were
converted to NMRPipe format without the template of output name such as
test%03d.fid but changed into 32scans.fid, 64scans.fid and so on.

* Step 2: addNMR was used as following:

- Option 1:
  addNMR � in1 32scans.fid �in2 64scans.fid �out test32_64.fid
  addNMR � in1 test32_64.fid �in2 96scans.fid �out 3DNCOCX.fid

- Option 2:
  addNMR �add � in1 32scans.fid �in2 64scans.fid �out test32_64.fid
  addNMR �add � in1 test32_64.fid �in2 96scans.fid �out 3DNCOCX.fid

In the 3D NCOCX experiments, the 1st dimension is N15 and the 2nd is CO, which
correspond to Z axis and Y axis in NMRPipe file, respectively.
When inspecting the first FID on Y or Z axis in 3DNCOCX.fid, I don't see any
significant differences from 32scans.fid, 64scans.fid, 96scans.fid. Trying to do
"auto process 1D" for the first FID, it gives me mainly noise spectrum.
Before recording 3D NCOCX experiments, I did 2D NCOCX experiment, 128 scans and
used the same pulse sequence and phase cycle, I got quite nice spectrum and see
all expected peaks on 1D projection.

Question for addNMR:
- Did I use the wrong program to add time domain data or the wrong way of using
addNMR?
- If addNMR is correct program to use, how can I check whether or not the
numbers of scans from different fid files were added?

Thank you very much for your help.
Best wishes,

Hoa
---------
Hoa Quynh Do, PhD student
Heinrich Heine University D�sseldorf
Germany


--- In nmrpipe@yahoogroups.com, "xiaohuxj83" <xpeng@...> wrote:
>
> I have two identical 3D solid state NMR spectra with 8 and 4 scans
> respectively and tried to add fids. After processing the added data,
> the spectrum looked completely different from the processed 8/4-scan
> spectrum.
> Does anyone have the experience of adding fids of solid state data?
> Thank you.
>

Sorry, this one got by us.  At least it is not a note about
"enhancement" ...

     Cheerful Regards,

     big fd

Quoting Gregg Siegal <g.siegal@...>:

>
>
>   That's a fairly presumptuous posting!
>
> Jeri Monika wrote:
>
>  A catalyst is a substance which asters the speed of a chemical
> reaction without itself undergoing any chemical change and the
> phenomenon is known as catalysis.
>
> -------------------------
> The INTERNET now has a personality. YOURS! See your Yahoo! Homepage.
>
> --
> signature Gregg Siegal
> Gorlaeus Laboratory
> University of Leiden
> Einsteinweg 55
> 2300-RA Leiden
> The Netherlands
> Phone (31) 71 527 4543
> Fax (31) 71 527 4603
> Lab Web Site[1]
>
> Links:
> ------
> [1] http://metprot.lic.gorlaeus.net/siegal/
> [2] mailto:?subject=Re: [nmrpipe] CATALYSIS
> [3] mailto:nmrpipe@yahoogroups.com?subject=Re: [nmrpipe] CATALYSIS
> [4]
>
http://groups.yahoo.com/group/nmrpipe/message/2011;_ylc=X3oDMTMyaGNpaDY5BF9TAzk3\
MzU5NzE0BGdycElkAzQzNTI5BGdycHNwSWQDMTcwNTA4MzE2NARtc2dJZAMyMDEyBHNlYwNmdHIEc2xr\
A3Z0cGMEc3RpbWUDMTI1OTY4ODEyNgR0cGNJZAMyMDEx
> [5]
>
http://groups.yahoo.com/group/nmrpipe/members;_ylc=X3oDMTJkYXZ1Zzk0BF9TAzk3MzU5N\
zE0BGdycElkAzQzNTI5BGdycHNwSWQDMTcwNTA4MzE2NARzZWMDdnRsBHNsawN2bWJycwRzdGltZQMxM\
jU5Njg4MTI2?o=6
> [6]
>
http://groups.yahoo.com/group/nmrpipe;_ylc=X3oDMTJjZTQ3M3AyBF9TAzk3MzU5NzE0BGdyc\
ElkAzQzNTI5BGdycHNwSWQDMTcwNTA4MzE2NARzZWMDdnRsBHNsawN2Z2hwBHN0aW1lAzEyNTk2ODgxM\
jY-
> [7]
>
http://groups.yahoo.com/group/nmrpipe/post;_ylc=X3oDMTJjMW5rYm1oBF9TAzk3MzU5NzE0\
BGdycElkAzQzNTI5BGdycHNwSWQDMTcwNTA4MzE2NARzZWMDZnRyBHNsawNudHBjBHN0aW1lAzEyNTk2\
ODgxMjY-
> [8]
>
http://us.ard.yahoo.com/SIG=14k2jhm8g/M=493064.13814333.13821539.13298430/D=grou\
ps/S=1705083164:MKP1/Y=YAHOO/EXP=1259695326/L=/B=Qd66JkPDhCs-/J=1259688126507839\
/K=ouKaeXZCp84NFolFuC9NJQ/A=5922843/R=0/SIG=11ckn2mo6/*http://advision.webevents\
.yahoo.com/green/
> [9]
>
http://us.ard.yahoo.com/SIG=14krdqkdu/M=493064.13814537.13821737.10835568/D=grou\
ps/S=1705083164:MKP1/Y=YAHOO/EXP=1259695326/L=/B=Qt66JkPDhCs-/J=1259688126507839\
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.yahoo.com/green/
> [10]
>
http://groups.yahoo.com/;_ylc=X3oDMTJiYXNta3ZpBF9TAzk3NDc2NTkwBGdycElkAzQzNTI5BG\
dycHNwSWQDMTcwNTA4MzE2NARzZWMDZnRyBHNsawNnZnAEc3RpbWUDMTI1OTY4ODEyNg--
> [11] mailto:nmrpipe-traditional@yahoogroups.com?subject=Change
> Delivery Format: Traditional
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> [13] mailto:nmrpipe-unsubscribe@yahoogroups.com?subject=Unsubscribe
> [14] http://docs.yahoo.com/info/terms/
>

There are several tools available that relate to this.

As mentioned, one is the stand-alone program "addNMR" which can
form weighted sums and differences of NMRPipe-format data in either
time or frequency domain.

There are also the nmrPipe processing functions COADD, and the more
general QMIX.  COADD uses a set of N coefficients to combine groups
of N input vectors to form a single output vector.  So, it can be used
to select odd or even channels (coefficients "1 0" or "0 1") sums (1 1)
and differences (1 -1) etc.

QMIX takes an NxM list of coefficients to combine N input vectors
to product M output vectors.

Some more notes are below.

And, the script "varAdjust.tcl" can be used to re-arrange the order of
vectors in raw varian "fid" data.  You can search for "varAdjust.tcl"
in the mailing list archives to find an example.

     Cheerful Regards,

     big fd

---
1. NMRPipe Processing Function COADD

This function can reduce a spectrum or FID by summing either
groups of two or more points within each 1D vector (-axis X)
OR by summing two or more adjacent 1D vectors (-axis Y).

Before summation, the given data is multiplied by the
coefficients given by "-cList" before summation.
So for example:

| nmrPipe -fn COADD -axis Y -cList 1 -1 -time \

will form a spectrum from the difference of each pair of
adjacent 1D slices. The "-time" argument is used to
reduce the recorded number of valid time-domain points
according to the reduction in the number of vectors.

2. NMRPipe Processing Function QMIX

The QMIX function takes a "matrix" of real or complex
coefficients which define how N input vectors are combined
to make M output vectors. Therefore, if N and M are different
values, the total number of vectors in the spectrum will be changed.

In the following example, groups of four input vectors (-ic 4)
are combined to produce groups of two output vectors (-oc 2),
reducing the total number of vectors by half.

The matrix element at row I, column J shows how much
of input vector J will be added to output vector I.
So, in the example below,

(output vector 1) = (input vector 1) - (input vector 3)
(output vector 2) = (input vector 2) - (input vector 4)

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

nmrPipe -in test.fid \
| nmrPipe -fn QMIX -ic 4 -oc 2 -cList $C -time \
-out ./testA.fid -verb -ov

The values for the matrix C are defined in "2D" form here
for readablity, however they could also be listed all in
one line. The "-time" argument will update the recorded
time-domain size to compensate for changes in the number
of vectors.



Quoting Sampo Mantylahti <pinegulf@...>:

> An exelent software. One question if I may.
>
> Situation: I'm working on a new sequence and I have one 3D fid,
> which contains both in-phase - and antiphase parts. Problem is that
> currently AP-part is pi/2 off from IP part. So I was planning to
> phasing the spectra separately and combining them with addnmr-command.
>
> Problem: My sequence has two variables (phase and phase2, phase has
> 4 states and phase2 has 2 states). As Varian fid-file contain all
> the coefficients in one file how can one separete them from each
> other? For example if I want to have just inphase part in VnmrJ I'd
> command  wft2d('ni2', 1 0 1 0  0 0 ...) Now when I convert var2pipe
> we don't have an option to specify myself how to combine the
> coefficients.
>
> Question: How can I define how to combine the coefficients when
> converting from Varian to Pipe? (Or is this even possible?)
>
>
>

A catalyst is a substance which asters the speed of a chemical reaction without itself undergoing any chemical change and the phenomenon is known as catalysis.

---

The INTERNET now has a personality. YOURS! See your Yahoo! Homepage.

I expect that this problem concerns the default shell for the particular
user.  As you all know, the various NMRPipe scripts expect that the user's
default shell is the C-shell.  This is mentioned more than 12 times
in the NMRPipe installation page. Of course, not everyone
in given a lab will get to see the installation page, so they
might miss out on this bit of NMRPipe wisdom.

Although the "mem.com" script is executed specifically as a C-shell,
since it begins with "#!/bin/csh" it may be that pipeline commands
inside of it would be executed by a combination of C-shell and whatever
other default shell the user has.  This might be why the single "echo $noise"
command would work but the "-noise $sigma" inside of a pipeline would not.

This is just a guess on my part, let us know what you find ...
if this isnt the issue, you might let us know exactly which hardware
and OS you're using (uname -a) ...

      Cheerful Regards,

      big fd


Quoting georgeluchina <j7lu@...>:

> I just tried out the 2D NUS demo. The $noise variable in the mem.com
>  script can be shown successfully in "echo $noise", but is not
> recognized in the nmrpipe lines "-sigma $noise".
>
> Otherwise, if I typed in a value for -sigma, the entire script would
>  run through with no errors.
>
> It might be some shell environment setup problem.
>
> Cheers,
> George
>
>
> --- In nmrpipe@yahoogroups.com, Frank Delaglio <delaglio@...> wrote:
>>
>>
>> Most Dear Colleagues,
>>
>> New demos for reconstruction of Non-Uniform Sampling (NUS) data
>> have just been posted at the NMRPipe download site ... the
>> NUS experimental data was kindly provided for us by Dr. Ryan McKay
>> of NANUC.
>>
>> The files "nusdemo2d.tar.Z" and "nusdemo3d.tar.Z" can be found
>> with the other sample data near the bottom of the web page:
>>
>>     http://spin.niddk.nih.gov/NMRPipe/install/
>>
>> Note that these NUS demos will require the **most recent** version
>> of NMRPipe, posted Oct 7 2009 or later ...
>>
>> If anyone gives these a try, let me know what you think ...
>>
>>     Cheerful Regards,
>>
>>     big fd
>>
>> PS:
>>
>> There are also new versions of the "relax" and "jmod" demos for
>> pseudo-3D analysis of peak height evolution.  The new versions
>> include examples using multiple copies of nmrDraw in
>> correlated "broadcast" mode to simultaneously view the
>> measured spectral data, the model, and the residual ... HUZZAH!!!
>>
>
>
>

I just tried out the 2D NUS demo. The $noise variable in the mem.com script can
be shown successfully in "echo $noise", but is not recognized in the nmrpipe
lines "-sigma $noise".

Otherwise, if I typed in a value for -sigma, the entire script would run through
with no errors.

It might be some shell environment setup problem.

Cheers,
George


--- In nmrpipe@yahoogroups.com, Frank Delaglio <delaglio@...> wrote:
>
>
> Most Dear Colleagues,
>
> New demos for reconstruction of Non-Uniform Sampling (NUS) data
> have just been posted at the NMRPipe download site ... the
> NUS experimental data was kindly provided for us by Dr. Ryan McKay
> of NANUC.
>
> The files "nusdemo2d.tar.Z" and "nusdemo3d.tar.Z" can be found
> with the other sample data near the bottom of the web page:
>
>     http://spin.niddk.nih.gov/NMRPipe/install/
>
> Note that these NUS demos will require the **most recent** version
> of NMRPipe, posted Oct 7 2009 or later ...
>
> If anyone gives these a try, let me know what you think ...
>
>     Cheerful Regards,
>
>     big fd
>
> PS:
>
> There are also new versions of the "relax" and "jmod" demos for
> pseudo-3D analysis of peak height evolution.  The new versions
> include examples using multiple copies of nmrDraw in
> correlated "broadcast" mode to simultaneously view the
> measured spectral data, the model, and the residual ... HUZZAH!!!
>

SORRY!!!

This problem has been discussed in earlier posts.
Just get a new version of the software.

Uncharacteristically for NMRPipe, "nlinLS" has a hard-wired upper
limit in the number of parameters that can be modeled in the
evolution dimension.  I didn't remove the limit, but I increased
it to 524.

Also, in case you haven't used it: these days, "nlinLS" is usually
operated indirectly via "autoFit.tcl".

Also also, current versions of NMRPipe have an interactive viewer
for displaying evolution curves (showEvolve.tcl) which includes
an option to send them to a fitting application (fitXY.tcl).

Examples are at the NMRPipe download site, files "relax.tar.Z" and
"jmod.tar.Z" ...

      Cheerful Regards,

      big fd


Quoting Sujoy Mukherjee <sujoyiit@...>:

> Hello,
>
> I'm having some problem with lineshape fitting usling the 'nlinLS'
> function. It gives some strange "memory allocation failure" error
> that I've not seen before. I've used this to fit lineshapes and
> extract intensities in pseudo3D datasets, consisting of multiple
> 1H-15N HSQC type experiments quite regularly for several datasets
> and worked fine. Its just that one particular dataset is having this
>  problem. Each of my spectra has ~90 peaks with ~20 peaks that are
> overlapped to some extent - and has been denoted properly using
> CLUSTID. There are 25 points (Z_A0 to Z_A25) that vary with a
> relaxation time. All of my spectra have been processed by nmrPipe
> with ~10Hz of GM linebroadening to give a gaussian lineshape to the
> peaks.
> I'm attaching a screenshot of the window that shows up while
> executing the nlinLS script.
> If someone has seen this kind of error or can provide some
> suggestion as to what could cause this, I would highly appreciate it.
> Many thanks in advance,
> Sujoy.
>
>
>
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