Dear All,

I have an hcch-tocsy experiment (hcchtocsy.fa) that can be processed on
Bruker using States in 13C and States in 1H indirect-detect
dimension.  This experiment does not process correctly in nmrPipe using any
of the following combinations

1H-direct 13C  1H-indirect
Complex States  States
DQD  States  States
Complex Complex Complex
DQD  Complex Complex
Complex States-TPPI States-TPPI
DQD  States-TPPI States-TPPI

Anyone seen this, or similar problem?  Suggestions?

Thanks in advance,

Norma Pawley

Dear NMRpipe’rs,

NANUC is happy to announce our 2003 training course.

Frank Delaglio will present his NMRPipe and other software packages at NANUC
(Canada’s National High Field NMR Centre, in Edmonton, Alberta, Canada) on
August 15 and 16, 2003. The list of topics that Frank will speak on
includes, but are not limited to:

General:
conversion (bruker/varian)
processing (nmrDraw nmrPipe xyz2pipe/pipe2xyz)
peak picking (nmrDraw)
spectral fitting (autoFit)

Special applications:
ipap assignment (ipap.tcl)
spectral series (autoProc pcaView titrView)
strip viewing and manipulation

New Applications:
talos
dipolar coupling analysis
nmr homology search (MFR)
and
structure calculation (DYNAMO)

In addition, Ryan McKay, NANUC’s in house instructional guru will present an
introduction to NMR Processing and NMRPipe; For Absolute Beginners.   Other
speakers may be included with time permitting.  As was the case last year,
the sessions will be held in the experiential lab at the Telus Centre for
Professional Development, located across the street from NANUC.  This
facility provides a computer terminal for each participant and was a great
success last year.

---------------------------------------------------------------------------

Registration is limited to 30 participants.
(First registration basis with cancellation waiting list.)

Registration forms are available now at:

http://www.nanuc.ca/resources/workshops.php

---------------------------------------------------------------------------

The cost for the sessions is $349 (Canada), $429 (United States), €429
(Europe) and £279 (Britain) and includes meals during the day (breakfast and
lunch), conference materials and a commemorative.

There will be a dinner on Friday night if interest is sufficient.

This event coincides with the Edmonton live theatre festival “The Fringe”.
The festival usually provides lots of opportunity to enjoy the hot summer
nights in Edmonton.

For further details please contact Bruce Lix directly at:
(780) 492-8530
email: bruce.lix@...



Ryan T. McKay
Scientific Director
National High Field NMR Centre (NANUC)
105 NANUC Bld.            Phone:  (780) 492-2700
University of Alberta     Fax:    (780) 492-9174
Edmonton, Alberta         Mobile: (780) 920-8871
Canada T6G2E1             http://www.nanuc.ca
email: ryan@...

Howdy to all...

Has anyone been able to get the drx2pipe script
working under Linux (specifically, RedHat 8.0) with
Bruker Avance data acquired using xwinnmr 2.6?

I keep trying to run the script, but I get an error
message after it tries to read the acqu data, claiming
that either the 1st FID was never properly completed,
or that the data doesn't come from an Avance.

Thanks in advance.

__________________________________
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Hi Ronald,

I have not tried it under Linux, so I have no idea if it should work.
However the error you get relates to the instrument name.  You either
need to edit the allowed string(s) for the instrument name in the
drx2pipe script (the line should be highlighted) or remove that section
altogether.  If you have not set an alias, the instrument name is
"spect", and this is not one of the default allowed names.  I put it in
because I like to check experiments as they are running, and this
ensures the parameters in the acqus files are correct - they are only
updated after the first FID is written to disk.

Good luck.

Duncan.


"Ronald Shin, PhD" wrote:
>
> Howdy to all...
>
> Has anyone been able to get the drx2pipe script
> working under Linux (specifically, RedHat 8.0) with
> Bruker Avance data acquired using xwinnmr 2.6?
>
> I keep trying to run the script, but I get an error
> message after it tries to read the acqu data, claiming
> that either the 1st FID was never properly completed,
> or that the data doesn't come from an Avance.
>
> Thanks in advance.
>
> __________________________________
> Do you Yahoo!?
> The New Yahoo! Search - Faster. Easier. Bingo.
> http://search.yahoo.com
>
>
>
>
> Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/

--

Duncan M Smith
Discovery Analytical Sciences
Mailstop 29-M-B
Amgen Inc.
One Amgen Center Drive
Thousand Oaks
CA 91320-1789
USA

Phone   (805) 447-3171
Fax     (805) 480-3015
E-mail  duncan@...

Hi, All:
	 I was trying to install the current version of NMRPipe
into two SGI O2 workstations (R5000 and R10000) running
OS IRIX6.5.  The graphics test failed during the installation.
Here are the test messages:

Testing the installation ...
Found the test program correctly ...
Executed the test program correctly ...
Found the test manual page correctly ...
Testing for X11 utilities ...
Found the X11 command xset ...
Found the X11 command xterm ...
Executing font initialization script ...
Testing the graphics, log file is graph.log ...
[1] 1726 1718
[1]  + Segmentation fault   xnotify -Wfsdb Executed the graphics test
correctly ... |& (core dumped)
        Done                 fgrep -iv ridiculous > graph.log
Error: graphics test generated errors/warnings.
----------------------------------------------------------------------
   *** Warning: Errors occurred during the installation.


	 When I looked at the graph.log file, I saw the following repeated
message:

XView warning: Notifier error: Bad file number

	 I am looking for your help to fix this problem.
	 Thanks a lot.

Jianyun Lu

Hello all,
	 Is there a command for setting the pivot for phase correction in
nmrPipe? I've tried to find one but cannot?
Thanks in advance
Mike

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Mike Osborne                         | Tel:   514-847-9494 (O)
  NMR Group                            |
  McGill Univeristy  		      |
  3655 Promenade Sir William Osler     | Fax:   514-389-7384
  Montreal, Quebec, H3G 1Y6            |
  Canada                               | e_mail: mike.osborne@...
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

How does one replace the first data points in an fid using LP?

Tara Sprules
Post-Doctoral Fellow
Department of Chemistry
University of Alberta
Edmonton, AB
Canada

from "man LP" ...

cheerful regards,

big FD


PARAMETERS FOR PREDICTION BEFORE
      When LP is used with the "-before" argument, it will work by
      replacing  points  before  the  selected data region, but it
      will not increase the size  of  the  data  (Note:  this  may
      change  in  later  implementations).  Therefore, in order to
      extend the data vectors by adding points at  the  beginning,
      the data size must first be adjusted "manually" by zero fil-
      ling and right-shifting. For example, if we start  with  100
      data  points,  and want to create 6 additional points before
      them:

         | nmrPipe -fn ZF -pad 6                           \
         | nmrPipe -fn RS -rs 6 -sw                        \
         | nmrPipe -fn LP -before -x1 7 -xn 106 -pred 6    \

      When the -before option is used, the default value  for  the
      -x1  parameter  is  set  to 1 plus the -pred value.  So, the
      following LP scheme is equivalent to the one above:

         | nmrPipe -fn ZF  -pad 6                 \
         | nmrPipe -fn RS  -rs 6 -sw              \
         | nmrPipe -fn LP  -before -pred 6        \

      these each mean "make room for 6 new points, move the origi-
      nal  data  over by 6 points, predict 6 new points before the
      original data which is now at points 7->106".

Hello all,
	 Does anyone have advice on using nmrDraw/nmrPipe for estimating
signal to noise. At the moment for 2D spectra I'm simply using the
"estimate noise" toggle in nmrDraw. I then pick the peaks and use the peak
heights to get the signal value. Is this a reasonable method? Or should I
pick a peak in a region of he spectrum where there are no peaks to get a
noise value.
	 In addition, is there a command that would allow me to get s/n of
a 1D spectrum?
Thanks in advance
Mike

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Mike Osborne                         | Tel:   514-847-9494 (O)
  NMR Group                            |
  McGill Univeristy  		      |
  3655 Promenade Sir William Osler     | Fax:   514-389-7384
  Montreal, Quebec, H3G 1Y6            |
  Canada                               | e_mail: mike.osborne@...
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                    __
                  .'  '.
                 :      :
                 | _  _ |
              .-.|(o)(o)|.-.        _._          _._
             ( ( | .--. | ) )     .',_ '.      .' _,'.
              '-/ (    ) \-'     / /' `\ \ __ / /' `\ \
               /   '--'   \     / /     \.'  './     \ \
               \ `"===="` /     `-`     : _  _ :      `-`
                `\      /'              |(o)(o)|
                  `\  /'                |      |
                  /`-.-`\_             /        \
            _..:;\._/V\_./:;.._       /   .--.   \
          .'/;:;:;\ /^\ /:;:;:\'.     |  (    )  |
         / /;:;:;:;\| |/:;:;:;:\ \    _\  '--'  /__
    jgs / /;:;:;:;:;\_/:;:;:;:;:\ \ .'  '-.__.-'   `-.

Hi:

I am trying to do LP in the two indirect dimensions of a 3D NOESY-HSQC. If
I do one after the other the result is not completetely satisfactory
since, besides a noticeable increase in resolution, there are some
artifacts, most intense cloe to the diagonal peaks. I know that the proper
thing to do is to LP one the dimensions, inverse FT the othe one and then
do LP on this.

According to my understanding of the LP man pages this is what I try to an
inverse FT of the indirect proton dimension (z) with the following script:


#!/bin/csh

xyz2pipe  -x -in fid/test%03d.fid \
| nmrPipe -fn SOL \
| nmrPipe -fn SP -off 0.50 -pow 2 -end 0.98 \
| nmrPipe -fn ZF -size 2048\
| nmrPipe -fn FT -auto \
| nmrPipe -fn PS -p0 -144.6 -p1  -7.0 -di \
| nmrPipe -fn EXT -left -sw \
| pipe2xyz -x -out ft/testx%03d.ft -verb -ov

xyz2pipe -z -in ft/testx%03d.ft \
| nmrPipe -fn SP -off 0.4 -pow 2 -end 0.98 -c 0.5\
| nmrPipe -fn ZF -size 256\
| nmrPipe -fn FT -auto \
| nmrPipe -fn PS -p0 -113.8 -p1 231.0 -di \
| pipe2xyz -z -out ft/testxz%03d.ft -verb -ov

xyz2pipe -y -in ft/testxz%03d.ft \
| nmrPipe -fn LP -fb \
| nmrPipe -fn SP -off 0.45 -pow 2 -end 0.98 -c 0.5\
| nmrPipe -fn ZF -size 128\
| nmrPipe -fn FT -auto \
| nmrPipe -fn PS -p0 -90.0 -p1  00.0 -di \
| pipe2xyz -y -out ft/testxyz%03d.ft -verb -ov

xyz2pipe -z -in ft/testxyz%03d.ft \
| nmrPipe  -fn HT  -auto                            \
| nmrPipe  -fn PS  -inv -hdr                        \
| nmrPipe  -fn FT  -inv                             \
| nmrPipe  -fn ZF  -inv                             \
| nmrPipe  -fn SP  -inv -hdr                        \
| nmrPipe  -fn LP  -fb                           \
| nmrPipe  -fn SP  -hdr                             \
| nmrPipe  -fn ZF  -auto                            \
| nmrPipe  -fn FT                                   \
| nmrPipe  -fn PS  -hdr -di                         \
| pipe2xyz -out ft/testxyz%03d.ft -z -inPlace -verb

xyz2pipe  -x -in ft/testxyz%03d.ft \
| nmrPipe -fn POLY -auto \
| pipe2xyz -x -out ft/testxyz%03d.ft -verb -ov
xyz2pipe  -z -in ft/testxyz%03d.ft \
| nmrPipe -fn POLY -auto \
| pipe2xyz -y -out ft/testxyz%03d.ft -verb -ov

The result is a strange spectrum with few signals and  strong artifacts
in the H-H plane. The spectrum has no resemblance at all with the
original one.

Thanks for your help.

--
Francisco Blanco
NMR group, Structural and Computational Biology Programme
Centro Nacional de Investigaciones Oncol�gicas
Melchor Fern�ndez Almagro 3, 28029 Madrid, Spain
Phone: 34 91 2246983  Fax: 34 91 2246976      www.cnio.es

Hi Francisco

I can see a possible couple of faults. You are not using first point
scaling correctly. If you have a first order (p1) phase correction of 0.0
then -c is 0.5. If p1 is not equal to zero then -c should be 1.0. Incorrect
use of -c will definitely cause baseplane distortions which may be further
distorted by LP.

Are you sure of your phase corrections in the indirect dimensions? It looks
like you started at half-dwell times and so p0 -90 p1 180 (or close to it)
should be used.

You also extract the left half of the spectrum after transforming your
first dimension. I suggest leaving that to the very end after base plane
corrections. This should also reduce baseplane distortions.

Good luck...Paul


At 10:05 PM 5/24/03 +0200, you wrote:

>Hi:
>
>I am trying to do LP in the two indirect dimensions of a 3D NOESY-HSQC. If
>I do one after the other the result is not completetely satisfactory
>since, besides a noticeable increase in resolution, there are some
>artifacts, most intense cloe to the diagonal peaks. I know that the proper
>thing to do is to LP one the dimensions, inverse FT the othe one and then
>do LP on this.
>
>According to my understanding of the LP man pages this is what I try to an
>inverse FT of the indirect proton dimension (z) with the following script:
>
>
>#!/bin/csh
>
>xyz2pipe  -x -in fid/test%03d.fid \
>| nmrPipe -fn SOL \
>| nmrPipe -fn SP -off 0.50 -pow 2 -end 0.98 \
>| nmrPipe -fn ZF -size 2048\
>| nmrPipe -fn FT -auto \
>| nmrPipe -fn PS -p0 -144.6 -p1  -7.0 -di \
>| nmrPipe -fn EXT -left -sw \
>| pipe2xyz -x -out ft/testx%03d.ft -verb -ov
>
>xyz2pipe -z -in ft/testx%03d.ft \
>| nmrPipe -fn SP -off 0.4 -pow 2 -end 0.98 -c 0.5\
>| nmrPipe -fn ZF -size 256\
>| nmrPipe -fn FT -auto \
>| nmrPipe -fn PS -p0 -113.8 -p1 231.0 -di \
>| pipe2xyz -z -out ft/testxz%03d.ft -verb -ov
>
>xyz2pipe -y -in ft/testxz%03d.ft \
>| nmrPipe -fn LP -fb \
>| nmrPipe -fn SP -off 0.45 -pow 2 -end 0.98 -c 0.5\
>| nmrPipe -fn ZF -size 128\
>| nmrPipe -fn FT -auto \
>| nmrPipe -fn PS -p0 -90.0 -p1  00.0 -di \
>| pipe2xyz -y -out ft/testxyz%03d.ft -verb -ov
>
>xyz2pipe -z -in ft/testxyz%03d.ft \
>| nmrPipe  -fn HT  -auto                            \
>| nmrPipe  -fn PS  -inv -hdr                        \
>| nmrPipe  -fn FT  -inv                             \
>| nmrPipe  -fn ZF  -inv                             \
>| nmrPipe  -fn SP  -inv -hdr                        \
>| nmrPipe  -fn LP  -fb                           \
>| nmrPipe  -fn SP  -hdr                             \
>| nmrPipe  -fn ZF  -auto                            \
>| nmrPipe  -fn FT                                   \
>| nmrPipe  -fn PS  -hdr -di                         \
>| pipe2xyz -out ft/testxyz%03d.ft -z -inPlace -verb
>
>xyz2pipe  -x -in ft/testxyz%03d.ft \
>| nmrPipe -fn POLY -auto \
>| pipe2xyz -x -out ft/testxyz%03d.ft -verb -ov
>xyz2pipe  -z -in ft/testxyz%03d.ft \
>| nmrPipe -fn POLY -auto \
>| pipe2xyz -y -out ft/testxyz%03d.ft -verb -ov
>
>The result is a strange spectrum with few signals and  strong artifacts
>in the H-H plane. The spectrum has no resemblance at all with the
>original one.
>
>Thanks for your help.
>
>--
>Francisco Blanco
>NMR group, Structural and Computational Biology Programme
>Centro Nacional de Investigaciones Oncol�gicas
>Melchor Fern�ndez Almagro 3, 28029 Madrid, Spain
>Phone: 34 91 2246983  Fax: 34 91 2246976      www.cnio.es
>
>
>
>
>
>Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/

Hi All,
I have a basic question. I would like to overlay 1D vector from two
different 2D spectra see the differnce in signal height. Can this be
don? Or is it possible to extract a 1D vecor and save this vector to
disk so i can read it back in later.
Tnakhs
Mike

Hi Mike and Everyone Else ...

As to estimating noise levels in NMRDraw:

In addition to the automated noise estimate from the "Draw/Estimate Nosie"
command, you can also find the statatistics of a manually-selected 2D
region (presumably an "empty" region of a given spectrum) and estimate
the noise level that way:

   1. Turn on the 2D Zoom Box (Mouse/2D Zoom).

   2. Adjust the zoom box with the mouse to surround the region of interest.

   3. Move the mouse pointer to the OUTSIDE border of the graphics area,
      click the MIDDLE mouse button: this will generate a pop-up window
      with statistical report and histogram of the intensities in the
      select region.  The standard deviation is reported as "SDev" ...

This option is also supposed to be available for the 1D case too,
but I found out recently that it didn't work (!!!!!!) ... recently
posted software should fix this ...

	 Cheerful Regards,

	 Big FD

Hi All ...

HN/N NOE experiments are often set up with a one-dwell delay
(P0=-180 P1=360) in the indirect 1H dimension.  This means
that the first point of the FID is missing, and should be
"replaced" by a zero-order baseline correction in the corresponding
spectrum.  This result then behaves like a spectrum with 0,0 phase,
and can have its imaginary data reconstructed by hilbert transform (HT)
with no distortion:

    xyz2pipe -z -in ft/testx%03d.ft \
    | nmrPipe -fn SP -off 0.5 -pow 2 -end 0.98 -c 1.0 \
    | nmrPipe -fn ZF -auto \
    | nmrPipe -fn FT \
    | nmrPipe -fn PS -p0 -180 -p1 360 -di \
    | nmrPipe -fn POLY -auto -ord 0 \
    | pipe2xyz -z -out ft/testxz%03d.ft -verb -ov

However, if the phase has some "intermediate" value, like the one given
in the example, the deleted imaginary data can not be reconstructed perfectly
later on during inverse processing -- also, such an intermediate phase value
will also always give rise to baseline distortions -- these are reasons
why the acquistion delay should be set with care:

    xyz2pipe -z -in ft/testx%03d.ft \
    | nmrPipe -fn SP -off 0.4 -pow 2 -end 0.98 -c 0.5\
    | nmrPipe -fn ZF -size 256 \
    | nmrPipe -fn FT -auto \
    | nmrPipe -fn PS -p0 -113.8 -p1 231.0 -di \
    | pipe2xyz -z -out ft/testxz%03d.ft -verb -ov

In this case, since ideal reprocessing of the 1H dimension is not possible,
it would be best to process the HN and 15N dimensions
first, linear predict and process the indirect 1H dimension,
and then re-process the 15N dimension.

Also: since we have to "divide" by the window function during
inverse processing, it is better to start with a more "gentle"
window function at first, maybe:

    | nmrPipe -fn SP -off 0.5 -pow 1 -end 0.95 -c 0.5 \

Also, about zero filling: we can't tell if the zero filling used
in the example scripts is reasonable, as we don't know the original
time-domain sizes of the FID.  In order to apply a hilbert transform
for inverse processing, the data must have been zero filled to at
least twice its original size.

For this reason, it is ually best to ALWAYS use "ZF -auto" rather than
a specific "-size" value ...

	 Cheerful Regards,

	 Big FD

Dear Frank,
Is there an archive site for NMRPIPE mailing list ?
thanks,
Padmanava
--- Frank Delaglio <delaglio@...>
wrote:
> Hi All ...
>
> HN/N NOE experiments are often set up with a
> one-dwell delay
> (P0=-180 P1=360) in the indirect 1H dimension.  This
> means
> that the first point of the FID is missing, and
> should be
> "replaced" by a zero-order baseline correction in
> the corresponding
> spectrum.  This result then behaves like a spectrum
> with 0,0 phase,
> and can have its imaginary data reconstructed by
> hilbert transform (HT)
> with no distortion:
>
>    xyz2pipe -z -in ft/testx%03d.ft \
>    | nmrPipe -fn SP -off 0.5 -pow 2 -end 0.98 -c 1.0
> \
>    | nmrPipe -fn ZF -auto \
>    | nmrPipe -fn FT \
>    | nmrPipe -fn PS -p0 -180 -p1 360 -di \
>    | nmrPipe -fn POLY -auto -ord 0 \
>    | pipe2xyz -z -out ft/testxz%03d.ft -verb -ov
>
> However, if the phase has some "intermediate" value,
> like the one given
> in the example, the deleted imaginary data can not
> be reconstructed perfectly
> later on during inverse processing -- also, such an
> intermediate phase value
> will also always give rise to baseline distortions
> -- these are reasons
> why the acquistion delay should be set with care:
>
>    xyz2pipe -z -in ft/testx%03d.ft \
>    | nmrPipe -fn SP -off 0.4 -pow 2 -end 0.98 -c
> 0.5\
>    | nmrPipe -fn ZF -size 256 \
>    | nmrPipe -fn FT -auto \
>    | nmrPipe -fn PS -p0 -113.8 -p1 231.0 -di \
>    | pipe2xyz -z -out ft/testxz%03d.ft -verb -ov
>
> In this case, since ideal reprocessing of the 1H
> dimension is not possible,
> it would be best to process the HN and 15N
> dimensions
> first, linear predict and process the indirect 1H
> dimension,
> and then re-process the 15N dimension.
>
> Also: since we have to "divide" by the window
> function during
> inverse processing, it is better to start with a
> more "gentle"
> window function at first, maybe:
>
>    | nmrPipe -fn SP -off 0.5 -pow 1 -end 0.95 -c 0.5
> \
>
> Also, about zero filling: we can't tell if the zero
> filling used
> in the example scripts is reasonable, as we don't
> know the original
> time-domain sizes of the FID.  In order to apply a
> hilbert transform
> for inverse processing, the data must have been zero
> filled to at
> least twice its original size.
>
> For this reason, it is ually best to ALWAYS use "ZF
> -auto" rather than
> a specific "-size" value ...
>
>  Cheerful Regards,
>
>  Big FD
>
>
>
>


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Hi All-

I am having a problem peak picking a 3D dataset. I've checked the
message board, and the only similar problem I saw was way back near the
beginnings of the list and dealt with directory write permissions (and
i'm working in my home directory and have write permissions to the
directory so there should be no problems). I get errors under Linux
(RedHat 8.0) and OS X.

When I execute the pick, i get the following errors:

"Error executing system command."
"Error detecting peaks."

The background output is as shown below. Not sure what I'm doing wrong
(I should add this is my first attempt at picking a 3D dataset in Pipe).

Any suggestions?

Thanks,
Doug Kojetin

----------------------------

ROI Name='./cocanophagelb1.dat' Length=-262458480 Orig Dim=2 Dim=3

ROI X: X_AXIS 1 -> 1531 1531 Pts 1 -> 1531 Align=None(0.000,0.000)
ROI Y: Y_AXIS 1 -> 130 130 Pts 1 -> 130 Align=None(0.000,0.000)

Memory allocation failure.
ReadROI Error: Error allocating ROI matrix.

      while executing
"readROI -roi 1 -ndim 3 -in $thisSpecName  -x X_AXIS $xFirst $xNext
         -y Y_AXIS $yFirst $yNext            -z Z_AXIS $zFirst $zNext
          ..."
      ("while" body line 5)
      invoked from within
"while {$xFirst <= 1 + $xN - $xExtra}  {
      set xNext [expr $xFirst+$xInc+2*$xExtra-1]
      if {$xNext > $xLast} {set xNext $xLast}

      readROI -roi 1 ..."
      ("while" body line 7)
      invoked from within
"while {$yFirst <= 1 + $yN - $yExtra}  {
      set yNext [expr $yFirst+$yInc+2*$yExtra-1]
      if {$yNext > $yLast} {set yNext $yLast}

      set xFirst  $x ..."
      ("while" body line 7)
      invoked from within
"while {$zFirst <= 1 + $zN - $zExtra} \
     {
      set zNext [expr $zFirst+$zInc+2*$zExtra-1]
      if {$zNext > $zLast} {set zNext $zLast}

      set yFirst ..."
      (file "./pk.tcl" line 43)

----------------------------

... sounds as if you've read the 3D spectrum in nmrDraw as a 2D
plane, or perhaps even saved the 3D in a single file, instead of the
"required" multi-plane output.

Be sure that the 3D result is saved during processing by "pipe2xyz" in the
usual way, and use the NMRDraw "Select File" command to select
the "3D Template" which represents the entire series of planes in
the 3D spectrum.

The clue about the problem is as follows ... when peak-picking a 3D,
the message should list the template name (with the "%03d") for example:

ROI Name='ft/test%03d.ft3' Length=5086900 Orig Dim=3 Dim=3

ROI X: X_AXIS 1 -> 130 130 Pts 1 -> 130 Align=None(0.000,0.000)
ROI Y: Y_AXIS 1 -> 301 301 Pts 1 -> 301 Align=None(0.000,0.000)
ROI Z: Z_AXIS 1 -> 130 130 Pts 1 -> 130 Align=None(0.000,0.000)

In your case though, it looks as if there is just a "single" file name,
in addition to a negative (= unusually large) data length:

ROI Name='./cocanophagelb1.dat' Length=-262458480 Orig Dim=2 Dim=3

ROI X: X_AXIS 1 -> 1531 1531 Pts 1 -> 1531 Align=None(0.000,0.000)
ROI Y: Y_AXIS 1 -> 130 130 Pts 1 -> 130 Align=None(0.000,0.000)

by the way, 1531 points sounds excessive for the direct dimension
of a triple-resonance spectrum ...

Many thanks for your help ... that was the problem.

Quick semi-unrelated question: Is it possible to draw all planes of a
3D (superimposed on a 2D) using nmrDraw?

Thanks,
Doug


> ... sounds as if you've read the 3D spectrum in nmrDraw as a 2D
> plane, or perhaps even saved the 3D in a single file, instead of the
> "required" multi-plane output.

Hi!

> Quick semi-unrelated question: Is it possible to draw all planes of a
> 3D (superimposed on a 2D) using nmrDraw?

"Draw/2D Settings", un-set the check box for "Auto Clear" ... then, when
you step through the planes of a 3D, the previous planes won't be erased.

For fun, here's a crude NMRWish TCL script that will do something similar.

Also, see the script "com/proj3D.tcl" which makes 2D projections of
the given 3D ...

	 Cheerful Regards,

	 big fd

--- ov2D.tcl:
#!/bin/sh
# The next line restarts using nmrWish \
exec nmrWish "$0" -- "$@"

set auto_path   "[split $env(TCLPATH) :] $auto_path"
set ARGV        [concat $argv0 $argv]
set ARGC        [llength $ARGV]

#
# Show command-line arguments if needed:

if {[flagLoc $ARGV -help]} \
    {
     puts "Draw Overlay of 2D Planes in a 3D Spectrum:"
     puts " -in inName \[ft/test%03d.ft3\]  Input 3D Spectrum."
     puts " -hi hi     \[Auto\]             Contour Height."
     puts "Plane Orientation Options (Use Only One):"
     puts " -xy -xz -yx -yz -zx -zy"
     exit 1
    }

#
# Extract command-line arguments:

set inName ft/test%03d.ft3
set aList  "X Y Z"
set hi     Auto

getArgD $ARGV -in inName
getArgD $ARGV -hi hi

if {[flagLoc $ARGV -xy]} {set aList "X Y Z"}
if {[flagLoc $ARGV -xz]} {set aList "X Z Y"}
if {[flagLoc $ARGV -yx]} {set aList "Y X Z"}
if {[flagLoc $ARGV -yz]} {set aList "Y Z X"}
if {[flagLoc $ARGV -zx]} {set aList "Z X Y"}
if {[flagLoc $ARGV -zy]} {set aList "Z Y X"}

set xName [lindex $aList 0]_AXIS
set yName [lindex $aList 1]_AXIS
set zName [lindex $aList 2]_AXIS

#
# Create window with ordinary TCL/TK:

wm geom  . +20+20
wm title . "Working ..."

set xSize 600
set ySize 580

set cx1 20
set cxn 500
set cy1 20
set cyn 500

canvas .c -width $xSize -height $ySize -border 0
button .b -text Quit -command exit
pack   .c .b -side top

#
# Create spectral drawing area with special NMRWish "pixmap" command.
# Define a drawing region with the NMRWish "defineCell" command.

.c create pixmap 0 0 -width $xSize -height $ySize -win 1

defineCell -x $cx1 $cxn -y $cy1 $cyn -cell 1 -verb -win 1
drawRec    -x 0% 100% -y 0% 100% -cell 1 -fg black

#
# Read the spectrum header.
# Find the number of planes to draw.
# Find the axis names for labeling the window.

set error [rdFDATA $inName fdata]

if {$error} {exit 1}

set zSize [getParmI $fdata NDSIZE  $zName]

set xLab  [getParmStr $fdata NDLABEL $xName]
set yLab  [getParmStr $fdata NDLABEL $yName]
set zLab  [getParmStr $fdata NDLABEL $zName]

#
# For each 2D plane:
#   Read the 2D plane as a ROI (region of interest)
#   Draw the 2D ROI plane.

for {set iz 1} {$iz <= $zSize} {incr iz} \
    {
     readROI -ndim 2 -roi 1 -in $inName -x $xName -y $yName -dz $zName $iz 0

     drawROI -roi 1 -cell 1 -hi $hi -bg None \
             -color1 multi -color2 multi -axis Bottom Right

     update
    }

wm title . "Done: $inName $xLab/$yLab $zSize $zLab Planes"

update

Hi folks,

I used a Bruker Avance 600 MHz instrument to record a
3D 15N NOESY-HSQC experiment (noesiif3gp), and the
processing looks fine when we do it from Xwin-NMR, but
when I try to process it using NMR-PIPE, and view the
two proton planes, while advancing / retreating in the
15N plane, the spectrum seems shifted.

The spectrum looks as if someone made a cut down the
middle of the indirect proton dimension, shifted the
lower half up, and then placed the former upper half
at the lower half of the screen (assuming that the
acquisition proton dimension is on the X-axis, and the
indirect proton dimension is on the Y-axis).  Each of
the "halves" are in their correct alignment, but are
shifted.

I am using this script:

#!/bin/csh

bruk2pipe -in ./ser -bad 0.0 -noaswap -DMX -decim 24
-dspfvs 12  \
   -xN              2048  -yN                50  -zN
            150  \
   -xT              1024  -yT                25  -zT
             75  \
   -xMODE            DQD  -yMODE  Echo-AntiEcho  -zMODE
    States-TPPI  \
   -xSW         7183.908  -ySW         2432.646  -zSW
       7183.908  \
   -xOBS         600.133  -yOBS          60.818  -zOBS
        600.133  \
   -xCAR           4.773  -yCAR         118.377  -zCAR
          4.773  \
   -xLAB              1H  -yLAB             15N  -zLAB
          H-ind  \
   -ndim               3  -aq2D          States
                \
   -out ./data/test%03d.pipe -verb -ov

sleep 5

sleep  1

#*********************************************************
# NMRPipe Data Processing Script
#! /bin/csh

echo 'Transforming 3-dimensional NMR data!'
echo 'Processing F3/F1 dimensions first'
xyz2pipe -in data/test%03d.pipe -x -verb  \
| nmrPipe -fn SOL -mode 1 -fl 16 -fs 1 -poly  \
| nmrPipe -fn CBF -last 12  \
| nmrPipe -fn SP -off 0.39 -end 0.98 -pow 3 -size 512
-c 0.5  \
| nmrPipe -fn ZF -size 2048  \
| nmrPipe -fn FT -verb  \
| nmrPipe -fn PS -p0 43 -p1 0 -di  \
| nmrPipe -fn EXT -left -sw -verb  \
| nmrPipe -fn TP  \
| nmrPipe -fn SP -off 0.39 -end 0.98 -pow 2 -size 25
\
| nmrPipe -fn ZF -size 128  \
| nmrPipe -fn FT -verb  \
| nmrPipe -fn PS -p0 90 -p1 0 -di  \
| pipe2xyz -out ft/test%03d.ft2 -y

xyz2pipe -in ft/test%03d.ft2 -z -verb  \
| nmrPipe -fn SP -off 0.39 -end 0.98 -pow 3 -size 75
-c 0.5 \
| nmrPipe -fn ZF -size 512  \
| nmrPipe -fn FT -verb  \
| nmrPipe -fn PS -p0 0 -p1 0 -di  \
| pipe2xyz -out ft/test%03d.ft3 -y


Can anyone tell me what I am doing wrong here?

Thanks.

Regards,

Ron

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try "FT -alt" ... (see "man FT" or "man bruk2pipe")

cheerful regards,
f

Thanks, Frank!  All works well.

Regards,

Ron


--- Frank Delaglio <delaglio@...>
wrote:
> try "FT -alt" ... (see "man FT" or "man bruk2pipe")


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Dear All,
I am running nmrPipe in Redhat Linux 8.0. I have all the scripts to
process the NMR data in csh which runs without any problem on SGI
machine. Could anyone suggest me, what changes I need to make in those
scripts to  run them in bash shell.
Thanks.
Sachchi.

Dear All,
I am running nmrPipe in Redhat Linux 8.0. I have all the scripts to
process the NMR data in csh which runs without any problem on SGI
machine. Could anyone suggest me, what changes I need to make in those
scripts to  run them in bash shell.
Thanks.
Sachchi.



Your use of Yahoo! Groups is subject to the Yahoo! Terms of Service.

-----Original Message-----
From: sachchi2000 [mailto:sachchi2000@...]
Sent: Wednesday, June 04, 2003 10:55 PM
To: nmrpipe@yahoogroups.com
Subject: [nmrpipe] runiing nmrpipe scripts in Bash

Dear All,
I am running nmrPipe in Redhat Linux 8.0. I have all the scripts to
process the NMR data in csh which runs without any problem on SGI
machine. Could anyone suggest me, what changes I need to make in those
scripts to  run them in bash shell.
Thanks.
Sachchi.



Your use of Yahoo! Groups is subject to the Yahoo! Terms of Service.

Hello all ...

This is from the "INSTALL" text file for NMRPipe:

            The scripts and environment of the NMRPipe system
            are intended for the C-shell.  Other shells, such
            as the Bourne shell "sh" or the "bash" shell may not
            be suitable.

Sorry, "bash" fans ...

f

The only way I could get nmrpipe to run in Redhat 8.0 was to change the login shell to tcsh.  Scripts did not work in bash for me.  Invoking a csh did not do it either as long as the login shell was bash.  That's my experience, others may have been able to get things to work.

 

Tamas

-----Original Message-----
From: sachchi2000 [mailto:sachchi2000@...]
Sent: Wednesday, June 04, 2003 10:55 PM
To: nmrpipe@yahoogroups.com
Subject: [nmrpipe] runiing nmrpipe scripts in Bash

Dear All,
I am running nmrPipe in Redhat Linux 8.0. I have all the scripts to
process the NMR data in csh which runs without any problem on SGI
machine. Could anyone suggest me, what changes I need to make in those
scripts to  run them in bash shell.
Thanks.
Sachchi.



Your use of Yahoo! Groups is subject to the Yahoo! Terms of Service.

Your use of Yahoo! Groups is subject to the Yahoo! Terms of Service.

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Hi,

I have a COSY, run with VNMR, phase=1. It has been collected correctly, as
I can process it in VNMR (wft2da (1,0,0,1), but I cannot get it right in
nmrpipe. With acquistion type chosen as "real" or "TPPI" and FT -auto or
-real, I get a "V" shaped diagonal whenever I process it. What am I
missing? Is it -aq2D that is wrong? It doesn't change with yMODE, and I
can't find the options for what can be there.

Thanks,

Tara


var2pipe -in ./fid -noaswap  \
   -xN              4096  -yN               512  \
   -xT              2048  -yT               512  \
   -xMODE        Complex  -yMODE           TPPI  \
   -xSW         8000.000  -ySW         8000.000  \
   -xOBS         599.934  -yOBS         599.934  \
   -xCAR           4.744  -yCAR           4.551  \
   -xLAB              H1  -yLAB              H1  \
   -ndim               2  -aq2D          States  \
   -out ./test.fid -verb -ov


nmrPipe -in test.fid \
| nmrPipe  -fn SP -off 0.5 -end 1.00 -pow 1 -c 1.0    \
| nmrPipe  -fn ZF -auto                               \
| nmrPipe  -fn FT -auto                               \
| nmrPipe  -fn PS -p0 0.00 -p1 0.00 -di -verb         \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn SP -off 0.5 -end 1.00 -pow 1 -c 1.0    \
| nmrPipe  -fn ZF -auto                               \
| nmrPipe -fn FT  -real                                 \
| nmrPipe  -fn PS -p0 0.00 -p1 0.00 -di -verb         \
    -ov -out test.ft2


Tara Sprules
Post-Doctoral Fellow
Department of Chemistry
University of Alberta
Edmonton, AB
Canada

maybe "-aq2D States" should be "-aq2D TPPI" ...