This message might appear if you try to run a TCL/TK script (such
as "bruker" or "varian") with no X11 graphics environment.
In particular, new Mac OS X users might see this, if they
haven't installed an X11 graphics server, then started the
graphics server before using NMRDraw et al. ... also,
if an X11 graphics system is already running, the "DISPLAY"
environment variable must also be set properly ("unix:0" to display
on the local machine) ...



On Fri, 31 Oct 2003, kunal bakshi wrote:

> hi all,
>      when i type "bruker " in the command line ,it shows' application specific
initialization failed ' same when i type "varian ".i am new to both linux and
NMRPipe.If anyone can help me out
> excuse me if this is silly,
>
> sincerely,
> Kunal Bakshi
> University of Connecticut.
>
>
>
> ---------------------------------
> Do you Yahoo!?
> Exclusive Video Premiere - Britney Spears

I have used nlinLS several times with success, but am now getting a
strange output.  I am reading in a .PCK from pipp and making a table.
Often when doing this, the last peak is repeated and I simply delete it.
This time the first peak is repeating with  a "-Inf" for x_axis and
volume.  I have used this many times before and have no idea why this
particular set of data is causing this problem.  Does anybody have any
ideas?

Thanks,
Martha

Hello,

I'm looking for an option in nmrpipe to save processed
data into ascii format.

Does anyone have an idea or a suggestion?

Thanks,

Luminita Duma
ENS-Lyon
Laboratoire de Chimie
Lyon/FRANCE


=====
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                Luminita DUMA
  Laboratoire de Chimie, ENS-Lyon
  46, Allee d'Italie, 69364 Lyon, FRANCE
  Tel: +33 (0)472 72 83 95 (Office)
  Fax: +33 (0)472 72 84 83 (Office)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

___________________________________________________________
Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en français !
Yahoo! Mail : http://fr.mail.yahoo.com

Hello,

look at the script:  yourpipedir/com/pipe2txt.tcl


Josef Chmelik

Hi All-

We are interested in reading in a text file (one column, with
intensities) and 'converting' it to nmrpipe.

I noticed txt2bin, txt2bin.tcl and bin2pipe programs/scripts in the com
directory, but I cannot find any documentation on them.  Can anyone
provide any assistance on a) the input format of the text file and b)
usage of these programs/scripts and/or c) which programs/scripts we
should use to convert a text file to nmrpipe data?

Many thanks,
Doug Kojetin

Hi-


I am also interested in saving my data in ASCII format. I looked at teh
pipe2txt.tcl file, and I was wondering what I needed to modify in the script do
that it will convert my .ft file.


Thanks,
Meredith :)



Quoting Josef Chmelik <xchmelik@...>:

> Hello,
>
> look at the script:  yourpipedir/com/pipe2txt.tcl
>
>
> Josef Chmelik
>
>
>
>
>
>
> Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
>
>
>


--
Meredith Newby Lambert, Ph. D.
Research Fellow
Department of Chemistry, University of Michigan
930 N. University, Ann Arbor, MI 48109-1055

Tel: (734) 615-4172
Fax: (734) 647-4865

Hi,

We are in the process of acquiring a Bruker NMR machine.  Bruker is now
offering host computers that run either windows or Linux.  I would like to
know from NMRPipe/NMRDraw users if they have had any problems processing
data acquired using either Windows or Linux?  Any suggestion will be
welcome.

Siddhartha

--
Siddhartha P. Sarma
Assistant Professor
Molecular Biophysics Unit
Indian Institute of Science
Bangalore, Karnataka - 560 012
INDIA

Tel: 80-2932839
      80-2932713
Fax: 80-3600535

Hi,

I think that you don't have to modify the script, just simply type:

pipe2txt.tcl yourfile.ft > yourfile.txt
for 3D: pipe2txt.tcl ft/yourfile*.ft3 > yourfile.txt (output file will be VERY
HUGE)

I've found one note in pipe2txt.tcl that requires that all files are real-only,
and have the same size


Good luck,

Josef Chmelik


Meredith Lambert wrote:

>Hi-
>
>
>I am also interested in saving my data in ASCII format. I looked at teh
>pipe2txt.tcl file, and I was wondering what I needed to modify in the script do
>that it will convert my .ft file.
>
>
>Thanks,
>Meredith :)
>
>

hi,

is it possible to symmetrize a 2D spectrum with nmrPipe? (or nmrview
or sparky, for that matter?)

i looked in the docs, but didn't find anything pertaining to that..

thanks!

jakob

Josef-

Thanks for the help!

-Meredith  :)



Quoting Josef Chmelik <xchmelik@...>:

> Hi,
>
> I think that you don't have to modify the script, just simply type:
>
> pipe2txt.tcl yourfile.ft > yourfile.txt
> for 3D: pipe2txt.tcl ft/yourfile*.ft3 > yourfile.txt (output file will be
> VERY HUGE)
>
> I've found one note in pipe2txt.tcl that requires that all files are
> real-only, and have the same size
>
>
> Good luck,
>
> Josef Chmelik
>
>
> Meredith Lambert wrote:
>
> >Hi-
> >
> >
> >I am also interested in saving my data in ASCII format. I looked at teh
> >pipe2txt.tcl file, and I was wondering what I needed to modify in the script
> do
> >that it will convert my .ft file.
> >
> >
> >Thanks,
> >Meredith :)
> >
> >
>
>
>
>
>
>
>
> Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
>
>
>


--
Meredith Newby Lambert, Ph. D.
Research Fellow
Department of Chemistry, University of Michigan
930 N. University, Ann Arbor, MI 48109-1055

Tel: (734) 615-4172
Fax: (734) 647-4865

Since it's been of interest lately, I attach a couple of scripts I've
written for extracting 1D slices from 2D nmrPipe data.  pipe1Dx and
pipe1Dy are simple modifications of the original pipe2txt.tcl script and
return a line along eiter x or y at specified ppm and allow for
integration in the orthogonal dimension.  They are decently commented
and can be modified to give 2D segments instead of 1D lines.  The last
script, pipe1Dat, implements the first two for a specific peak in the
spectrum, as directed by some peak list file, e.g. a sparky .save file.

...  Caveat:  I will not offer advice on how to use these, just thought
some might find them useful.  Read the comments.

Hope this is useful.  Jim Kempf.

#!/bin/sh
#
# pipe1Dy  -  This script is based on the pipe2txt.tcl script found
#             in the /usr/local/nmrDraw/com directory on worf.
#             Description given below is sent to screen when no
#             arguments provided with call to script.
#
# 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]

# If no arguments supplied, explain usage.
if {$ARGC == 1 || [flagLoc $ARGV -help]} \
{
   puts stderr "\n\
     Display 1D slice along y from NMRPipe 2D Data as text.\n\
     \t x is the directly detected dimension (typically 1H).\n\
     \t y is the indirectly detected dimension (typically 15N or 13C).\n\n\
     Usage:  pipe1Dy inFile a b c d e f g h > outFile\n\
     where a b c d e f g h all in ppm and\n\
     \t a = slice location in constant (x) dimension\n\
     \t b = peak location in selected (y) dimension\n\
     \t c = range of integration (use 0.0 for non-integrated 1D slice)\n\
     \t c = range of 1D slice to include as output\n\
     \t b = spectral width x dimension\n\
     \t c = start position x dimension (i.e., lowest value)\n\
     \t d = spectral width y dimension\n\
     \t e = start position y dimension (i.e., lowest value)\n\n\
     - When providing SW and start position values consider whether\n\
       the inFile contains extracted data. The extracted SW and start\n\
       are the relevant values.\n\
     - Tacking on '> outFile' pipes 1D data output to outFile.\n\
     - Script requires that all files are real-only.\n"
   exit 0
}

set inName [lindex $argv 0]

rdFDATA $inName fdata

# Get numPts in each dimension.
# Notice reversal of xy terminology.
set xSize [getParmI $fdata NDSIZE CUR_YDIM]
set ySize [getParmI $fdata NDSIZE CUR_XDIM]
set n     [expr $xSize*$ySize]

set rdata [sysMalloc $n float]

set inName [lindex $argv [expr 0]]
set inUnit [sysOpen $inName r]

set   sLoc [lindex $argv [expr 1]]
set   pLoc [lindex $argv [expr 2]]
set   iRng [lindex $argv [expr 3]]
set   kRng [lindex $argv [expr 4]]
set    SWx [lindex $argv [expr 5]]
set xStart [lindex $argv [expr 6]]
set    SWy [lindex $argv [expr 7]]
set yStart [lindex $argv [expr 8]]

sysRead $inUnit $fdata $FDATASIZE
sysRead $inUnit $rdata $n

sysClose $inUnit

# Calculate and round off the point number in x dimension that
# corresponds to the input constant ppm valule, $sLoc.
set ixTemp [expr ( $xSize*(1 - ($sLoc - $xStart)/$SWx) )]
for {set j 1} {$j <= $xSize} {incr j} \
{  if {$ixTemp > $j} {set ix $j}
}
set temp [expr ($ixTemp - $ix) ]
if {$temp >= 0.5} { incr ix }

# Convert iRng (= integration range) to iRange, the number
# of 1D slices to sum for integration.
set iRange 0
set iR [expr ( ($iRng/$SWx)*$xSize ) ]
for {set j 1} {$j <= $iR} {incr j} \
{  if {$iR > $j} {set iRange $j}
}
#if {$iRng > 0.0} { puts stderr [format "\n\niRange = \t%i" $iRange] }


#Output selected 1D slice as (chem shift, amp) pairs.
set i [expr ( $ySize*$ix )]
for {set iy 1} {$iy <= $ySize} {incr iy} \
{
  #  Calc chem shift at current point, and, if within $kRange
  #  of peak center ($pLoc), include in output.
   set cs [expr ( ($yStart + $SWy) - ($iy - 1)*((1.0*$SWy)/(1.0*$ySize)) )]
   set dist [expr ($pLoc - $cs)]
   if {$dist < 0} {set dist [expr ($cs - $pLoc)] }

   set r 0.0
   if {$dist < [expr ($kRng/2.0)]} \
   {
    # Integrate over indicated range.
     if {$iRng > 0.0} \
     { for {set ni 0} {$ni <= $iRange} {incr ni} \
       { set j    [expr ( $i - $ySize*( $ni - $iRange/2) )]
         set rNow [getPtrVal $rdata $j]
         set r    [expr ($r + $rNow)]
       }
       set r [expr ($r/$iRange)]
     }
    # ...or get 1D slice w/out integration
     if {$iRng <= 0.0} { set r [getPtrVal $rdata $i] }

    puts   [format "\t%14.5f \t%14.5f" $cs $r]
   }
   incr i
}

exit 0

#!/bin/sh
#
# pipe1Dx  -  This script is based on the pipe2txt.tcl script found
#             in the /usr/local/nmrDraw/com directory on worf.
#             Description given below is sent to screen when no
#             arguments provided with call to script.
#
# 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]

# If no arguments supplied, explain usage.
if {$ARGC == 1 || [flagLoc $ARGV -help]} \
{
   puts stderr "\n\
     Display 1D slice along x from NMRPipe 2D Data as text.\n\
     \t x is the directly detected dimension (typically 1H).\n\
     \t y is the indirectly detected dimension (typically 15N or 13C).\n\n\
     Usage:  pipe1Dx inFile a b c d e f g h > outFile\n\
     where a b c d e f g h are all in ppm and\n\
     \t a = slice location in constant (y) dimension\n\
     \t b = peak location in selected (x) dimension\n\
     \t c = range of integration (use 0.0 for non-integrated 1D slice)\n\
     \t d = range of 1D slice to include as output
     \t e = spectral width x dimension\n\
     \t f = start position x dimension (i.e., lowest value)\n\
     \t g = spectral width y dimension\n\
     \t h = start position y dimension (i.e., lowest value)\n\n\
     - When providing SW and start position values consider whether\n\
       the inFile contains extracted data. The extracted SW and start\n\
       are the relevant values.\n\
     - Tacking on '> outFile' pipes 1D data output to outFile.\n\
     - Script requires that all files are real-only.\n"
   exit 0
}

set inName [lindex $argv 0]

rdFDATA $inName fdata

# Get numPts in each dimension.
# Notice reversal of xy terminology.
set xSize [getParmI $fdata NDSIZE CUR_YDIM]
set ySize [getParmI $fdata NDSIZE CUR_XDIM]
set n     [expr $xSize*$ySize]

set rdata [sysMalloc $n float]

set inName [lindex $argv [expr 0]]
set inUnit [sysOpen $inName r]

set   sLoc [lindex $argv [expr 1]]
set   pLoc [lindex $argv [expr 2]]
set   iRng [lindex $argv [expr 3]]
set   kRng [lindex $argv [expr 4]]
set    SWx [lindex $argv [expr 5]]
set xStart [lindex $argv [expr 6]]
set    SWy [lindex $argv [expr 7]]
set yStart [lindex $argv [expr 8]]

sysRead $inUnit $fdata $FDATASIZE
sysRead $inUnit $rdata $n

sysClose $inUnit

# Calculate and floor the point number in y dimension that
# corresponds to the input constant ppm value, $sLoc.
set iyTemp [expr ( $ySize*(1 - ($sLoc - $yStart)/$SWy) )]
for {set j 1} {$j <= $ySize} {incr j} \
{  if {$iyTemp > $j} {set iy $j}
}

# Convert iRng (= integration range) to # of 1D
# slices to sum, $iRange, and ensure it is odd.
set iR [expr ( ($iRng/$SWy)*$ySize ) ]
for {set j 1} {$j <= $iR} {incr j} \
{  if {$iR > $j} {set iRange $j}
}
#if {$iRng > 0.0} { puts stderr [format "iRange = \t%i" $iRange] }


#Output selected 1D slice as (chem shift, amp) pairs.
set i 0
for {set ix 1} {$ix <= $xSize} {incr ix} \
{
  # Calc chem shift at current point, and, if within $kRange
  # of peak center ($pLoc), include in output.
   set cs [expr ( ($xStart + $SWx) - ($ix - 1)*((1.0*$SWx)/(1.0*$xSize)) )]
   set dist [expr ($pLoc - $cs)]
   if {$dist < 0} {set dist [expr ($cs - $pLoc)] }

   set r 0.0
   if {$dist < [expr ($kRng/2.0)]} \
   {
    # Integrate over indicated range.
    if {$iRng > 0.0} \
    { for {set ni 0} {$ni <= $iRange} {incr ni} \
      { set  i     [expr ( $ySize*($ix - 1) + ($iy - $iRange/2 + $ni) )]
        set  rNow  [getPtrVal $rdata $i]
        set  r     [expr ($r + $rNow)]
      }
      set r [expr ($r/$iRange)]
     }
    # ...or get 1D slice w/out integration.
    if {$iRng <= 0.0} \
    { set  i  [expr ( $ySize*($ix - 1) + $iy )]
      set  r  [getPtrVal $rdata $i]
    }

    puts  [format "\t%14.5f \t%14.5f" $cs $r]
   }

}

exit 0

#!/usr/bin/perl
#
# pipe1Dat expN res dim verb iRange kRange
#
#  This script gets a 1D slice corresponding to the position of residue = res
#  as read from the file expN.sp.save. The 1D slice is taken from the file
#  expN.ft2, along either 15N or 1H dimension according to dim = 0 or 1.
#  Integration in the orthogonal dimension over range iRange is used unless
#  iRange = 0.0, while kRange specifies the spectral range of data to keep
#  from along the 1D slice.
#
#  Hardwired paramers for the 1H and 15N spectal widths and starting frequencies
#  in nmrDraw's .ft2 file are specified in the first few lines and must be
changed
#  according to the extraction, etc., used in producing that file.
#
#  Defaults for iRange and kRange are also specified with values typically
#  appropriate for the 1H-15N HSCQ spectrum of RNase A.
#

$ext1 = ".sp.save";  $ext2 = ".ft2";

# Default spectral parameters (ppm).
# $startH =   5.5; $stopH =  11.0;  $swH = 1.0*($stopH - $startH);
# $startN = 103.0; $stopN = 135.0;  $swN = 1.0*($stopN - $startN);
  $startH =   5.5; $stopH =  11.5;  $swH = 1.0*($stopH - $startH);
  $startN =   0.0; $stopN =  30.0;  $swN = 1.0*($stopN - $startN);
  $iRngH = 0.25;  $kRngH = 0.25;
  $iRngN = 0.05;  $kRngN = 1.50;

if ($#ARGV < 2)
{ print "\n\n";
   print "Usage: pipe1Dat expN res dim iRange kRange verb\n\n";
   print " where dim = 0 (1) gives the 1D slice through the 2D NMR data\n";
   print " at residue = res along the 15N (1H) dimension.\n\n";
   print " - Peak location is read from file expN.sp.save\n";
   print "   and the 1D slice taken from file expN.ft2.\n";
   print " - Assumed spectral ranges in expN.ft2:\n";
   print "       1H --> {$startH, $stopH} ppm\n";
   print "      15N --> {$startN, $stopN} ppm\n";
   print " - Integration and keep ranges (iRange & kRange) default to \n";
   print "   $iRngH & $kRngH ppm (1H) or $iRngN & $kRngN ppm (15N).\n\n";
   print "Optional parameter verb = 0 turns off messages.\n\n";
   exit;
}

$input = $ARGV[0];  $myRes = $ARGV[1];  $dim = $ARGV[2];  $verb = 1;

# Notify user of assumed parameters.
   print "\n\n !!! NOTE !!!  Assumed spectral ranges:\n";
   print "                1H --> {$startH, $stopH} ppm\n";
   print "               15N --> {$startN, $stopN} ppm\n";

# Default integration and keep ranges are dimension specific and based
# on typical peak widths in the 1H-15N HSCQ of RNase A.
  if ($dim == 1) { $iRng = $iRngH;  $kRng = $kRngH; }
  if ($dim == 0) { $iRng = $iRngN;  $kRng = $kRngN; }

if ($#ARGV > 3) {$iRng = $ARGV[3];  $kRng = $ARGV[4];}
if ($#ARGV > 5) { $verb = $ARGV[5]; }
if ($dim != 0 && $dim != 1)
{ print "\n\nMust choose dim = 0 or 1, $dim invalid.\n\n ";  exit; }

# Get {15N,1H} coordinate of requested residue.
  open (in1, $input.$ext1);
  # Read ornament info from in1 file and get coords of desired peak.
  while (($line=<in1>) !~ /<ornament>/) { }
  $search = 1;
  while ($search)
  {
    while ( ($line = <in1>) !~ /type label/ )
    { @temp= split(/\s+/, $line);
      if ($temp[0] =~ /pos/) { $coordN = $temp[1]; $coordH = $temp[2]; }
      if ($temp[0] =~ /rs/)  { @rtemp = split(/\|/, $temp[1]);
                               $res = $rtemp[1]; }
      if ($line =~ /<end ornament>/)
      { print "\n$myRes not found.\n\n"; exit; }
    }
    if ($res =~ $myRes)
    { # if ($verb) { print "\n\t $res\{15N,1H}: {$coordH, $coordN}\n\n"; }
      $search = 0; }
  }
  close in1;


# Get 1D slice through freq domain at {15N,1H} coordinate.
  $in2 = $input.$ext2;
  if ($dim == 0) { $dS1 = "15N";  $dS2 = "1H";  $const = $coordH; }
  if ($dim == 1) { $dS1 = "1H";  $dS2 = "15N";  $const = $coordN; }
  $iRpm = $iRng/2.0;  $kRpm = $kRng/2.0;

  $ofile = $res.".".$input.".".$dS1.".dat";
  if ($dim == 0) { `pipe1Dy $in2 $coordH $coordN $iRng $kRng $swH $startH $swN
$startN > $ofile`; }
  if ($dim == 1) { `pipe1Dx $in2 $coordN $coordH $iRng $kRng $swH $startH $swN
$startN > $ofile`; }
  if ($verb) { print "\n Complete.\n";
               print "  1D $dS1 slice for $res at ($coordH,$coordN) ppm. \n";
               print "   - Peak integrated over +/-$iRpm about $const $dS2
ppm.\n";
               print "   - Kept +/-$kRpm ppm about peak along $dS1 dimension.\n";
               print "  Data written to $ofile.\n\n";
             }

Greetings all ...

There is a crude symmetrization macro "diag.M" that is suitable only for
square datasets with the diagonal signal at the actual "diagonal" of
the spectral matrix S (diagonal of S(i,j) whenever i = j).

By default, it replaces points S(i,j) and S(j,i) with which ever
is smaller in magnitude.

If you need a specific symmetrization function (min, max, retain sign,
product, avg) copy and adjust the macro.

mrPipe -in test.ft2 \
| nmrPipe -fn MAC -macro $NMRTXT/diag.M -noRd -noWr -all \
    -out sym.ft2 -verb -ov

Note that many consider symmetrization a bad practice, because it
can distort real signals, and make correlated noise ridges look
like real signals.

	 Cheerful Regards,

	 Big FD

On Wed, 12 Nov 2003, jakobjlopez wrote:

> hi,
>
> is it possible to symmetrize a 2D spectrum with nmrPipe? (or nmrview
> or sparky, for that matter?)
>
> i looked in the docs, but didn't find anything pertaining to that..
>
> thanks!
>
> jakob
>
>
>
>
>
>
> Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
>
>
>

i consider it bad practice as well. but my boss wants a 'nice spectrum'.

cheers!

jakob

On Wednesday 12 November 2003 18:07, Frank Delaglio wrote:
>  Greetings all ...
>
>  There is a crude symmetrization macro "diag.M" that is suitable only for
>  square datasets with the diagonal signal at the actual "diagonal" of
>  the spectral matrix S (diagonal of S(i,j) whenever i = j).
>
>  By default, it replaces points S(i,j) and S(j,i) with which ever
>  is smaller in magnitude.
>
>  If you need a specific symmetrization function (min, max, retain sign,
>  product, avg) copy and adjust the macro.
>
>  mrPipe -in test.ft2 \
>
>  | nmrPipe -fn MAC -macro $NMRTXT/diag.M -noRd -noWr -all \
>
>     -out sym.ft2 -verb -ov
>
>  Note that many consider symmetrization a bad practice, because it
>  can distort real signals, and make correlated noise ridges look
>  like real signals.
>
>        Cheerful Regards,
>
>        Big FD
>
>  On Wed, 12 Nov 2003, jakobjlopez wrote:
>  > hi,
>  >
>  > is it possible to symmetrize a 2D spectrum with nmrPipe? (or nmrview
>  > or sparky, for that matter?)
>  >
>  > i looked in the docs, but didn't find anything pertaining to that..
>  >
>  > thanks!
>  >
>  > jakob
>  >
>  >
>  >
>  >
>  > 
>  >
>  > Your use of Yahoo! Groups is subject to
>  > http://docs.yahoo.com/info/terms/
>
> Yahoo! Groups Sponsor
>
>
>
> ADVERTISEMENT
>
>
>
>
>
>
>  Your use of Yahoo! Groups is subject to the Yahoo! Terms of Service.

Howdy All-

I have more questions concerning the txt2bin/bin2pipe conversion
process.  I figured out how to convert a text file to bin using the
txt2bin.tcl script.  As as test case, I took a 2D dataset that we had
processed, converted it to a text file, and wanted to convert it back
to an nmrPipe file to see how everything works -- but the end result is
not good.  Can anyone look at the following steps to see what we are
doing wrong?

Step 1: convert from pipe TO text
  > pipe2txt.tcl data.dat > data.txt

Step 2: convert from text TO bin
  > txt2bin.tcl < data.txt > data.bin

Step 3: use bin2pipe to make final file
  > bin2pipe.com (see below for script)

#!/bin/sh

bin2pipe -in data.bin \
    -xN          1024    -yN         54  \
    -xT           512    -yT         27   \
    -xMODE     Real   -yMODE     Real \
    -xSW       8000.0    -ySW       3400.00  \
    -xOBS      599.736    -yOBS     150.829  \
    -xCAR        5.159    -yCAR     56.00  \
         -xFT             Freq  -yFT             Freq  \
    -xLAB           NH    -yLAB       CA    \
    -ndim            2    -aq2D     States \
          -out newdata.dat  -verb -ov


We originally had MODE = Complex (in the original conversion script; we
used the same parameters in the bin2pipe conversion that we used for
var2pipe) -- changed them to Real but it did not help.  Any
hints/pointers?  Is this all that is needed (bin2pipe conversion -- no
further processing?)?

Thanks,
Doug

Hi everyone-

I received the recent post that included scripts to transform a horizontal or
vertical slice of a 2D experiment, but are there any scripts floating around
that will 1D transform a 2D experiment, i.e., basically take 2D data and just
do a 1D transform of it? I'm very new to NMRPipe- what's the simplest way to do
this- anybody know?

Thanks so much,
Meredith  :)


--
Meredith Newby Lambert, Ph. D.
Research Fellow
Department of Chemistry, University of Michigan
930 N. University, Ann Arbor, MI 48109-1055

Tel: (734) 615-4172
Fax: (734) 647-4865

Dear Meredith,
I am not sure if I understood well what you are asking about, but let me
try to answer anyway.  If you want to process one dimension only at a tim,
it is a given, as the processing takes care of a set of one-dimensional
vectors arranged in the x direction.  You can always interrupt the
processing at that point and write out the (intermediate) results.
Best regards,
Istvan

wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
Istvan Pelczer, Ph.D. 	       	 Email: ipelczer@...
Senior NMR Spectroscopist, Lecturer
Princeton University
Department of Chemistry, Frick Lab.,  		 ph#  (609) 258 2342
Washington Road 				 fax#  (609) 258 6746
Princeton,  NJ 08544, USA 	 Web:  www.princeton.edu/~nmr




On Thu, 13 Nov 2003, Meredith Lambert wrote:

> Hi everyone-
>
> I received the recent post that included scripts to transform a horizontal or
> vertical slice of a 2D experiment, but are there any scripts floating around
> that will 1D transform a 2D experiment, i.e., basically take 2D data and just
> do a 1D transform of it? I'm very new to NMRPipe- what's the simplest way to
do
> this- anybody know?
>
> Thanks so much,
> Meredith  :)
>
>
> --
> Meredith Newby Lambert, Ph. D.
> Research Fellow
> Department of Chemistry, University of Michigan
> 930 N. University, Ann Arbor, MI 48109-1055
>
> Tel: (734) 615-4172
> Fax: (734) 647-4865
>
>
>
>
> Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
>
>
>

Greetings Colleagues,

The nmrDraw command "Proc/NMRPipe Command" will provide a one-line
command window, where individual nmrPipe processing functions and
their arguments can be entered one at a time (like "FT" "ZF" etc).
The functions will operate on whatever 1D slice is currently being viewed.

The nmrDraw command "Proc/Auto Proc 1D" will execute a nifty little
pre-defined script to process the current 1D slice being viewed:

1. If the data is in the time-domain, it will be processed with
    an SP cosine window, zero fill and FT.  If the axis name happens
    to be "HN", a solvent filter will be used, and the left half of
    the data will be processed.

2. If the data is in the freq domaini (try it!): it will be inverse
    processed, including removal of the window function and zero filling.
    This is a nice way to see interferogram data, to test LP
    on individual 1D vectors, and to diagnose problems in the
    spectra such as prematurely terminated experiments.

    FYI, for this inverse processing to work properly, you have to
    use a window function that does not have zero values
    (e.g. "SP -off 0.5 -end 0.98" instead of "SP -off 0.5 -end 1.0")


   	 Cheerful Regards,

	 big fd


On Thu, 13 Nov 2003, Meredith Lambert wrote:

> Hi everyone-
>
> I received the recent post that included scripts to transform a horizontal or
> vertical slice of a 2D experiment, but are there any scripts floating around
> that will 1D transform a 2D experiment, i.e., basically take 2D data and just
> do a 1D transform of it? I'm very new to NMRPipe- what's the simplest way to
do
> this- anybody know?
>
> Thanks so much,
> Meredith  :)
>
>
> --
> Meredith Newby Lambert, Ph. D.
> Research Fellow
> Department of Chemistry, University of Michigan
> 930 N. University, Ann Arbor, MI 48109-1055
>
> Tel: (734) 615-4172
> Fax: (734) 647-4865
>
>
>
>
> Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
>
>
>

Thanks!

That hgelps a lot!

-Meredith  :)

Quoting Frank Delaglio <delaglio@...>:

>
> Greetings Colleagues,
>
> The nmrDraw command "Proc/NMRPipe Command" will provide a one-line
> command window, where individual nmrPipe processing functions and
> their arguments can be entered one at a time (like "FT" "ZF" etc).
> The functions will operate on whatever 1D slice is currently being viewed.
>
> The nmrDraw command "Proc/Auto Proc 1D" will execute a nifty little
> pre-defined script to process the current 1D slice being viewed:
>
> 1. If the data is in the time-domain, it will be processed with
>    an SP cosine window, zero fill and FT.  If the axis name happens
>    to be "HN", a solvent filter will be used, and the left half of
>    the data will be processed.
>
> 2. If the data is in the freq domaini (try it!): it will be inverse
>    processed, including removal of the window function and zero filling.
>    This is a nice way to see interferogram data, to test LP
>    on individual 1D vectors, and to diagnose problems in the
>    spectra such as prematurely terminated experiments.
>
>    FYI, for this inverse processing to work properly, you have to
>    use a window function that does not have zero values
>    (e.g. "SP -off 0.5 -end 0.98" instead of "SP -off 0.5 -end 1.0")
>
>
>     Cheerful Regards,
>
>  big fd
>
>
> On Thu, 13 Nov 2003, Meredith Lambert wrote:
>
> > Hi everyone-
> >
> > I received the recent post that included scripts to transform a horizontal
> or
> > vertical slice of a 2D experiment, but are there any scripts floating
> around
> > that will 1D transform a 2D experiment, i.e., basically take 2D data and
> just
> > do a 1D transform of it? I'm very new to NMRPipe- what's the simplest way
> to do
> > this- anybody know?
> >
> > Thanks so much,
> > Meredith  :)
> >
> >
> > --
> > Meredith Newby Lambert, Ph. D.
> > Research Fellow
> > Department of Chemistry, University of Michigan
> > 930 N. University, Ann Arbor, MI 48109-1055
> >
> > Tel: (734) 615-4172
> > Fax: (734) 647-4865
> >
> >
> >
> >
> > Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
> >
> >
> >
>
>
>
>
> Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
>
>
>


--
Meredith Newby Lambert, Ph. D.
Research Fellow
Department of Chemistry, University of Michigan
930 N. University, Ann Arbor, MI 48109-1055

Tel: (734) 615-4172
Fax: (734) 647-4865

Thanks for you help!

-Meredith  :)


Quoting Istvan Pelczer <ipelczer@...>:

>
> Dear Meredith,
> I am not sure if I understood well what you are asking about, but let me
> try to answer anyway.  If you want to process one dimension only at a tim,
> it is a given, as the processing takes care of a set of one-dimensional
> vectors arranged in the x direction.  You can always interrupt the
> processing at that point and write out the (intermediate) results.
> Best regards,
> Istvan
>
> wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
> Istvan Pelczer, Ph.D. 	       	 Email: ipelczer@...
> Senior NMR Spectroscopist, Lecturer
> Princeton University
> Department of Chemistry, Frick Lab.,  		 ph#  (609) 258 2342
> Washington Road 				 fax#  (609) 258 6746
> Princeton,  NJ 08544, USA 	 Web:  www.princeton.edu/~nmr
>
>
>
>
> On Thu, 13 Nov 2003, Meredith Lambert wrote:
>
> > Hi everyone-
> >
> > I received the recent post that included scripts to transform a horizontal
> or
> > vertical slice of a 2D experiment, but are there any scripts floating
> around
> > that will 1D transform a 2D experiment, i.e., basically take 2D data and
> just
> > do a 1D transform of it? I'm very new to NMRPipe- what's the simplest way
> to do
> > this- anybody know?
> >
> > Thanks so much,
> > Meredith  :)
> >
> >
> > --
> > Meredith Newby Lambert, Ph. D.
> > Research Fellow
> > Department of Chemistry, University of Michigan
> > 930 N. University, Ann Arbor, MI 48109-1055
> >
> > Tel: (734) 615-4172
> > Fax: (734) 647-4865
> >
> >
> >
> >
> > Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
> >
> >
> >
>
>
>
> Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
>
>
>


--
Meredith Newby Lambert, Ph. D.
Research Fellow
Department of Chemistry, University of Michigan
930 N. University, Ann Arbor, MI 48109-1055

Tel: (734) 615-4172
Fax: (734) 647-4865

Hi everyone.

Can someone tell me if there is a way for NMRPipe to
read/process bruker data that have been acquired with
a 3-1-2 order (instead of 3-2-1)?

I have a 3D-HNHA that is giving me problems...

Thanks

Barbara

________________________________________________________________________
Want to chat instantly with your online friends?  Get the FREE Yahoo!
Messenger http://mail.messenger.yahoo.co.uk

Barbara,

This is a processing script for a Bruker DMX / DRX
N15-NOESY-HSQC experiment (noesiif3gp).  It's a
similar situation, where F2 is N15, and F3/F1 are
proton:

#!/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 2 -size 512
-c 0.5  \
| nmrPipe -fn ZF -size 1024  \
| nmrPipe -fn FT -verb  \
| nmrPipe -fn PS -p0 43 -p1 0 -di  \
| nmrPipe -fn TP  \
| nmrPipe -fn SP -off 0.39 -end 0.98 -pow 2 -size 25
-c 0.5  \
| nmrPipe -fn ZF -size 128  \
| nmrPipe -fn FT -verb  \
| nmrPipe -fn PS -p0 90 -p1 0 -di  \
| pipe2xyz -out lp/test%03d.ft2 -y

echo 'Processing F2'
xyz2pipe -in lp/test%03d.ft2 -z -verb  \
| nmrPipe -fn LP -f -ord 30 -x1 2 -xn 75 -pred 53 -fix
-fixMode 1 -after  \
| nmrPipe -fn SP -off 0.39 -end 0.98 -pow 2 -size 128
-c 0.5  \
| nmrPipe -fn ZF -size 512  \
| nmrPipe -fn FT -alt -verb  \
| nmrPipe -fn PS -p0 0 -p1 0 -di  \
| pipe2xyz -out lp/test%03d.ft3 -y


Normally, in the last line, it's supposed to end in
-z, but in this script, -z was changed to -y.  This
will then display the two proton dimensions, and you
can scroll through the nitrogen planes.



__________________________________
Do you Yahoo!?
Protect your identity with Yahoo! Mail AddressGuard
http://antispam.yahoo.com/whatsnewfree

Hoping I can get a clarification on use of the QMIX function for
separating interleaved NOE/no_NOE data.  "Quick" background and my
specific question follow.

I've run 1H,15N NOE experiments in an interleaved manner with using
satflg=1,2 and phase=1,2 (arrayed in that order). My psequence saturates
1H for ~5s when satflg=1 (NOE) and incorporates a pulse-free delay when
satflg=2 (no_NOE). As usual, phase=1,2 is for coherence selection (here,
P,N-type Rance-Kay) in 15N.

Because satflg is arrayed, I must separate the two 2D spectra contained
in the raw data (a Varian fid file).  I've done this using two scripts
fid.com, then separate.com printed below.  fid.com is straighforward to
generate... Just type 'varian', read params and then manually edit to
double yN (yielding yN=4*ni, but leave yT=ni) to account for the fact
that the raw data contains two spectra.

The separate.com script is one I inherited.  It uses the QMIX nmrPipe
function with

    set C = ( x 0 \
              0 x \
              y 0 \
              0 y )

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

where x,y=1,0 or 0,1 yields test.fid as the NOE or no_NOE data,
respecitvely.  I do not understand why the C matrix requires ic*oc=8
elements, when the data contains only four components: P & N-types for
satflg=1 and 2.

My problem is that if I don't understand the meaning of the elements in
C, then how do I know I've chosen x and y, or the zeros for that matter,
properly?

I'd very much appreciate clarification.
Thanks in advance!
Jim Kempf.


/***  Begin fid.com macro. ***/
#!/bin/csh

var2pipe -in ./fid -noaswap  \
   -xN              4000  -yN               620  \
   -xT              2000  -yT               155  \
   -xMODE        Complex  -yMODE      Rance-Kay  \
   -xSW        15625.000  -ySW         4000.000  \
   -xOBS         799.499  -yOBS          81.022  \
   -xCAR           4.821  -yCAR         119.995  \
   -xLAB              H1  -yLAB             N15  \
   -ndim               2  -aq2D          States  \
   -out ./test.fid -verb -ov
/***  End fid.com macro. ***/


/***  Begin separate.com macro. ***/
#!/bin/csh
echo
echo "NOE data sent to /noe/test.fid"
set C = ( 1 0 \
           0 1 \
           0 0 \
           0 0 )
nmrPipe -in test.fid \
| nmrPipe -fn QMIX -ic 4 -oc 2 -cList $C -time   \
    -verb -ov -out ./noe/test.fid

echo
echo "no_NOE data sent to /no_noe/test.fid"
set C = ( 0 0 \
           0 0 \
           1 0 \
           0 1 )
nmrPipe -in test.fid \
| nmrPipe -fn QMIX -ic 4 -oc 2 -cList $C -time   \
    -verb -ov -out ./no_noe/test.fid
echo
/***  End of separate.com macro. ***/

--
Postdoctoral Fellow
Yale University
Department of Chemistry
225 Prospect St.
P.O. Box 208107
New Haven, CT 06520-8107

  phone: (203) 432-5728
    FAX: (203) 432-6144

Many Greetings ...

Here's some info on interleaved data that some might find interesting,
including a note about the QMIX function ...

	 Cheerful Regards,

	 big fd


There are several methods for making combinations of spectral data,
and for manipulating interleaved data:

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.

3. NMRPipe Processing Function MAC (see the manual page for MAC)
    Examples include any of the gradient shuffling macros, such
    as "nmrtxt/bruk_ranceY.M".

4. Stand-alone macro interpreter "M"

    This program can be invoked directly to execute a macro in the
    "MAC" macro language.  One example can be found in the 3D projection
    macro "nmrtxt/projZ.M"

5. Stand-alone program "addNMR"

    This program forms algebraic combinations (sum, difference, etc)
    of two NMRPipe format FIDs or spectra (1D-4D), for example:

    addNMR -in1 A.dat -in2 B.dat -sub -out A-B.dat

    addNMR -in1 fid/A%03d.fid -in2 fid/B%03d.fid -add -out fid/sum%03d.fid

6. An NMRWish TCL macro (one example, "com/peCOSY.tcl")

A question about fitting the window function to the indirect dimension
size...

I have an indirect dimension acquired with 120 increments
(Echo/A-Echo), and the
following 8 increments are padded out with zeros by the spectrometer
(GE Omega).
Should I:

a) use a conversion script that gives -yT as 120, which would lead to
a window
function of the same size and therefore avoid truncation artefacts,

or should I

b) use a conversion script that gives -yT as 128, then linear predict
the final 8
points, or do something clever with the window function to avoid
truncation
artefacts. (If it's something clever then any tips would help,
thanks).

Further to this, is it unadvisable for any reason not to acquire with
a number of
increments that is a power of two? I heard it may affect the linear
prediction
performance.

Cheers,

Charlie

Many Greetings,

In this case, there are 128 complex points recorded on the disk,
but only 120 of them are valid.  It's for cases like these that
we have different conversion arguments for the two kinds of information.

The general rules:

    The "-xN" "-yN" etc will be set to the total (real+imaginary) number of
    points actually recorded in the file.

    The "-xT" "-yT" etc will be set to the desired number of points in
    the window function.  For complex data with no "missing" points,
    this means that the "-xT" "-yT" ... values will be exactly half
    of the corresponding "-xN" "-yN" ... values.  However, if there
    are missing data points, the "-xT" "-yT" values are reduced
    accordingly.

So, in Charlie's case:

   "-yN 256 -yT 120"

As to sizes which are powers of two: this is not a requirement,
and will not effect the quality of processing.  However, FT steps
will be slower; for this reason, we usually use "ZF -auto", which
doubles the data size, then rounds up to a power of two if needed.


	 Cheerful Regards,

	 big fd

On Fri, 28 Nov 2003, dark_isnewcdt wrote:

> A question about fitting the window function to the indirect dimension
> size...
>
> I have an indirect dimension acquired with 120 increments
> (Echo/A-Echo), and the
> following 8 increments are padded out with zeros by the spectrometer
> (GE Omega).
> Should I:
>
> a) use a conversion script that gives -yT as 120, which would lead to
> a window
> function of the same size and therefore avoid truncation artefacts,
>
> or should I
>
> b) use a conversion script that gives -yT as 128, then linear predict
> the final 8
> points, or do something clever with the window function to avoid
> truncation
> artefacts. (If it's something clever then any tips would help,
> thanks).
>
> Further to this, is it unadvisable for any reason not to acquire with
> a number of
> increments that is a power of two? I heard it may affect the linear
> prediction
> performance.
>
> Cheers,
>
> Charlie
>
>
>
>
>
>
> Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
>
>
>

This has been asked before but I think it's worth asking again in case
anyone has any new insight.

For solvent suppression, example scripts on the web seem to always
use "SOL" or "POLY -avg -nw 16 -fx1 NW+4 -nc (SIZE/(2*NW+1)" (more
commonly known as "POLY -time").

Does anyone have advice on optimising these parameters, or whether it
is worth time spent varying them?

Charlie

Hi,

I have run a gHCCH_TOCSY, but cannot seem to process it using nmrview- no
matter what combinations/permutations of complex and rance-kay I use I
always end up with a mirror plane in one of the indirect dimensions. It
does process correctly with VNMR, so I know the data is fine. I ran it
with both phase and phase2 of 1,2. Does anyone have a processing script
for this experiment?

Thanks,

Tara

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

Tara,

The array parameter ('phase, phase2', or 'phase2', 'phase') determines aqORD
(1 or 0, respectively).  What is your "array"?  Could this be a problem?  It
seems to me gHCCH_TOCSY is not gradient selected, i.e., no Rance-Kay.

Hsin

--
Hsin Wang, Ph.D.
NMR Facility Manager
College of Staten Island
2800 Victory Boulevard
Staten Island, NY 10314
Phone: 718-982-3809
Fax: 718-982-3910
Email: wang@...

> -----Original Message-----
> From: Tara Sprules [mailto:tara.sprules@...]
> Sent: Monday, December 01, 2003 4:21 PM
> To: nmrpipe@yahoogroups.com
> Subject: [nmrpipe] gHCCH_TOCSY
>
>
>
> Hi,
>
> I have run a gHCCH_TOCSY, but cannot seem to process it using nmrview- no
> matter what combinations/permutations of complex and rance-kay I use I
> always end up with a mirror plane in one of the indirect dimensions. It
> does process correctly with VNMR, so I know the data is fine. I ran it
> with both phase and phase2 of 1,2. Does anyone have a processing script
> for this experiment?
>
> Thanks,
>
> Tara
>
> Tara Sprules
> Post-Doctoral Fellow
> Department of Chemistry
> University of Alberta
> Edmonton, AB
> Canada
>
>
>
>
>
>
> Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
>
>
>

Thanks! This was the one that finally worked, once I added -aqORD 1.

FYI: I recorded my expt on varian, using array phase,phase2 (with
phase=1,2 and phase2=1,2).

Tara

On Tue, 2 Dec 2003, [euc-kr] Á¤Áø¿ø wrote:

> Hi,
>
> please try this script.
>
> -----------
>
> #!/bin/csh
>
> var2pipe -in ./fid -swap  \
>   -xN              1024  -yN               100  -zN                96  \
>   -xT               512  -yT                50  -zT                48  \
>   -xMODE        Complex  -yMODE Complex         -zMODE  Complex        \
>   -xSW         8000.000  -ySW         8000.000  -zSW         9427.292  \
>   -xOBS         499.863  -yOBS         499.863  -zOBS         125.694  \
>   -xCAR           4.773  -yCAR           4.773  -zCAR          37.599  \
>   -xLAB              H1  -yLAB              H1  -zLAB             C13  \
>   -ndim               3  -aq2D          States                         \
> | nmrPipe -fn MAC -macro $NMRTXT/var_ranceY.M -noRd -noWr \
> | nmrPipe  -fn MAC -macro $NMRTXT/var_ranceZ.M -noRd -noWr \
> | pipe2xyz -out ./data/test%03d.fid -verb -ov
>
> ----
>
> >
> >
> > -----¿øº»¸Þ½ÃÁö-----
> > º¸³½»ç¶÷: "TaraSprules"
> > ¹Þ´Â»ç¶÷: nmrpipe@yahoogroups.com
> > ³¯Â¥: 2003/12/02(È­)06:21
> > Á¦¸ñ: [nmrpipe] gHCCH_TOCSY
> >
> >
> > Hi,
> >
> > I have run a gHCCH_TOCSY, but cannot seem to process it using nmrview- no
> > matter what combinations/permutations of complex and rance-kay I use I
> > always end up with a mirror plane in one of the indirect dimensions. It
> > does process correctly with VNMR, so I know the data is fine. I ran it
> > with both phase and phase2 of 1,2. Does anyone have a processing script
> > for this experiment?
> >
> > Thanks,
> >
> > Tara
> >
> > Tara Sprules
> > Post-Doctoral Fellow
> > Department of Chemistry
> > University of Alberta
> > Edmonton, AB
> > Canada
> >
> >
> >
> >
> >
> >
> > Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
> >
> >
>

+----------------------------------------+
| Jung, Jinwon. PhD Student,             |
| HTSD-NMR Laboratory. Yonsei University |
| Seoul, KOREA                           |
+----------------------------------------+

Do you know @MESSAGE? Powered by 3R Soft, Inc.



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