Hi
I have a series of 1D spectra that I would like to present as a stackplot.
These spectra have been processed using NMRPipe. What is the best way to
do this?  Any help/scripts etc would be much appreciated.
Thanks in advance.

Siddhartha




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

Tel: 80-3092839

Hi all,

I am pretty new at this 3D stuff, so I hope I am not stating the
obvious here.

I have been trying to process HNCOCA data from a Bruker Avance using
XWinNMR 3.1. I have observed that the 'bruker' conversion program
interprets the parameters not exactly right. Things I had to modify
are:

Acquisition Mode :
  z - Complex -> States-TPPI
Spectral Width :
  y -> acqu2s
  z -> acqu3s
Observe Freq (MHz) : also adjusts the center positions
  y : SFO3 (= SFO1 in acqu2s)
  z : SFO2 (= SFO1 in acqu3s)
Center Position: now this is strange, the SFOx positions in the popup
are not right, I got for 15N 116.106, while according to Bruker it
was 116 (13C pipe:56.765; bruker:54). I was under the impression that
these values should be O1/BF1 from the acqu files for each of the
dimensions.
  x : 4.802 -> should be from acqus : O1/BF1
  y : fixed wrongly to SFO3 (= O1/BF1 in acqu2s)
  z : fixed already to SFO2 (= O1/BF1 in acqu3s)

This makes me wonder why the program does not automatically use the
parameters from the acqus, acqu2s and acqu3s files. It should need
only SW_h, SFO1, O1, (since BF1 = SFO1-O1) to get the frequencies
right. Am I missing something here?

I am also not sure whether the aq2D should be States when the data
are echo/antiecho in y and DQD in x.

Finally the echo/antiecho shuffling done by the (automatically called
bruk_ranceY.M) seems to give me a y dimension that needs a -90 phase
shift and a reversal. I recall something about Bruker changing the
echo/antiecho acquisition in the Avance or XWinNMR 3.x versions. What
is the best way to fix this problem. Should I just copy the
var_ranceY.M to bruk_ranceY.M in the nmrtext directory?

Sorry about the long message. Thank you for reading it all, and
thanks in advance for any help or suggestions you may have. (The one
I hope for is: we have this update and that fixes everything!!)

Thanks,
René Kanters
--------
René P.F Kanters, Ph.D.
Director of Computer Assisted Science Education
Department of Chemistry
University of Richmond, Virginia 23173
Phone: (804) 287-6873
Fax: (804) 287-1897
Email: rkanters@...
Web: http://www.richmond.edu/~rkanters

Hi Rene,

You could try using my suite of scripts "drx2pipe" which is downloadable
from the BMRB website.  They will create an NMRPipe conversion script
for Bruker Avance data for 1D-4D data.  If you have any problems
downloading or using them, please let me know.

Good luck!

Duncan.


rpfkanters2 wrote:
>
> Hi all,
>
> I am pretty new at this 3D stuff, so I hope I am not stating the
> obvious here.
>
> I have been trying to process HNCOCA data from a Bruker Avance using
> XWinNMR 3.1. I have observed that the 'bruker' conversion program
> interprets the parameters not exactly right. Things I had to modify
> are:
>
> Acquisition Mode :
>  z - Complex -> States-TPPI
> Spectral Width :
>  y -> acqu2s
>  z -> acqu3s
> Observe Freq (MHz) : also adjusts the center positions
>  y : SFO3 (= SFO1 in acqu2s)
>  z : SFO2 (= SFO1 in acqu3s)
> Center Position: now this is strange, the SFOx positions in the popup
> are not right, I got for 15N 116.106, while according to Bruker it
> was 116 (13C pipe:56.765; bruker:54). I was under the impression that
> these values should be O1/BF1 from the acqu files for each of the
> dimensions.
>  x : 4.802 -> should be from acqus : O1/BF1
>  y : fixed wrongly to SFO3 (= O1/BF1 in acqu2s)
>  z : fixed already to SFO2 (= O1/BF1 in acqu3s)
>
> This makes me wonder why the program does not automatically use the
> parameters from the acqus, acqu2s and acqu3s files. It should need
> only SW_h, SFO1, O1, (since BF1 = SFO1-O1) to get the frequencies
> right. Am I missing something here?
>
> I am also not sure whether the aq2D should be States when the data
> are echo/antiecho in y and DQD in x.
>
> Finally the echo/antiecho shuffling done by the (automatically called
> bruk_ranceY.M) seems to give me a y dimension that needs a -90 phase
> shift and a reversal. I recall something about Bruker changing the
> echo/antiecho acquisition in the Avance or XWinNMR 3.x versions. What
> is the best way to fix this problem. Should I just copy the
> var_ranceY.M to bruk_ranceY.M in the nmrtext directory?
>
> Sorry about the long message. Thank you for reading it all, and
> thanks in advance for any help or suggestions you may have. (The one
> I hope for is: we have this update and that fixes everything!!)
>
> Thanks,
> René Kanters
> --------
> René P.F Kanters, Ph.D.
> Director of Computer Assisted Science Education
> Department of Chemistry
> University of Richmond, Virginia 23173
> Phone: (804) 287-6873
> Fax: (804) 287-1897
> Email: rkanters@...
> Web: http://www.richmond.edu/~rkanters
>
>
>
> Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/

--

Duncan M Smith                  \  "We trained hard, but it seemed that
Discovery Analytical Sciences   /  every time we were beginning to form
Mailstop 29-M-B                 \  into teams, we would be reorganized.
Amgen Inc.                      /  I was to learn later in life that we
One Amgen Center Drive          \  tend to meet any new situation by re-
Thousand Oaks                   /  organizing, and a wonderful method it
CA 91320-1789                   \  can be for creating the illusion of
USA                             /  progress, while producing confusion,
                                 \  inefficiency and demoralization."
Phone   (805) 447-3171          /
Fax     (805) 480-3015          \  Gaius Petronius
E-mail  duncan@...        /  Roman Centurion  AD 66

I recall hearing of a version of NMRPipe for Windows NT... anyone
have experinece with this, and is it as good as 'nix versions? I'm
currently using pipe in linux, but it's the only software I'm
using... Sparky has drawing problems on my machines and only works
properly in Windows, and since CNS is available for NT, it seems
silly not to run everything on a single platform.

Hello all,
	 I was wondering if someone could help with a problem I am
encountering processing an hncacb dataset acquired on a DRX-600. Basically
I have severe truncation in both the indirect 15N and 13C dimensions. I am
using Linear prediction to help overcome this. As recommended I make sure
that the other dimensions are previously fourier transformed. My strategy
has been to FT the 1H and 15N deminesions first and then FT the 13C
dimension with LP. I then inverse FT retransform the 15N with LP (the
script is attached below). However, the 15N dimension still showed severe
truncation. When I compared the 15N dimension to the non-lp'd transform,
the non lp'd one looked better. Somehow applying the inv ft and subsequent
LP seemed to introduce further truncation in my case. I checked this by
taking out the 15N vectors and apllying a 1d transfrom on them. IF the FID
had not been previously transformed I managed to apply LP and the normal
cosine bell window and force the fid to zero. However, when I took out a a
FT'd 15N vector after HT and inv FT (as applied on the macro below) the
fid was not forced to zero which is likely the reason for truncation.  Is
there something I am doing wrong (I guess there must be). If anyone could
give me some advice I would be grateful.
Thanks in advance
MIke
############################################################################

xyz2pipe -in fid/hnca%03d.DAT -x  \
| nmrPipe  -fn PS -p1 27720  \
| nmrPipe  -fn SOL \
| nmrPipe  -fn PS -p1 -27720  \
| nmrPipe  -fn SP -off .5 -end .98 -pow 2 -c 0.5 \
| nmrPipe  -fn ZF -auto \
| nmrPipe  -fn FT -auto \
| nmrPipe  -fn PS -p0 -87 -p1 0.0 -di -verb 2 \
| nmrPipe  -fn EXT -x1 10.0ppm -xn 6.5ppm -sw \
| pipe2xyz -out lp/test%03d.ft3 -x  -ov

echo DONE.
       xyz2pipe -in lp/test%03d.ft3 -z -verb               \
       | nmrPipe  -fn SP -off 0.5 -end 0.95 -pow 1 -c 0.5  \
       | nmrPipe  -fn ZF -auto                             \
       | nmrPipe  -fn FT   -auto                               \
       | nmrPipe  -fn PS -p0 0.0 -p1 0.0 -di               \
       | pipe2xyz -out lp/test%03d.ft31 -z -inPlace -ov -nofs


       xyz2pipe -in lp/test%03d.ft31 -y -verb               \
       | nmrPipe  -fn SP -off 0.5 -end 0.95 -pow 1 -c 0.5 \
       | nmrPipe  -fn LP -fb -ord 8                             \
       | nmrPipe  -fn ZF -auto                             \
       | nmrPipe  -fn FT  -auto                              \
       | nmrPipe  -fn PS -p0 0 -p1 0 -di               \
       | pipe2xyz -out lp/test%03d.ft32 -y  -ov

       xyz2pipe -in lp/test%03d.ft32 -z -verb               \
       | 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 -ord 8                          \
       | nmrPipe  -fn SP  -hdr                             \
       | nmrPipe  -fn ZF  -auto                            \
       | nmrPipe  -fn FT  -auto                                  \
       | nmrPipe  -fn PS  -hdr -di                         \
       | pipe2xyz -out lp/test%03d.ft33 -z



xyz2pipe -in lp/test%03d.ft33 | pipe2xyz -nv -out hncbcalp.nv




~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Mike Osborne                         | Tel:   514-496-7617 (O)
  McGill University                   | Fax:   514-496-5143
  Montreal, Quebec, H4P 2R2            |
  Canada                               | e_mail: mike.osborne@...
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                    __
                  .'  '.
                 :      :
                 | _  _ |
              .-.|(o)(o)|.-.        _._          _._
             ( ( | .--. | ) )     .',_ '.      .' _,'.
              '-/ (    ) \-'     / /' `\ \ __ / /' `\ \
               /   '--'   \     / /     \.'  './     \ \
               \ `"===="` /     `-`     : _  _ :      `-`
                `\      /'              |(o)(o)|
                  `\  /'                |      |
                  /`-.-`\_             /        \
            _..:;\._/V\_./:;.._       /   .--.   \
          .'/;:;:;\ /^\ /:;:;:\'.     |  (    )  |
         / /;:;:;:;\| |/:;:;:;:\ \    _\  '--'  /__
    jgs / /;:;:;:;:;\_/:;:;:;:;:\ \ .'  '-.__.-'   `-.

Sometimes, unexpected truncation in the final dimension is a sign
that the experiment was not fully completed.  This is especially
so with Bruker data, since an entire "blank" (or random) ser file
is created at the start of the experiment.

This kind of problem can usually be diagnosed by inspecting the
FID or interferograms to see how many data points were actually
measured in the final dimension.  The time-domain data can then
be converted again with reduced time-domain sizes (e.g. 3D -zN and -zT)
to compensate.

f

Hi Mike,

We finally got started with the acquisition of some 3D spectra on our
new 500.

Seeing your script made me wonder why you need such a big phase
correction in p0 and p1 of your observation domain:

xyz2pipe -in fid/hnca%03d.DAT -x  \
| nmrPipe  -fn PS -p1 27720  \
| nmrPipe  -fn SOL \
| nmrPipe  -fn PS -p1 -27720  \

Is your conversion script working the way it should, i.e., having the
proper -decim and -dspfvs (on our machine we get -decim 24 -dspfvs 12)
and using DQD in acquisition? It looks like the digital filter is not
properly processed during the conversion process.

René

PS I will need to get back to the NMRView stuff sometime, but currently
I am very much pulled into trying to get some (3,2) GFT sequences to
work so we can get the HNCA 3D information with only 3 2D spectra....
This idea is based on the Szyperski paper in JACS 2003, 125, 1385-1393
where he reports a (5,2) GFT seqeunce to get HA CA CO N HN information
with 15 2D spectra...

Hi Rene,
	 The large first order phase corrections are for shifting the water
signal to the center of the spectrum (we used frequency shifting) becuase
the SOL command will "suppress" signal at the carrier. A First order phase
correction on the time domain data is equivalent to a frequency shift on
the processed data. The DSPFVS and DECIM commands are correct and change
depending on the sweep width (I think!). I still cannot seem to get over
the problem I was having though!
Cheers
Mike

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Mike Osborne                         | Tel:   514-496-7617 (O)
  Biotechnology Research Institute     |        514-948-3405 (H)
  National Research Council Canada     |
  6100 Royalmount Avenue               | Fax:   514-496-5143
  Montreal, Quebec, H4P 2R2            |
  Canada                               | e_mail: mike.osborne@...
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                    __
                  .'  '.
                 :      :
                 | _  _ |
              .-.|(o)(o)|.-.        _._          _._
             ( ( | .--. | ) )     .',_ '.      .' _,'.
              '-/ (    ) \-'     / /' `\ \ __ / /' `\ \
               /   '--'   \     / /     \.'  './     \ \
               \ `"===="` /     `-`     : _  _ :      `-`
                `\      /'              |(o)(o)|
                  `\  /'                |      |
                  /`-.-`\_             /        \
            _..:;\._/V\_./:;.._       /   .--.   \
          .'/;:;:;\ /^\ /:;:;:\'.     |  (    )  |
         / /;:;:;:;\| |/:;:;:;:\ \    _\  '--'  /__
    jgs / /;:;:;:;:;\_/:;:;:;:;:\ \ .'  '-.__.-'   `-.


On Thu, 20 Mar 2003, René Kanters wrote:

> Hi Mike,
>
> We finally got started with the acquisition of some 3D spectra on our
> new 500.
>
> Seeing your script made me wonder why you need such a big phase
> correction in p0 and p1 of your observation domain:
>
> xyz2pipe -in fid/hnca%03d.DAT -x  \
> | nmrPipe  -fn PS -p1 27720  \
> | nmrPipe  -fn SOL \
> | nmrPipe  -fn PS -p1 -27720  \
>
> Is your conversion script working the way it should, i.e., having the
> proper -decim and -dspfvs (on our machine we get -decim 24 -dspfvs 12)
> and using DQD in acquisition? It looks like the digital filter is not
> properly processed during the conversion process.
>
> René
>
> PS I will need to get back to the NMRView stuff sometime, but currently
> I am very much pulled into trying to get some (3,2) GFT sequences to
> work so we can get the HNCA 3D information with only 3 2D spectra....
> This idea is based on the Szyperski paper in JACS 2003, 125, 1385-1393
> where he reports a (5,2) GFT seqeunce to get HA CA CO N HN information
> with 15 2D spectra...
>
>
> Yahoo! Groups Sponsor
>
> ADVERTISEMENT
> width
> width
> Your use of Yahoo! Groups is subject to the Yahoo! Terms of Service.
>

Hello Mike, don't you want to do the LP before SP in this section ...

>
>       xyz2pipe -in lp/test%03d.ft31 -y -verb               \
>       | nmrPipe  -fn SP -off 0.5 -end 0.95 -pow 1 -c 0.5 \
>       | nmrPipe  -fn LP -fb -ord 8                             \
>       | nmrPipe  -fn ZF -auto                             \
>       | nmrPipe  -fn FT  -auto                              \
>       | nmrPipe  -fn PS -p0 0 -p1 0 -di               \
>       | pipe2xyz -out lp/test%03d.ft32 -y  -ov
>

Take care, Sean

--
----------------------------------------------------
Sean Cahill, Dept. of Biochemistry NMR Facility
Albert Einstein College of Medicine
1300 Morris Park Ave, Bronx, NY  10461
Office: Ullmann-B8  E-mail: cahill@...
Phone: (718) 430-2035

Hi Everyone,
I just wanted to update on this message. bAsically the yT and ZT commands
were not half yN and zN. It seems (to me at keast) that this made little
difference with processing without doing HT  and the inv FT; hwoever, when
you need to do this the incorrect parameters for the fid size etc are
present.
Cheers and thanks for the repsonses
MIke

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Mike Osborne                         | Tel:   514-496-7617 (O)
  Biotechnology Research Institute     |        514-948-3405 (H)
  National Research Council Canada     |
  6100 Royalmount Avenue               | Fax:   514-496-5143
  Montreal, Quebec, H4P 2R2            |
  Canada                               | e_mail: mike.osborne@...
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                    __
                  .'  '.
                 :      :
                 | _  _ |
              .-.|(o)(o)|.-.        _._          _._
             ( ( | .--. | ) )     .',_ '.      .' _,'.
              '-/ (    ) \-'     / /' `\ \ __ / /' `\ \
               /   '--'   \     / /     \.'  './     \ \
               \ `"===="` /     `-`     : _  _ :      `-`
                `\      /'              |(o)(o)|
                  `\  /'                |      |
                  /`-.-`\_             /        \
            _..:;\._/V\_./:;.._       /   .--.   \
          .'/;:;:;\ /^\ /:;:;:\'.     |  (    )  |
         / /;:;:;:;\| |/:;:;:;:\ \    _\  '--'  /__
    jgs / /;:;:;:;:;\_/:;:;:;:;:\ \ .'  '-.__.-'   `-.


On Wed, 19 Mar 2003, Mike Osborne wrote:

>
> Hello all,
>       I was wondering if someone could help with a problem I am
> encountering processing an hncacb dataset acquired on a DRX-600. Basically
> I have severe truncation in both the indirect 15N and 13C dimensions. I am
> using Linear prediction to help overcome this. As recommended I make sure
> that the other dimensions are previously fourier transformed. My strategy
> has been to FT the 1H and 15N deminesions first and then FT the 13C
> dimension with LP. I then inverse FT retransform the 15N with LP (the
> script is attached below). However, the 15N dimension still showed severe
> truncation. When I compared the 15N dimension to the non-lp'd transform,
> the non lp'd one looked better. Somehow applying the inv ft and subsequent
> LP seemed to introduce further truncation in my case. I checked this by
> taking out the 15N vectors and apllying a 1d transfrom on them. IF the FID
> had not been previously transformed I managed to apply LP and the normal
> cosine bell window and force the fid to zero. However, when I took out a a
> FT'd 15N vector after HT and inv FT (as applied on the macro below) the
> fid was not forced to zero which is likely the reason for truncation.  Is
> there something I am doing wrong (I guess there must be). If anyone could
> give me some advice I would be grateful.
> Thanks in advance
> MIke
> ############################################################################
>
> xyz2pipe -in fid/hnca%03d.DAT -x  \
> | nmrPipe  -fn PS -p1 27720  \
> | nmrPipe  -fn SOL \
> | nmrPipe  -fn PS -p1 -27720  \
> | nmrPipe  -fn SP -off .5 -end .98 -pow 2 -c 0.5 \
> | nmrPipe  -fn ZF -auto \
> | nmrPipe  -fn FT -auto \
> | nmrPipe  -fn PS -p0 -87 -p1 0.0 -di -verb 2 \
> | nmrPipe  -fn EXT -x1 10.0ppm -xn 6.5ppm -sw \
> | pipe2xyz -out lp/test%03d.ft3 -x  -ov
>
> echo DONE.
>       xyz2pipe -in lp/test%03d.ft3 -z -verb               \
>       | nmrPipe  -fn SP -off 0.5 -end 0.95 -pow 1 -c 0.5  \
>       | nmrPipe  -fn ZF -auto                             \
>       | nmrPipe  -fn FT   -auto                               \
>       | nmrPipe  -fn PS -p0 0.0 -p1 0.0 -di               \
>       | pipe2xyz -out lp/test%03d.ft31 -z -inPlace -ov -nofs
>
>
>       xyz2pipe -in lp/test%03d.ft31 -y -verb               \
>       | nmrPipe  -fn SP -off 0.5 -end 0.95 -pow 1 -c 0.5 \
>       | nmrPipe  -fn LP -fb -ord 8                             \
>       | nmrPipe  -fn ZF -auto                             \
>       | nmrPipe  -fn FT  -auto                              \
>       | nmrPipe  -fn PS -p0 0 -p1 0 -di               \
>       | pipe2xyz -out lp/test%03d.ft32 -y  -ov
>
>       xyz2pipe -in lp/test%03d.ft32 -z -verb               \
>       | 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 -ord 8                          \
>       | nmrPipe  -fn SP  -hdr                             \
>       | nmrPipe  -fn ZF  -auto                            \
>       | nmrPipe  -fn FT  -auto                                  \
>       | nmrPipe  -fn PS  -hdr -di                         \
>       | pipe2xyz -out lp/test%03d.ft33 -z
>
>
>
> xyz2pipe -in lp/test%03d.ft33 | pipe2xyz -nv -out hncbcalp.nv
>
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Mike Osborne                         | Tel:   514-496-7617 (O)
> McGill University                   | Fax:   514-496-5143
> Montreal, Quebec, H4P 2R2            |
> Canada                               | e_mail: mike.osborne@...
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>                    __
>                  .'  '.
>                 :      :
>                 | _  _ |
>              .-.|(o)(o)|.-.        _._          _._
>             ( ( | .--. | ) )     .',_ '.      .' _,'.
>              '-/ (    ) \-'     / /' `\ \ __ / /' `\ \
>               /   '--'   \     / /     \.'  './     \ \
>               \ `"===="` /     `-`     : _  _ :      `-`
>                `\      /'              |(o)(o)|
>                  `\  /'                |      |
>                  /`-.-`\_             /        \
>            _..:;\._/V\_./:;.._       /   .--.   \
>          .'/;:;:;\ /^\ /:;:;:\'.     |  (    )  |
>         / /;:;:;:;\| |/:;:;:;:\ \    _\  '--'  /__
>    jgs / /;:;:;:;:;\_/:;:;:;:;:\ \ .'  '-.__.-'   `-.
>
>
>
>
>
> Yahoo! Groups Sponsor
>
> ADVERTISEMENT
> width
> width
> Your use of Yahoo! Groups is subject to the Yahoo! Terms of Service.
>

I installed succefully NMRPipe on Macos X.2.4 but I got that

Xlib:  extension "XFree86-Misc" missing on display ":0.0".
X Error of failed request:  86
   Major opcode of failed request:  51 (X_SetFontPath)
   Serial number of failed request:  8
   Current serial number in output stream:  10
X Error of failed request:  86
   Major opcode of failed request:  51 (X_SetFontPath)
   Serial number of failed request:  8
   Current serial number in output stream:  10

I run X11 from Apple. Probably this error is related to that. How can I fix
that ?
Laurent
--
Dr Laurent Ettouati
Universite Claude Bernard Lyon I
Institut des Sciences Pharmaceutiques et Biologiques
Laboratoire de Chimie therapeutique
8 avenue Rockefeller
69373 Lyon cedex 08 France
Ph +33 (0)4 78 77 70 82 - Fax  +33 (0)4 78 77 75 49
E-mail. : ettouati@...

Hello

Could anyone please tell me how to use NMR pipe to convert the data from
Bruker to Varian software?

Viji

Vijayalekshmi Sarojini
Dept of Chemistry
Rensselaer Polytechnic Institute
Troy, NY-12180
Phone: 00 1 518 276 8173

no

:)

From: Laurent Ettouati <Laurent.Ettouati@...>
Reply-To: nmrpipe@yahoogroups.com
Date: Thu, 27 Mar 2003 17:32:59 +0100
To: <nmrpipe@yahoogroups.com>
Subject: [nmrpipe] Nmrpipe install and  X11 from Apple

I installed succefully NMRPipe on Macos X.2.4 but I got that

Xlib:  extension "XFree86-Misc" missing on display ":0.0".
X Error of failed request:  86
  Major opcode of failed request:  51 (X_SetFontPath)
  Serial number of failed request:  8
  Current serial number in output stream:  10
X Error of failed request:  86
  Major opcode of failed request:  51 (X_SetFontPath)
  Serial number of failed request:  8
  Current serial number in output stream:  10

I run X11 from Apple. Probably this error is related to that. How can I fix
that ?
Laurent
--
Dr Laurent Ettouati
Universite Claude Bernard Lyon I
Institut des Sciences Pharmaceutiques et Biologiques
Laboratoire de Chimie therapeutique
8 avenue Rockefeller
69373 Lyon cedex 08 France
Ph +33 (0)4 78 77 70 82 - Fax  +33 (0)4 78 77 75 49
E-mail. : ettouati@...


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Viji,

I assume that you have VNMR.  Why not use VNMR to convert Bruker data to
Varian readable format?  There is a vnmr macro "convertbru" that might meet
your needs.  I am no longer familiar with what it does, but you can look in
AMMRL webpage, or simply read VNMR manpages.

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: Vijayalekshmi [mailto:vijays@...]
Sent: Thursday, March 27, 2003 2:37 PM
To: nmrpipe@yahoogroups.com
Subject: [nmrpipe] NMR pipe: Bruker to Varian


Hello

Could anyone please tell me how to use NMR pipe to convert the data from
Bruker to Varian software?

Viji

Vijayalekshmi Sarojini
Dept of Chemistry
Rensselaer Polytechnic Institute
Troy, NY-12180
Phone: 00 1 518 276 8173





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Hello

I am sure this is a trivial question, but I am not used to nmrPipe yet, and
cannot seem to find this in the man pages. How do I get 1D projections from a
2D spectrum?

Many thanks for an answer!

Jakob

--
____________________________________
Dr. Jakob J. Lopez

Johann Wolfgang Goethe University
Institute for Biophysical Chemistry
Biocentre, N202, Room 0.04
Marie-Curie Str. 9
D-60439 Frankfurt am Main

email:   lopez@...
phone:  work    ++49 69 798 29902
            mobile  ++49 171 456 9264

Hi Jakob,

You find some TCL scripts for projections on the executable path
in the "com" directory: proj2D.tcl and proj3D.tcl

	 Cheerful Regards,

	 Frank

proj2D.tcl -help

proj2D.tcl: Create 1D projections from 2D data.
  -in inName [test.ft2]         Name of 2D Input.
  -skyline                      Skyline Projection (Default).
  -sum                          Summation projection.

Dear Frank,

Sometime back I had asked for some help in making stack pots of 1D
spectra processed using NMRPipe.  Do you have any suggestions?


Siddhartha



On Thu, 3 Apr 2003, Frank Delaglio wrote:

> Hi Jakob,
>
> You find some TCL scripts for projections on the executable path
> in the "com" directory: proj2D.tcl and proj3D.tcl
>
>  Cheerful Regards,
>
>  Frank
>
> proj2D.tcl -help
>
> proj2D.tcl: Create 1D projections from 2D data.
>  -in inName [test.ft2]         Name of 2D Input.
>  -skyline                      Skyline Projection (Default).
>  -sum                          Summation projection.
>
>
>
>
>
> Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
>
>

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

Tel: 80-3942839
      80-3942713
Fax: 80-3600535

Hello everybody,

I have some problems in processing  noesyhsqc tocsyHsqc from Bruker DRX
800MHZ.
Does anyone have nmrpipe script for processing these data.
thanks

Hi everyone,
I use new Sun machine (Blade 2000, two processors) running Solaris 9 (64-
bit system). I have installed precompiled version of Nmrpipe (sol).
However, the performance is not such I expect. Don't you have any
suggestion where could be the problem?
Cheers and thanks for the repsonses.
 
Vaclav Veverka
NMRc, Leicester

Hi,

I am trying to use a macro to add and subtract two 2D slices in a
pseudo 3D (3,2)GFT spectrum. The statement I try is (in a pipeline):

nmrPipe -fn MAC 32GFT \

I keep getting the message:

XYZ2Pipe Partition: Plane 1 to 2 of 2
NMRPipe Error extracting arguments.
NMRPipe Aborting with null header.
NMRPipe Error Status: 1
NMRPipe Function MAC

What I am doing wrong here?

Three asides:
1) the bruker conversion program seems to think that a (pseudo) 3D
file with only 2 2D spectra in them is a 2D file. I know that only 2
points can not be FT'd, but I don't have to FT them but add/subtract
them later.
2) do I have to do something special with the -noRd and -noWr
options, since the macro reads and writes?
3) Is there somewhere more extensive information about the macro
language and the functions in nmrPipe (besides `man nmrPipe`?).

Thanks,
René Kanters

PS The 32GFT.M file exists in the /usr/local/NMRPipe/nmrtext
directory and is basically a slight modification of the echo-antiecho
unshuffling:
if (!(sliceCode != 1))
    {
     exit( 0 );
    };

float sumR[size], sumI[size], difR[size], difI[size];

(void) dReadB( inUnit, rdata, wordLen*size );
(void) dReadB( inUnit, idata, wordLen*size );
(void) dReadB( inUnit, difR,  wordLen*size );
(void) dReadB( inUnit, difI,  wordLen*size );

(void) vvCopy( sumR, rdata, size );
(void) vvCopy( sumI, idata, size );

(void) vvAdd( sumR, difR, size );
(void) vvAdd( sumI, difI, size );
(void) vvSub( difR, rdata, size );
(void) vvSub( difI, idata, size );

(void) vNeg( difR, size );
(void) vNeg( difI, size );

(void) dWrite( outUnit, sumR, wordLen*size );
(void) dWrite( outUnit, sumI, wordLen*size );
(void) dWrite( outUnit, difI, wordLen*size );
(void) dWrite( outUnit, difR, wordLen*size );

Hi,

I made a mistake in my macro for the previous message. I should be
added and subtracting 2D slices (z), not 1D slices (y). But the question on=
  how to avoid the errors I mentioned in my previous message reamins.

What I have are 2 2D datasets stored in a 3D dataset. The first has a
cosine modulated co-evolution of Ca on N (acquired echo-antiecho) the
second one has the sine modulated signal. What I need to do is
perform a 90 phase shift on the second one, relative to the phase of
the first one, and in one case add it to the first 2D, in another
case subtract it, in order to get 2D datasets with peaks at N + C and
N - C respectively, where C is the Ca frequency away from the 13C
offset.

I think that it is very similar to the echo-antiecho type shuffling
(but in Z).

Any suggestions?
Thanks,
René Kanters

Greetings all ...

A little more about the macro language can be found in the "MAC" man page.

As Rene suggestion, NMRPipe macros which read and write their own data
(via dRead and dWrite functions) should use the "-noRd" and "-noWr"
arguments ... this tells NMRPipe not to read and write data on
behalf of the macro.

As to conversion parameters for Bruker pseudo-3D: if the data are actually
acquired as a series of 2D planes rather than interleaved vectors,
you can always reset the number of dimensions to "3" manually
and fill in parameters for a pseudo Z axis. In particular,
this would give you the chance to process the planes of the
result seperately if desired, and then recombine them
with the "addNMR" program to form sums and differences.

By the way, as to forming combinations of data, the following
are available for your enjoyment:

1. The stand-alone program "addNMR" (try addNMR -help) which can
    combine NMRPipe format spectra and FIDs to form sums
    and differences.

2. NMRWish TCL scripts (see com/peCOSY.tcl for an example).

3. Macros via the nmrPipe MAC function or the stand-alone
    macro interpreter "M".

4. NMRPipe 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 \

         will form a spectrum from the difference of each pair of
         adjacent 1D slices.

5. NMRPipe 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.

Hi,

I just ran into a error message when the bruker conversion program read the=
  parameters. The error occurred while parsing the hncogp3d.3 pulseprogram, w=
hen it encountered the line

   "if (d30 > d21-p16-d16-4u) { d28=3u; }"

it turns out that the program first strips everything after the ; and later=
  tries to balance the " (which it can't do anymore).

So if you see a message like like I did, you may want to remove the ; from =
that line (or ones like that).

Cheers,
René

... most recent version of "bruker" seems to be able to handle
     the problematic construct that Rene was kind enough to
     illustrate ...

cheerful regards,

big fd

   "if (d30 > d21-p16-d16-4u) { d28=3u; }"

In response to the recent comments about running nmrPipe on a Sun Blade
2000, I thought I would add our experience.

When carrying out the identical simple 2D macro on a Sun Blade 2000 with 2
900 MHz processors running Solaris 8 and on an SGI Octane 2 with 2 400
MHz R12000 processors running Irix 6.5, I found the SGI to be about three
times as fast. Running the macro under the time command the results were

                 Sun Blade               SGI

User              2.11s                 1.759s

Kernel            0.49s                 0.95s

Elapsed           7.76s                 2.31s

CPU               33.3%                116.8%

There appears to be a more efficient use of CPU resources on the SGI. The
fact that the CPU use is given as more than 100% for the SGI indicates
that it is using the second processor as well. This has to do with the way
the operating system handles the commands, since I had done nothing to set
up nmrPipe to use more than one processor. I don't know whether the
difference reflects hardware, operating system or compilation issues.

David Live                              Office 1-130 BSBE Bldg
Research Associate Professor            Phone 612-626-3805
Structural NMR Resource                 Fax   612-624-5121
Biochemistry Department
University of Minnesota
6-155 Jackson Hall
321 Church St. SE
Minneapolis, MN 55455

Hello!

Can anybody please send me the scripts for processing the N15-HSQC-IPAP in
both ways aquired on Varian 600 Unity plus and Bruker Avance 500.

Thanking in advance...

	 Neel

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D-230                               +91-22-2215-2182(direct, NMR lab)
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Mumbai 400 005 INDIA                           Mumbai 400 005 INDIA

Homepage  : http://www.tifr.res.in/~neelsb
Cell: +91-9869115302
**********************************************************************

Thanks David ...

Here's a comment though: a short 2D processing scheme may not be
a good choice for a processing speed benchmark.  A 3D case that
takes a more substantial amount of time is a better choice ...

IPAP conversion and processing schemes can differ substantially
based on:

1. Whether the data are gradient enhanced.

2. Whether the IP/AP loop is the innermost one of the pulse sequence,
    or the real/imaginary loop is the inner one.

Generally, the nmrPipe function "COADD" is used to select or combine
the IP/AP channels.

I find it helpful to process the IP and AP channels separately,
and then combine them after processing.  This makes it possible
to inspect the data to choose a scaling factor that will lead
to the best IP/AP cancelation.

The stand-alone program "addNMR" can also be used to re-combine
processed IP or AP data.

Some examples are below.


	 Cheerful Regards,

	 big fd

-------------------------------------------------------------------------
If the IP/AP channel is in the innermost loop, the selection or
combination of AP/IP data should be done at the start of processing:

nmrPipe -in ./test.fid                                  \
| nmrPipe  -fn COADD -cList 1 -1.11 -axis Y -time       \
| nmrPipe  -fn SP -off 0.4 -end 0.98 -pow 2.0 -c 1.0    \
| nmrPipe  -fn ZF -size 4096                            \
| nmrPipe  -fn FT -verb                                 \
| nmrPipe  -fn PS -p0 -80.0 -p1 -180.0 -di              \
| nmrPipe  -fn EXT -x1 10ppm -xn 6.0ppm -sw             \
| nmrPipe  -fn TP                                       \
| nmrPipe  -fn SP -off 0.4 -end 0.98 -pow 1.0 -c 1      \
| nmrPipe  -fn ZF -size 4096                            \
| nmrPipe  -fn FT -verb                                 \
| nmrPipe  -fn PS -p0 -90 -p1 180.0 -di                 \
| nmrPipe  -fn CS -rs -1ppm -neg -sw                    \
| nmrPipe  -fn TP                                       \
    -ov -out A-B.DAT

-------------------------------------------------------------------------
If the IP/AP loop is outside the real/imaginary loop, the selection
of combination of AP/IP data should be done after the direct dimension
is processed.

Note that in this case, one IP/AP channel is 90 degrees out of phase
with respect to the other:

#!/bin/csh

var2pipe -in ./fid -noaswap  \
   -xN              1024  -yN               484  \
   -xT               512  -yT               242  \
   -xMODE        Complex  -yMODE        Complex  \
   -xSW         6999.738  -ySW         2000.000  \
   -xOBS         499.628  -yOBS          50.633  \
   -xCAR           4.773  -yCAR         118.860  \
   -xLAB              HN  -yLAB               N  \
   -ndim               2  -aq2D          States  \
   -out ./test.fid -verb -ov

nmrPipe -in test.fid \
| nmrPipe  -fn SOL                                    \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5    \
| nmrPipe  -fn ZF -auto                               \
| nmrPipe  -fn FT                                     \
| nmrPipe  -fn PS -p0 177 -p1 0.0 -di                 \
| nmrPipe  -fn EXT -left -sw -verb                    \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn COADD -cList 1 0 -time                 \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5    \
| nmrPipe  -fn ZF -auto                               \
| nmrPipe  -fn FT                                     \
| nmrPipe  -fn PS -p0 0 -p1 0 -di                     \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn POLY -auto                             \
    -verb -ov -out A.ft2

nmrPipe -in test.fid \
| nmrPipe  -fn SOL                                    \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5    \
| nmrPipe  -fn ZF -auto                               \
| nmrPipe  -fn FT                                     \
| nmrPipe  -fn PS -p0 177 -p1 0.0 -di                 \
| nmrPipe  -fn EXT -left -sw -verb                    \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn COADD -cList 0 1 -time                 \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5    \
| nmrPipe  -fn ZF -auto                               \
| nmrPipe  -fn FT                                     \
| nmrPipe  -fn PS -p0 -90 -p1 0 -di                   \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn POLY -auto                             \
    -verb -ov -out B.ft2

addNMR -in1 A.ft2 -in2 B.ft2 -out A+B.ft2 -c1 1.0 -c2 1.25 -add
addNMR -in1 A.ft2 -in2 B.ft2 -out A-B.ft2 -c1 1.0 -c2 1.25 -sub