AHOY!!!

Ok, "don't like to play with each other" is maybe not the most
specific way to describe the problem, so I can't offer a specific
answer for sure.

In other cases, such as with NMRPipe and NMRView, which incidentally
love to play with each other, there are nevertheless sometimes
problems regarding settings for TCL/TK.

The most recently posted version of NMRPipe uses "private" environment
variables NMRPIPE_TCL_LIB and NMRPIPE_TK_LIB over the generic ones
(TCL_LIBRARY and TK_LIBRARY) used by other TCL/TK-based applications.

This new NMRPipe environment scheme has not been widely tested,
so it might yet require adjustment.  Accordingly, the NMRPipe initialization
script still sets both versions of these variables, but it should be
possible to adjust it so that it only sets the "private" versions,
so as not to interfere with other software.

I could also imagine that problems could arise regarding
dynamic link libraries used by different software systems.
There haven't been any reports of this that I know of,
but depending on the operating system, an NMRPipe installation
might have its own dynamic link libraries for:
"libtcl" "libtk" "libBLT24" "libxview" and "libolgx"

Problems of this sort might be approached by resetting
the system link library path (system dependent: LD_LIBRARY_PATH
DYLD_LIBRARY_PATH SHLIB_PATH) when appropriate.

On Tue, 6 Feb 2007, djbuijs wrote:

> Hello,
>
> I'm trying to get my configurations streamlined and I've noticed that
> with default settings, nmrPipe, Aria2.1 and CCPNMR don't like to play
> with each other.=20
>
> Does anyone have a single .cshrc that works with all of them, or are
> people writing custom startup scripts for each?
>
> I can get all of these programs working independently, if I remove the
> environment settings for the others, but there has to be a way to get
> them all working together.=20
>
> Any thoughts?
>
> Dan Buijs
> Health Canada
>
>

Hello,

Thanks Frank, that did it. The most recent version of nmrpipe works
with Aria2.1 and CCPNMR Analysis with a single .cshrc file, with some
small modifications.

I am using the most recent version of Fedora Core 6, which has all the
pre-reqs for CCPNMR and Aria included in its base repositories. Both
of these applications are ok with Fedora's TCL/TK 8.4 and Python 2.4.

As Frank says, nmrpipe seems to be ok with just its own private
variables.

I removed the entries for BLT_LIBRARY, TCLPATH, TCL_LIBRARY, and
TK_LIBRARY from nmrInit.linux9.com, as well as commenting out all the
alias commands. I also added the NMR_CONT variable here.

The LD_LIBRARY_PATH variable didn't need adjustment on my system (so far).

I had to add explicit TK_LIBRARY and TCL_LIBRARY pointers in the
.cshrc (you don't have to if you're not sourcing nmrInit.linux9.com,
oddly enough).

With these minor adjustments, everything seems to work without any
further customisation. I can send my full configuration details to
anyone who e-mails me directly.

Cheers,

Dan Buijs
Health Canada
--- In nmrpipe@yahoogroups.com, "Frank Delaglio, Ph.D. (CONTRACTOR)"
<delaglio@...> wrote:
>
>
> AHOY!!!
>
> Ok, "don't like to play with each other" is maybe not the most
> specific way to describe the problem, so I can't offer a specific
> answer for sure.
>
> In other cases, such as with NMRPipe and NMRView, which incidentally
> love to play with each other, there are nevertheless sometimes
> problems regarding settings for TCL/TK.
>
> The most recently posted version of NMRPipe uses "private" environment
> variables NMRPIPE_TCL_LIB and NMRPIPE_TK_LIB over the generic ones
> (TCL_LIBRARY and TK_LIBRARY) used by other TCL/TK-based applications.
>
> This new NMRPipe environment scheme has not been widely tested,
> so it might yet require adjustment.  Accordingly, the NMRPipe
initialization
> script still sets both versions of these variables, but it should be
> possible to adjust it so that it only sets the "private" versions,
> so as not to interfere with other software.
>
> I could also imagine that problems could arise regarding
> dynamic link libraries used by different software systems.
> There haven't been any reports of this that I know of,
> but depending on the operating system, an NMRPipe installation
> might have its own dynamic link libraries for:
> "libtcl" "libtk" "libBLT24" "libxview" and "libolgx"
>
> Problems of this sort might be approached by resetting
> the system link library path (system dependent: LD_LIBRARY_PATH
> DYLD_LIBRARY_PATH SHLIB_PATH) when appropriate.
>
> On Tue, 6 Feb 2007, djbuijs wrote:
>
> > Hello,
> >
> > I'm trying to get my configurations streamlined and I've noticed that
> > with default settings, nmrPipe, Aria2.1 and CCPNMR don't like to play
> > with each other.=20
> >
> > Does anyone have a single .cshrc that works with all of them, or are
> > people writing custom startup scripts for each?
> >
> > I can get all of these programs working independently, if I remove the
> > environment settings for the others, but there has to be a way to get
> > them all working together.=20
> >
> > Any thoughts?
> >
> > Dan Buijs
> > Health Canada
> >
> >
>

Dear all,

When I process Varian data, I use a macro
(e.g.: |   nmrPipe  -fn MAC -macro $NMRTXT/ranceZ.M -noRd -noWr )
immediately after the arguments of var2pipe almost under all
circumstances.

On how to decide which macro should be used, I usually reference to
the processing scripts of previous data in our lab. but I don't know
the reason why I should use the MAC.

All the previous data in our lab were collected on Varian
spectrometers. Recently, one member of our lab collected a set of data
on a Bruker machine.

He processed the 3D data following the scheme below (no MACs were used):

1. Read the parameters of the data with "NMRPipe Conversion Utility
[Bruker(NIH)]". Check the DECIM, DSPFVS, TD, FnMODE, SW, SFO1 values
and save the fid.com files. Then execute "fid.com".

2. Adjust the phases of xy and xz planes in NMRDraw.
File > Macro Edit > Process 2D > XY Plane of 3D  and XZ Plane of 3D

when executing the script, nmrPipe prompted him to use the -alt flag
for the function  FT.

then he added the -alt flag after "| nmrPipe  -fn FT" and executed the
script again.

3. Edit a 3D processing script and execute the script.


Some of the spectra are now displayed properly in NMRDraw, but some
are not.


Should we use MAC options? And How to determine which MAC we should use?

This set of data were collected using standard Bruker pulses.

The 3D spectra involve HNCACB, CBCA(CO)NH, HNCO, HN(CA)CO, C(CCO)NH,
H(CCCO)NH, CCH-COSY, HCCH-TOCSY, 15N-NOESY-HSQC and 13C-NOESY-HSQC.


Regards,

Liwen

Dear Colleagues,

I am trying to determine amide pKa from chemical shift
titration of 15N. Does nmrPipe have a way to do the
curve fitting to extract the pKa from titration data?
Or anyone has or knows a program running on linux  box
to do the curve fitting.

Thanks a lot.

--- djbuijs <dbuijs@...> wrote:

> Hello,
>
> I'm trying to get my configurations streamlined and
> I've noticed that
> with default settings, nmrPipe, Aria2.1 and CCPNMR
> don't like to play
> with each other.
>
> Does anyone have a single .cshrc that works with all
> of them, or are
> people writing custom startup scripts for each?
>
> I can get all of these programs working
> independently, if I remove the
> environment settings for the others, but there has
> to be a way to get
> them all working together.
>
> Any thoughts?
>
> Dan Buijs
> Health Canada
>
>

dear Weidong,

>       I am trying to determine amide pKa from chemical
>      shift
>       titration of 15N.

Do you really mean the pKa of protein backbone amides? Or
do you mean to use backbone amides as reporters of nearby
charged side chains (in which case you will have to be
very cautious in the interpretation, there are much better
experiments for that measuring 13C shifts)?

>       Or anyone has or knows a program running on linux
>       box
>       to do the curve fitting.

XMGR would be an obvious suggestion, but the fitting may
not be transparent (I haven't checked). I am sure other
people have good suggestions. If you have access to MATLAB
or mathematica then you would have full control over your
procedure (simplex, steepest descent, and many other
algorithms). Should be no problem.

frans



Dr. Frans Mulder
Biophysical Chemistry
Groningen University
Nijenborgh 4
9747 AG  Groningen
the Netherlands

tel: +31-50-3634339
fax: +31-50-3634398
email: f.a.a.mulder@...

Hi,

concerning xmgr: the descendant of XMGR seems to be Grace; you can download at
http://plasma-gate.weizmann.ac.il/Grace/

Bye,
Marco


Citando "F.A.A.Mulder" <f.a.a.mulder@...>:

>
> dear Weidong,
>
>>       I am trying to determine amide pKa from chemical
>>      shift
>>       titration of 15N.
>
> Do you really mean the pKa of protein backbone amides? Or
> do you mean to use backbone amides as reporters of nearby
> charged side chains (in which case you will have to be
> very cautious in the interpretation, there are much better
> experiments for that measuring 13C shifts)?
>
>>       Or anyone has or knows a program running on linux
>>       box
>>       to do the curve fitting.
>
> XMGR would be an obvious suggestion, but the fitting may
> not be transparent (I haven't checked). I am sure other
> people have good suggestions. If you have access to MATLAB
> or mathematica then you would have full control over your
> procedure (simplex, steepest descent, and many other
> algorithms). Should be no problem.
>
> frans
>
>
>
> Dr. Frans Mulder
> Biophysical Chemistry
> Groningen University
> Nijenborgh 4
> 9747 AG  Groningen
> the Netherlands
>
> tel: +31-50-3634339
> fax: +31-50-3634398
> email: f.a.a.mulder@...
>



Dr.Marco Sette, Ph.D.

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

Dear Marco,

Thank you for providing me this information. I already
downloaded grace 5.1.20. I think it should be good
enough for my purpose.

Best wishes,

--- sette@... wrote:

>
> Hi,
>
> concerning xmgr: the descendant of XMGR seems to be
> Grace; you can download at
> http://plasma-gate.weizmann.ac.il/Grace/
>
> Bye,
> Marco
>
>
> Citando "F.A.A.Mulder" <f.a.a.mulder@...>:
>
> >
> > dear Weidong,
> >
> >>       I am trying to determine amide pKa from
> chemical
> >>      shift
> >>       titration of 15N.
> >
> > Do you really mean the pKa of protein backbone
> amides? Or
> > do you mean to use backbone amides as reporters of
> nearby
> > charged side chains (in which case you will have
> to be
> > very cautious in the interpretation, there are
> much better
> > experiments for that measuring 13C shifts)?
> >
> >>       Or anyone has or knows a program running on
> linux
> >>       box
> >>       to do the curve fitting.
> >
> > XMGR would be an obvious suggestion, but the
> fitting may
> > not be transparent (I haven't checked). I am sure
> other
> > people have good suggestions. If you have access
> to MATLAB
> > or mathematica then you would have full control
> over your
> > procedure (simplex, steepest descent, and many
> other
> > algorithms). Should be no problem.
> >
> > frans
> >
> >
> >
> > Dr. Frans Mulder
> > Biophysical Chemistry
> > Groningen University
> > Nijenborgh 4
> > 9747 AG  Groningen
> > the Netherlands
> >
> > tel: +31-50-3634339
> > fax: +31-50-3634398
> > email: f.a.a.mulder@...
> >
>
>
>
> Dr.Marco Sette, Ph.D.
>
> Department of Chemical Sciences and Technology
> University of Rome, "Tor Vergata"
> via della Ricerca Scientifica, 00133, Rome, Italy
> e-mail:        sette@...
> Tel.:          +39-0672594424
> Fax:           +39-0672594328
>
>
>


Dr. Weidong Hu
Immunology Division, BRI, City of Hope
1500 Duarte Rd., Duarte, CA 91010
Tel: 626 359-8111, ext: 63416
Fax: 626 301-8186

I'm a new nmrpipe user
I'm trying to determine the noise in 1D spectrum. Is there any
function to find out the noise level or how I can find out.

Regards

Sudhakar

Greetings all,

NMRPipe includes a general-purpose XY fitting script called
"fitXY.tcl", which includes estimation of fitted parameter
errors via Monte Carlo analysis.

The are also NMRPipe tools specifically for extracting chemical
shift evolution data from HSQC series.  If these are of interest,
write directly to: delaglio@...

	 Cheerful Regards,

	 big fd


On Tue, 13 Feb 2007, Weidong Hu wrote:

> Dear Marco,
>
> Thank you for providing me this information. I already
> downloaded grace 5.1.20. I think it should be good
> enough for my purpose.
>
> Best wishes,
>
> --- sette@... wrote:
>
> >
> > Hi,
> >
> > concerning xmgr: the descendant of XMGR seems to be
> > Grace; you can download at
> > http://plasma-gate.weizmann.ac.il/Grace/
> >
> > Bye,
> > Marco
> >
> >
> > Citando "F.A.A.Mulder" <f.a.a.mulder@...>:
> >
> > >
> > > dear Weidong,
> > >
> > >>       I am trying to determine amide pKa from
> > chemical
> > >>      shift
> > >>       titration of 15N.
> > >
> > > Do you really mean the pKa of protein backbone
> > amides? Or
> > > do you mean to use backbone amides as reporters of
> > nearby
> > > charged side chains (in which case you will have
> > to be
> > > very cautious in the interpretation, there are
> > much better
> > > experiments for that measuring 13C shifts)?
> > >
> > >>       Or anyone has or knows a program running on
> > linux
> > >>       box
> > >>       to do the curve fitting.
> > >
> > > XMGR would be an obvious suggestion, but the
> > fitting may
> > > not be transparent (I haven't checked). I am sure
> > other
> > > people have good suggestions. If you have access
> > to MATLAB
> > > or mathematica then you would have full control
> > over your
> > > procedure (simplex, steepest descent, and many
> > other
> > > algorithms). Should be no problem.
> > >
> > > frans
> > >
> > >
> > >
> > > Dr. Frans Mulder
> > > Biophysical Chemistry
> > > Groningen University
> > > Nijenborgh 4
> > > 9747 AG  Groningen
> > > the Netherlands
> > >
> > > tel: +31-50-3634339
> > > fax: +31-50-3634398
> > > email: f.a.a.mulder@...
> > >
> >
> >
> >
> > Dr.Marco Sette, Ph.D.
> >
> > Department of Chemical Sciences and Technology
> > University of Rome, "Tor Vergata"
> > via della Ricerca Scientifica, 00133, Rome, Italy
> > e-mail:        sette@...
> > Tel.:          +39-0672594424
> > Fax:           +39-0672594328
> >
> >
> >
>
>
> Dr. Weidong Hu
> Immunology Division, BRI, City of Hope
> 1500 Duarte Rd., Duarte, CA 91010
> Tel: 626 359-8111, ext: 63416
> Fax: 626 301-8186
>

Ahoy!!

There are a few ways, and the automated methods tend to be better for
2D/3D then they are with 1D, depending on the nature of the spectrum.

1. Automated, stand-alone, rough estimate (also for 2D-3D data):

    showApod -in test1d.dat

REMARK Effect of Processing on Peak Parameters and Noise for test.dat
REMARK Automated Noise Std Dev in Processed Data: 1492.19
REMARK Noise Std Dev Before Processing H1: 48.3569

VARS   AXIS LABEL  TSIZE FSIZE LW_ADJ LW_FINAL HI_FACTOR VOL_FACTOR SIGMA_FACTOR
FORMAT %s   %-8s   %4d   %4d   %7.4f  %7.4f    %.4e      %.4e       %.4e

   X    H1      8192  16384 2.5718 4.8340   9.0766e-04 1.2207e-04 3.2407e-02

2. Automated estimate within nmrDraw: use the menu option
    "Draw/Estimate Noise".

3. Manual Noise Estimate in nmrDraw:

    i.   Use "Mouse/1D Zoom" to get a zoom box (use "2D Zoom" for 2D data)

    ii.  Adjust the zoom box so that it surrounds a region of
         baseline only.

    iii. Move the mouse pointer to the right-hand border
         of the nmrDraw window, just outside the spectral
         drawing area.  Then click the MIDDLE mouse button,
         which will generate a histogram and statistical report
         of the selected region; the "SDev" value is the standard
         deviation of the selected region:

   -292.090 |  25 |***
   -154.351 |  71 |*********
    -16.612 | 124 |****************
    121.127 | 264 |**********************************
    258.866 | 350 |*********************************************
    396.605 | 460 |************************************************************
    534.344 | 413 |*****************************************************
    672.083 | 334 |*******************************************
    809.822 | 225 |*****************************
    947.561 | 112 |**************
   1085.300 |  57 |*******
   1223.039 |  21 |**
   1360.778 |   7 |
   1498.516 |   7 |
   1636.255 |   5 |
   1773.994 |   3 |
   1911.733 |   5 |
   2049.472 |   7 |
   2187.211 |   3 |
One * = 7.67 obs; 2493 Total Points;
Min: -292.09 Max: 2324.95 Sum: 1.33944e+06 Avg: 537.279
SDev: 334.546 Var: 111921  ADev: 254.126
Skew: 0.795512 Kurt: 2.62328 Chi2: 21063.5 PNorm: 0



A On Thu, 15 Feb 2007, psudhakar07 wrote:

> I'm a new nmrpipe user
> I'm trying to determine the noise in 1D spectrum. Is there any
> function to find out the noise level or how I can find out.
>
> Regards
>
> Sudhakar
>
>

Thankyou very much

Sudhakar

--- In nmrpipe@yahoogroups.com, "Frank Delaglio, Ph.D. (CONTRACTOR)"
<delaglio@...> wrote:
>
>
> Ahoy!!
>
> There are a few ways, and the automated methods tend to be better for
> 2D/3D then they are with 1D, depending on the nature of the spectrum.
>
> 1. Automated, stand-alone, rough estimate (also for 2D-3D data):
>
>    showApod -in test1d.dat
>
> REMARK Effect of Processing on Peak Parameters and Noise for test.dat
> REMARK Automated Noise Std Dev in Processed Data: 1492.19
> REMARK Noise Std Dev Before Processing H1: 48.3569
>
> VARS   AXIS LABEL  TSIZE FSIZE LW_ADJ LW_FINAL HI_FACTOR VOL_FACTOR
SIGMA_FACTOR
> FORMAT %s   %-8s   %4d   %4d   %7.4f  %7.4f    %.4e      %.4e       %.4e
>
>   X    H1      8192  16384 2.5718 4.8340   9.0766e-04 1.2207e-04
3.2407e-02
>
> 2. Automated estimate within nmrDraw: use the menu option
>    "Draw/Estimate Noise".
>
> 3. Manual Noise Estimate in nmrDraw:
>
>    i.   Use "Mouse/1D Zoom" to get a zoom box (use "2D Zoom" for 2D
data)
>
>    ii.  Adjust the zoom box so that it surrounds a region of
>         baseline only.
>
>    iii. Move the mouse pointer to the right-hand border
>         of the nmrDraw window, just outside the spectral
>         drawing area.  Then click the MIDDLE mouse button,
>         which will generate a histogram and statistical report
>         of the selected region; the "SDev" value is the standard
>         deviation of the selected region:
>
>   -292.090 |  25 |***
>   -154.351 |  71 |*********
>    -16.612 | 124 |****************
>    121.127 | 264 |**********************************
>    258.866 | 350 |*********************************************
>    396.605 | 460
|************************************************************
>    534.344 | 413 |*****************************************************
>    672.083 | 334 |*******************************************
>    809.822 | 225 |*****************************
>    947.561 | 112 |**************
>   1085.300 |  57 |*******
>   1223.039 |  21 |**
>   1360.778 |   7 |
>   1498.516 |   7 |
>   1636.255 |   5 |
>   1773.994 |   3 |
>   1911.733 |   5 |
>   2049.472 |   7 |
>   2187.211 |   3 |
> One * = 7.67 obs; 2493 Total Points;
> Min: -292.09 Max: 2324.95 Sum: 1.33944e+06 Avg: 537.279
> SDev: 334.546 Var: 111921  ADev: 254.126
> Skew: 0.795512 Kurt: 2.62328 Chi2: 21063.5 PNorm: 0
>
>
>
> A On Thu, 15 Feb 2007, psudhakar07 wrote:
>
> > I'm a new nmrpipe user
> > I'm trying to determine the noise in 1D spectrum. Is there any
> > function to find out the noise level or how I can find out.
> >
> > Regards
> >
> > Sudhakar
> >
> >
>

Dear All

Does anyone know if we can get the 1D spectrum (F2 or
F1 dimension, which can be saved as .ft1 ) from a 2D
(or even 3D) fid ?

Thank you!

Lei



________________________________________________________________________________\
____
Be a PS3 game guru.
Get your game face on with the latest PS3 news and previews at Yahoo! Games.
http://videogames.yahoo.com/platform?platform=120121

Dear all,
  I am a new NMRPipe user , please tell me some how to
convert a test.ft file to UCSF fomat ,which is
required for SPARKY ......

                    parichita

Parichita Mazumder
Junior Research Fellow
C/O Dr. Chaitali Mukhopadhayay
Department of Chemistry
University of Calcutta
92,A P C Road
Kolkata-700009
India.





__________________________________________________________
Yahoo! India Answers: Share what you know. Learn something new
http://in.answers.yahoo.com/

There are several ways to extract 1D data, here are two:

INTERACTIVE:

From inside "nmrDraw", if you are viewing a 1D from any dimension,
you can save it this way:

Use the command "Proc/NMRPipe Command" ... this will create
a one-line pop-up window where individual nmrPipe processing
functions and their arguments can be entered (such as "SP -off 0.5",
"ZF", "FT" etc).  Use the "SAVE" function, for example:

    SAVE -name test1d.dat

FROM THE COMMAND-LINE:

You can use the stand-alone command "readROI" to extract and save
1D vectors and projections.  This command is actually a TCL script.

The direction and location of the extracted data is specified using the
spectral axis names, as set by "-xLAB" "-yLAB" etc during conversion.
The axis names must be unique.

For example, if the axis names are "HN" and "N", the following
command will extract the 1D 15N vector from the point closest
to 7.2ppm:

    readROI -in hsqc.ft2 -ndim 1 -x N -dy HN 7.2ppm -out test1d.dat

See "readROI -help" and "man readROI" for some more info ...

On Mon, 19 Feb 2007, Lei Li wrote:

> Dear All
>
> Does anyone know if we can get the 1D spectrum (F2 or
> F1 dimension, which can be saved as .ft1 ) from a 2D
> (or even 3D) fid ?
>
> Thank you!
>
> Lei
>
>
>
>
________________________________________________________________________________\
____
> Be a PS3 game guru.
> Get your game face on with the latest PS3 news and previews at Yahoo! Games.
> http://videogames.yahoo.com/platform?platform=120121
>

Dear all,
I am a new NMRPipe user , please tell me some how to
convert a test.ft file to UCSF fomat ,which is
required for SPARKY ......

parichita

Parichita Mazumder
Junior Research Fellow
C/O Dr. Chaitali Mukhopadhayay
Department of Chemistry
University of Calcutta
92,A P C Road
Kolkata-700009
India.


__________________________________________________________
Yahoo! India Answers: Share what you know. Learn something new
http://in.answers.yahoo.com/

Parichita

Go to the directory where sparky is loaded in DOS mode and type bruk2ucsf if you have bruker data or vnmr2ucsf if you have varian data.
This worked for me few days back.

Cheers

Sudhakar

parichita parichita <parichitamajumdar@yahoo.co.in> wrote:

Dear all,
I am a new NMRPipe user , please tell me some how to
convert a test.ft file to UCSF fomat ,which is
required for SPARKY ......

parichita

Parichita Mazumder
Junior Research Fellow
C/O Dr. Chaitali Mukhopadhayay
Department of Chemistry
University of Calcutta
92,A P C Road
Kolkata-700009
India.


__________________________________________________________
Yahoo! India Answers: Share what you know. Learn something new
http://in.answers.yahoo.com/

---

Everyone is raving about the all-new Yahoo! Mail beta.

Dear All,

I am not sure if i did it right. but it seems that my
Pipe doesn't work very well for SOME topspin data. For
example, it works well for 2D HSQC, but it does not
work for a 3D HSQC-TOCSY data.

Is it possible my Pipe too old? How do I know the
version of my pipe?
(I know my version of nmrDraw is: 2.3 REV
2005.356.10.50 )

Thank you!

Lei



________________________________________________________________________________\
____
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Everyone is raving about the all-new Yahoo! Mail beta.
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Hi,

I am having problems with the fonts for scroll.tcl.
I am using Ubuntu (dapper).

The HN ppm labels for each strip are huge, and offset wrong.

I initiate scroll.tcl using a short startup script:

#!/bin/sh

scroll.tcl $* -cmnd  \
-scale small -type1 small -type2 small  \
-tab hn.tab -lab INDEX  \
-in ./hncocacb2H/ft/test%03d.ft3 ./hncacb2H/ft/test%03d.ft3 \
-hi 2.0e+4  2.0e+4 \
-xOff    0.00 \
-z1  75.0ppm \
-zn  15.0ppm  \
-cursors 2 2 \
-colorC  white yellow  \
-title "HNCOCACB" "HNCACB"

The command window, Index labels and titles are fine, normal font
size.  The HN ppm labels at the bottom are the problem.

I have tried reinstalling NMRPipe, reinstalling 75 and 100 dpi fonts,
pulling the defined fonts from a friend who had Arch Linux (scroll.tcl
works fine for him) and replacing my fonts with his, and replacing
tk/tcl8.4 with tk/tcl8.3 to see if a different tcllib would help.

I can send a screenshot if necessary so people can see the problem.

if anyone can offer any advice I would be very appreciative.

Thanks so much

Nicole Freedman
Graduate Student
Institute for Tuberculosis Research
University of Illinois Chicago

Ah, how sad.  Let's see what can be done.

1. There are no arguments "-scale" "-type1" and "-type2" for
    "scroll.tcl".  These are arguments for "nmrDraw".  Try
    "scroll.tcl -help" ...

2. Current "nmrWish" applications like "scroll.tcl" are set to
    use these as the small and large fonts:

    "-*-lucida-medium-r-*-*-*-140-*-*-*-*-*-*"
    "-*-lucida-medium-r-*-*-*-180-*-*-*-*-*-*"

      or, if those can't be found, then:

    "-*-helvetica-medium-r-*-*-*-140-*-*-*-*-*-*"
    "-*-helvetica-medium-r-*-*-*-180-*-*-*-*-*-*"

    These are similar to fonts used by nmrDraw. So:

      * Does "nmrDraw" seem to work correctly?

      * Can you start an xterm using the fonts above without
        problem, for example:

        xterm -fn '-*-lucida-medium-r-*-*-*-140-*-*-*-*-*-*'

3. The current NMRPipe installation files attempt to test
    whether or not a Linux installation needs extra fonts.
    This is a fairly recent addition, as most versions of
    Linux previously seemed to have all of the required fonts.
    Since this Linux/font feature is so new, it may still need
    to be adjusted to work on every system ...

    In the current install procedure, fonts are provided whether
    they are needed or not, and a file "com/font.com" is created
    which will add the fonts to the font path.  Have a look at
    this file, and see if the fonts directories etc have actually
    been installed.  If the font files have been installed, try
    executing "com/font.com", and then try running "scroll.tcl" again ...



On Sat, 3 Mar 2007, nkjvcjs wrote:

> Hi,
>
> I am having problems with the fonts for scroll.tcl.
> I am using Ubuntu (dapper).
>
> The HN ppm labels for each strip are huge, and offset wrong.
>
> I initiate scroll.tcl using a short startup script:
>
> #!/bin/sh
>
> scroll.tcl $* -cmnd  \
> -scale small -type1 small -type2 small  \
> -tab hn.tab -lab INDEX  \
> -in ./hncocacb2H/ft/test%03d.ft3 ./hncacb2H/ft/test%03d.ft3 \
> -hi 2.0e+4  2.0e+4 \
> -xOff    0.00 \
> -z1  75.0ppm \
> -zn  15.0ppm  \
> -cursors 2 2 \
> -colorC  white yellow  \
> -title "HNCOCACB" "HNCACB"=20
>
> The command window, Index labels and titles are fine, normal font
> size.  The HN ppm labels at the bottom are the problem.
>
> I have tried reinstalling NMRPipe, reinstalling 75 and 100 dpi fonts,
> pulling the defined fonts from a friend who had Arch Linux (scroll.tcl
> works fine for him) and replacing my fonts with his, and replacing
> tk/tcl8.4 with tk/tcl8.3 to see if a different tcllib would help.
>
> I can send a screenshot if necessary so people can see the problem.
>
> if anyone can offer any advice I would be very appreciative.
>
> Thanks so much
>
> Nicole Freedman
> Graduate Student
> Institute for Tuberculosis Research
> University of Illinois Chicago
>
>

Thank you for your quick reply:

> Ah, how sad.  Let's see what can be done.
>
> 1. There are no arguments "-scale" "-type1" and "-type2" for
>    "scroll.tcl".  These are arguments for "nmrDraw".  Try
>    "scroll.tcl -help" ...

Oops, that was a line I added just to try, and since it did nothing,
forgot to remove it.


>      * Does "nmrDraw" seem to work correctly?

With the scale arguments, it works perfectly.  Without the scale
arguments the axis labels are very large.

>      * Can you start an xterm using the fonts above without
>        problem, for example:
>
>        xterm -fn '-*-lucida-medium-r-*-*-*-140-*-*-*-*-*-*'


Yes, the xterm window opens with no problem, however even the 140 is
huge.  Changing to 80 or 100 gives a more reasonable size.  Maybe this
is key?

>    Have a look at
>    this file, and see if the fonts directories etc have actually
>    been installed.  If the font files have been installed, try
>    executing "com/font.com", and then try running "scroll.tcl" again

Xview/fonts/gz/75dpi and /misc are there.
Executed font.com. No change when running scroll.tcl afterward.
Tried editing 'gz' to 'bdf' in font.com (I know I don't have an sgi,
but it was worth a try <vbg>) and still no change.

Again Thank you very much.

Nicole Freedman
Graduate Student
Institute for Tuberculosis Research
University of Illinois Chicago

I love a thorough reply!  Our young colleague here deserves
a solution just for that.

Anyway, these font choices are currently "hard wired" into the
software, perhaps somewhat unwisely done on my part.  I'll
amend this soon.

In the meanwhile: what display resolution is being used?
The software will probably not look so nice at resolutions
under 1024x768.  So, as possible, update your graphics driver
if needed, and set the graphics resolution to the highest
value that your graphics display supports clearly.

If this is not an option, you can write to me directly,
and I'll give you news about updated versions of the
software which will allow you to adjust the fonts.

	 Cheerful Regards,

	 big fd



On Sat, 3 Mar 2007, nkjvcjs wrote:

> Thank you for your quick reply:
> =20
> > Ah, how sad.  Let's see what can be done.
> >=20
> > 1. There are no arguments "-scale" "-type1" and "-type2" for
> >    "scroll.tcl".  These are arguments for "nmrDraw".  Try
> >    "scroll.tcl -help" ...
>
> Oops, that was a line I added just to try, and since it did nothing,
> forgot to remove it.
>
> =20
> >      * Does "nmrDraw" seem to work correctly?
>
> With the scale arguments, it works perfectly.  Without the scale
> arguments the axis labels are very large.
> =20
> >      * Can you start an xterm using the fonts above without
> >        problem, for example:
> >=20
> >        xterm -fn '-*-lucida-medium-r-*-*-*-140-*-*-*-*-*-*'
>
>
> Yes, the xterm window opens with no problem, however even the 140 is
> huge.  Changing to 80 or 100 gives a more reasonable size.  Maybe this
> is key?
>
> >    Have a look at
> >    this file, and see if the fonts directories etc have actually
> >    been installed.  If the font files have been installed, try
> >    executing "com/font.com", and then try running "scroll.tcl" again
> =20
> Xview/fonts/gz/75dpi and /misc are there.
> Executed font.com. No change when running scroll.tcl afterward.
> Tried editing 'gz' to 'bdf' in font.com (I know I don't have an sgi,
> but it was worth a try <vbg>) and still no change.
>
> Again Thank you very much.
>
> Nicole Freedman
> Graduate Student
> Institute for Tuberculosis Research
> University of Illinois Chicago
>
>

Dear all,

I run NMRPipe on my PC (Red Hat Linux 9 on x86). Recently, I've found
that some people use the "-swap" option for "var2pipe".


var2pipe -in ./fid -swap -aqORD 1 \

Must I use the option too? Why should I use this option?

And should I use this option when processing Bruker data?

i.e.,
bruk2pipe -in ./ser -bad 0.0 -swap -DMX -decim 24 -dspfvs 12  \


Thanks in advance!


Regards,

Liwen

This is from the bruk2pipe/var2pipe manual page:

                -swap or -noswap: depending on the computer platforms
                involved, spectrometer format data may require each
                four bytes of input to be reversed before conversion.
                This is called byte-swapping.  It can be enabled or
                suppressed via these flags.  Having the byte-swap mode
                set incorrectly will cause large numbers of "Bad
                Points", which will have unusually large intensities.
                More recently, complementary options -aswap and
                -noaswap have been added; these are system-dependant
                byte-swap options whose meanings change depending on
                the computer platform.  The intent is that conversion
                commands which use the -aswap and -noaswap options
                should work consistantly when given the same input
                data, regardless of the computer platform used for the
                conversion.

The conversion utilities "bruker" and "varian" should set the
byte swap flags automatically.


On 10 Mar 2007, liwenfu24 wrote:

>
> Dear all,
>
> I run NMRPipe on my PC (Red Hat Linux 9 on x86). Recently, I've found
> that some people use the "-swap" option for "var2pipe".
>
>
> var2pipe -in ./fid -swap -aqORD 1 \
>
> Must I use the option too? Why should I use this option?
>
> And should I use this option when processing Bruker data?
>
> i.e.,
> bruk2pipe -in ./ser -bad 0.0 -swap -DMX -decim 24 -dspfvs 12  \
>
>
> Thanks in advance!
>
>
> Regards,
>
> Liwen
>
>
>
>

Dear Frank,

Thank you very much! Following what you mationed, I've tested these
four options with a cbca(co)nh spectrum acquired on Bruker AVANCE 500
MHz spectrometer, processed on Intel PC running Red Hat Linux 9.
The results are:

"-swap" = "-aswap" = "-noswap" : correct
"-noswap" = "": "unusually large intensities"

Thanks again!

Regards,

Liwen


--- In nmrpipe@yahoogroups.com, "Frank Delaglio, Ph.D. (CONTRACTOR)"
<delaglio@...> wrote:
>
>
>
> This is from the bruk2pipe/var2pipe manual page:
>
>                -swap or -noswap: depending on the computer platforms
>                involved, spectrometer format data may require each
>                four bytes of input to be reversed before conversion.
>                This is called byte-swapping.  It can be enabled or
>                suppressed via these flags.  Having the byte-swap mode
>                set incorrectly will cause large numbers of "Bad
>                Points", which will have unusually large intensities.
>                More recently, complementary options -aswap and
>                -noaswap have been added; these are system-dependant
>                byte-swap options whose meanings change depending on
>                the computer platform.  The intent is that conversion
>                commands which use the -aswap and -noaswap options
>                should work consistantly when given the same input
>                data, regardless of the computer platform used for the
>                conversion.
>
> The conversion utilities "bruker" and "varian" should set the
> byte swap flags automatically.
>
>
> On 10 Mar 2007, liwenfu24 wrote:
>
> >
> > Dear all,
> >
> > I run NMRPipe on my PC (Red Hat Linux 9 on x86). Recently, I've found
> > that some people use the "-swap" option for "var2pipe".
> >
> >
> > var2pipe -in ./fid -swap -aqORD 1 \
> >
> > Must I use the option too? Why should I use this option?
> >
> > And should I use this option when processing Bruker data?
> >
> > i.e.,
> > bruk2pipe -in ./ser -bad 0.0 -swap -DMX -decim 24 -dspfvs 12  \
> >
> >
> > Thanks in advance!
> >
> >
> > Regards,
> >
> > Liwen
> >
> >
> >
> >
>

Hi,
  I have a 2D spectrum "test.ft". I need to extract 1D pojections along
x-axis and y-axis. Which is the command in nmrPipe to get the projections.
thanks
nrs

proj2D.tcl -in test.ft

The input spectrum should have unique axis names, as established
during conversion via "-xLAB" and "-yLAB" ...

% proj2D.tcl -help
/u/delaglio/com/proj2D.tcl: Create 1D projections from 2D data.
  -in inName [test.ft2]         Name of 2D Input.
  -skyline                      Skyline Projection (Default).
  -sum                          Summation projection.
  -abs                          Use Absolute Value.


On Fri, 16 Mar 2007, neeraj_sinha23 wrote:

> Hi,
>  I have a 2D spectrum "test.ft". I need to extract 1D pojections along
> x-axis and y-axis. Which is the command in nmrPipe to get the projections.
> thanks
> nrs
>
>
>

-- Dr. Frans Mulder
Biophysical Chemistry
Groningen University
Nijenborgh 4
9747 AG Groningen
the Netherlands
tel: +31-50-3634339
fax: +31-50-3634398
email: f.a.a.mulder@...
URL: www.rug.nl/gbb/nmr