Dear Olivier,
The issue, I would assume, is that you have used Bruker Topspin or
XWinNMR and have not taken a difference in the ncproc parameter into
account. This can be seen in the replicated spectra of 'T2_32ms1':
Assignment w1 w2 Data Height
L3N-HN 122.461 8.416 2901924
I8N-HN 116.473 7.845 367875
G9N-HN 115.613 8.139 390567
E10N-HN 118.029 8.243 570286
G12N-HN 113.878 7.570 351431
E14N-HN 114.407 8.855 599796
T15N-HN 107.526 7.683 410404
S17N-HN 112.398 8.680 371010
D18N-HN 123.107 7.708 537122
Y19N-HN 119.260 7.776 485032
and 'T2_32ms2':
Assignment w1 w2 Data Height
L3N-HN 122.457 8.415 84734
I8N-HN 116.457 7.847 11680
G9N-HN 115.598 8.140 12639
E10N-HN 118.017 8.245 19195
G12N-HN 113.852 7.571 9156
E14N-HN 114.386 8.856 14600
T15N-HN 107.482 7.680 9844
S17N-HN 112.405 8.681 9324
D18N-HN 123.113 7.710 14935
Y19N-HN 119.250 7.777 13343
'ncproc' is a Bruker specific spectra intensity scaling factor
(relating to the retarded and ancient integer format storage in the
ser FID file). My guess is that the ncproc value difference between
the 2 spectra is 5! If this is not the case, I have absolutely no
idea why the second data set is 30 to 40 times (ncproc diff of 5 is
2**5 times = 32) smaller than the first. This is where the errors in
peak height are determined from, hence the error is orders of
magnitude bigger than the values themselves. I hope this information
helps.
Regards,
Edward
On Tue, Jul 21, 2009 at 11:52 AM, Olivier
Serve<NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
URL:
<http://gna.org/bugs/?13993>
Summary: Not reasonnable R2 fitting calculation time
Project: relax
Submitted by: oserve
Submitted on: mardi 21.07.2009 à 09:52
Category: relax's source code
Severity: 3 - Normal
Priority: 5 - Normal
Status: None
Privacy: Public
Assigned to: None
Originator Name:
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Release: 1.3.3
Operating System: GNU/Linux
_______________________________________________________
Details:
Hi,
Using my data (sparky format) to extract R2 from the relaxation experiments
and the relaxation fitting sample script provided with relax, I have an
unexpected behaviour. First the calculation time is really long (4~5 ) hours
on a recent 2.66 Ghz Xeon, and finally error estimation is very high.
I am even more suprised that, it worked perfectly with T1 data. NMRViewJ
gave
also coherent results for both T1 and T2 experiments.
I joined a archive containing the peak list files (reduced to 10 residues),
a
pdb file and the modified relax script.
I hope it can be fixed, I would like to use relax for the analyis of
relaxation data of course.
Thank you for your help
Best regards,
Olivier Serve
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: mardi 21.07.2009 à 09:52 Name: bug-relax.tar.gz Size: 66 ko By:
oserve
<http://gna.org/bugs/download.php?file_id=6235>
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?13993>
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Re: [bug #13993] Not reasonnable R2 fitting calculation time