Hi Edward,
I have sent an email to them, so it should get sorted out. I checked
the
numbers exported against the peak lists within the program, where it
shows
both height and volume and it looks like it is exporting volume
unfortunately.
---------------------------- Original Message
----------------------------
Subject: Re: [Fwd: Re: [bug #17341] Compatibility with CCPN Analysis2.1
(fwd)]
From: "Edward d'Auvergne" <edward@xxxxxxxxxxxxx>
Date: Mon, January 10, 2011 9:51 am
To: "Maddy Strickland" <M.Strickland@xxxxxxxxxxxxx>
Cc: relax-users@xxxxxxx
--------------------------------------------------------------------------
Hi,
I would guess that this problem is not so bad as it seems. It is
probably a superficial bug in the conversion to Sparky format, but
that it actually contains the peak heights from Analysis rather than
the volumes as it indicates. This will have to be clarified with the
CCPN people though.
Regards,
Edward
On 6 January 2011 11:28, Maddy Strickland <M.Strickland@xxxxxxxxxxxxx>
wrote:
Hi Jo,
Thanks for that, you're right is it exporting the volume rather than
the
peak height. I definitely will email them as this error has undone
about
a year's worth of work for me! I suppose it will be quicker the second
time round though. Looking forwards to recalculating T1, T2, NOE and
Lipari-Szabo for 4 proteins at 2 fields!
Maddy
---------------------------- Original Message
----------------------------
Subject: Re: [bug #17341] Compatibility with CCPN Analysis2.1 (fwd)
From: "Jolyon Claridge" <jolyon.claridge@xxxxxxxxxxxxxx>
Date: Wed, January 5, 2011 5:34 pm
To: "Edward d'Auvergne" <edward@xxxxxxxxxxxxx>
Cc: "M Strickland, Science 04" <M.Strickland@xxxxxxxxxxxxx>
"relax-users@xxxxxxx" <relax-users@xxxxxxx>
--------------------------------------------------------------------------
Hi,
It would appear that the Format Converter in Analysis is exporting the
peak volume rather than the height and I think you are using box sum
integration, hence the bx. This is a bug in the Format Converter as
Analysis is able to measure both height and volume. Can you send it in
to the CCPNMR mailing list as a bug? As an aside, is it really
necessary
to convert the files to sparky format at all? I usually just use the
'export' function directly from the peaklist editing window in Analysis
and then create a text file which relax will be able to handle without
any further trouble.
Regards,
Jo
Edward d'Auvergne wrote:
Hi,
It shouldn't be a problem at all. I have no idea what the bx means
then either, it's strange that they put that there. I hope it really
is a hight integration that it's doing :S Well, if you have all
spectra duplicated, then you will be able to have an error estimate
per spectrum. For a sanity check, this should be similar to the value
of the RMSD of the baseplane noise in each spectra.
Regards,
Edward
On 20 December 2010 14:47, M Strickland, Science 04
<M.Strickland@xxxxxxxxxxxxx> wrote:
I don't know what the bx means, I've been removing it in my final
files.
Analysis just gives the option between height and intensity and I
pick
height. Unfortunately, I don't know how they measure it, but I
generally
get duplicate spectra for all my results, and at two field strengths,
so it
shouldn't be an issue for my calculations?
---------- Forwarded Message ----------
Date: 17 December 2010 20:33 +0100
From: Edward d'Auvergne <edward@xxxxxxxxxxxxx>
To:
Cc: m.strickland@xxxxxxxxxxxxx, relax-devel@xxxxxxx
Subject: Re: [bug #17341] Compatibility with CCPN Analysis2.1
Hi Maddy,
I'm in the process of adding this data to the relax test suite, and
noticed that the integrated values have 'bx' after it. Would you
know
what that is? Are you using box integration, or measuring peak
heights? Can CCPN Analysis measure peak heights? If you are using
box integration without duplicate spectra, this significantly
complicates the analysis as you will need to know the exact number of
points used in each box. Peak heights are a much better way of
determining the peak intensities as one advantage is that the errors
are much easier to ascertain.
Regards,
Edward
On 17 December 2010 16:48, anonymous
<NO-REPLY.INVALID-ADDRESS@xxxxxxx>
wrote:
URL:
<http://gna.org/bugs/?17341>
Summary: Compatibility with CCPN Analysis2.1
Project: relax
Submitted by: None
Submitted on: Fri 17 Dec 2010 03:48:15 PM UTC
Category: relax's source code
Severity: 2 - Minor
Priority: 5 - Normal
Status: None
Privacy: Public
Assigned to: None
Originator Name: Madeleine Strickland
Originator Email: M.Strickland@xxxxxxxxxxxxx
Open/Closed: Open
Discussion Lock: Any
Release: 1.3.5
Operating System: GNU/Linux
_______________________________________________________
Details:
When using FormatConverter (with CCPN Analysis2.1) you can output
'Sparky'
format peak lists for use with curve fitting in Relax. These have a
different format to those expected by Relax1.3.5. Differences are:
Relax: Two header lines, Analysis: One header line
Relax: V1504N-HN, Analysis: V1504N-V1504HN
Relax: Peaks in order, Analysis: Random order of peaks
Attached: R1.py script, lists for two residues, log file of output
from
Relax, sequence
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Fri 17 Dec 2010 03:48:15 PM UTC Name: log.txt Size: 24kB
By:
None
<http://gna.org/bugs/download.php?file_id=11610>
-------------------------------------------------------
Date: Fri 17 Dec 2010 03:48:15 PM UTC Name: peak_lists.tar.gz
Size:
645B
By: None
<http://gna.org/bugs/download.php?file_id=11611>
-------------------------------------------------------
Date: Fri 17 Dec 2010 03:48:15 PM UTC Name: R1A.py Size: 4kB By:
None
<http://gna.org/bugs/download.php?file_id=11612>
-------------------------------------------------------
Date: Fri 17 Dec 2010 03:48:15 PM UTC Name: sequence.out Size: 44B
By:
None
<http://gna.org/bugs/download.php?file_id=11613>
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?17341>
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Message sent via/by Gna!
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---------- End Forwarded Message ----------
----------------------
M Strickland, Science 04
ms4225@xxxxxxxxxxxxx
_______________________________________________
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--
Dr. Jolyon Claridge
Research Associate
Laboratory of Molecular Biophysics jolyon.claridge@xxxxxxxxxxxxxx
University of Oxford Tel: ++44 (0)1865 613200
Oxford, U.K., OX1 3QU
Madeleine Strickland
MCJC Group
N317, School of Chemistry, Bristol University
_______________________________________________
relax (http://nmr-relax.com)
This is the relax-users mailing list
relax-users@xxxxxxx
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
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Madeleine Strickland
MCJC Group
N317, School of Chemistry, Bristol University
Re: [Fwd: Re: [Fwd: Re: [bug #17341] Compatibility with CCPN Analysis2.1 (fwd)]]