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List: relax-users
Subject: Re: [Fwd: Re: [bug #17341] Compatibility with CCPN Analysis2.1 (fwd)]
From: "Edward d'Auvergne" <edward () domain ! hid>
Date: 2011-01-10 9:51:38
Message-ID: AANLkTike0n9jgjbYdB2zBMg_ge1m2Rdkh71ZrpBjEm_z () domain ! hid
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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@domain.hid> 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@domain.hid>
> Date: Wed, January 5, 2011 5:34 pm
> To: "Edward d'Auvergne" <edward@domain.hid>
> Cc: "M Strickland, Science 04" <M.Strickland@domain.hid>
> "relax-users@domain.hid" <relax-users@domain.hid>
> --------------------------------------------------------------------------
>
> 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@domain.hid> 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@domain.hid>
>>> To:
>>> Cc: m.strickland@domain.hid, relax-devel@domain.hid
>>> 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@gna.org>
>>> 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@domain.hid
>>>> 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>
>>>>
>>>> _______________________________________________
>>>> Message sent via/by Gna!
>>>> http://gna.org/
>>>>
>>>>
>>>> _______________________________________________
>>>> relax (http://nmr-relax.com)
>>>>
>>>> This is the relax-devel mailing list
>>>> relax-devel@domain.hid
>>>>
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>>>>
>>>>
>>> ---------- End Forwarded Message ----------
>>>
>>>
>>>
>>> ----------------------
>>> M Strickland, Science 04
>>> ms4225@domain.hid
>>>
>>> _______________________________________________
>>> relax (http://nmr-relax.com)
>>>
>>> This is the relax-users mailing list
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>>>
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>>>
>>>
>>
>> _______________________________________________
>> relax (http://nmr-relax.com)
>>
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>
>
> --
> Dr. Jolyon Claridge
> Research Associate
> Laboratory of Molecular Biophysics jolyon.claridge@domain.hid.uk
> 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@domain.hid
>
> To unsubscribe from this list, get a password
> reminder, or change your subscription options,
> visit the list information page at
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