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List: relax-users
Subject: Re: [Fwd: Re: [Fwd: Re: [bug #17341] Compatibility with CCPN Analysis2.1 (fwd)]]
From: "Edward d'Auvergne" <edward () domain ! hid>
Date: 2011-01-10 12:33:28
Message-ID: AANLkTinp--8A99G33ip85sqt8bXons1pHfj-5gQRW+S3 () domain ! hid
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That's good news! I'll try to work out what that volume bug is
though. If you could submit a bug report for that, it would be much
appreciated.
Cheers,
Edward
On 10 January 2011 11:59, Maddy Strickland <M.Strickland@domain.hid> wrote:
> Hi Edward,
>
> They have now changed it to peak heights, I have checked by exporting some
> data. All you need to do is update by clicking 'project>updates' and it's
> now sorted out - to check it's updated correctly, when you export a Sparky
> peak list it should say height instead of intensity. Glad that's sorted
> out! Won't take too long to convert now...
>
> Maddy
>
>
> On Mon, January 10, 2011 10:52 am, Edward d'Auvergne wrote:
>> Oh, if it is volumes, then that would be a problem. Hopefully it is
>> easy for them to sort out at their end, and also easy for you to
>> convert your old data to heights.
>>
>> Regards,
>>
>> Edward
>>
>>
>> On 10 January 2011 11:50, Maddy Strickland <M.Strickland@domain.hid>
>> wrote:
>>> 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@domain.hid>
>>> Date: Mon, January 10, 2011 9:51 am
>>> To: "Maddy Strickland" <M.Strickland@domain.hid>
>>> Cc: relax-users@domain.hid
>>> --------------------------------------------------------------------------
>>>
>>> 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
>>>>>>>
>>>>>>> To unsubscribe from this list, get a password
>>>>>>> reminder, or change your subscription options,
>>>>>>> visit the list information page at
>>>>>>> https://mail.gna.org/listinfo/relax-devel
>>>>>>>
>>>>>>>
>>>>>> ---------- End Forwarded Message ----------
>>>>>>
>>>>>>
>>>>>>
>>>>>> ----------------------
>>>>>> M Strickland, Science 04
>>>>>> ms4225@domain.hid
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>>> https://mail.gna.org/listinfo/relax-users
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>> https://mail.gna.org/listinfo/relax-users
>>>>>
>>>>
>>>>
>>>> --
>>>> Dr. Jolyon Claridge
>>>> Research Associate
>>>> Laboratory of Molecular Biophysics jolyon.claridge@domain.hid.ac.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
>>>> https://mail.gna.org/listinfo/relax-users
>>>>
>>>
>>>
>>> Madeleine Strickland
>>>
>>> MCJC Group
>>> N317, School of Chemistry, Bristol University
>>>
>>>
>>
>
>
> Madeleine Strickland
>
> MCJC Group
> N317, School of Chemistry, Bristol University
>
>
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