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 <[email protected]> > 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" <[email protected]> >> Date: Mon, January 10, 2011 9:51 am >> To: "Maddy Strickland" <[email protected]> >> Cc: [email protected] >> -------------------------------------------------------------------------- >> >> 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 <[email protected]> >> 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" <[email protected]> >>> Date: Wed, January 5, 2011 5:34 pm >>> To: "Edward d'Auvergne" <[email protected]> >>> Cc: "M Strickland, Science 04" <[email protected]> >>> "[email protected]" <[email protected]> >>> -------------------------------------------------------------------------- >>> >>> 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 >>>> <[email protected]> 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 <[email protected]> >>>>> To: >>>>> Cc: [email protected], [email protected] >>>>> 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 >>>>> <[email protected]> >>>>> 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: [email protected] >>>>>> 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 >>>>>> [email protected] >>>>>> >>>>>> 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 >>>>> [email protected] >>>>> >>>>> _______________________________________________ >>>>> relax (http://nmr-relax.com) >>>>> >>>>> This is the relax-users mailing list >>>>> [email protected] >>>>> >>>>> 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 >>>> [email protected] >>>> >>>> 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 [email protected] >>> 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 >>> [email protected] >>> >>> 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 _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] 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
