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
