Indeed most likely a referencing problem. Gotchas with HCCH TOCSY type expts include:
The shifted offset trick: in order to maximize digital resolution in the indirect 1H dimension, the pulse sequences often include a 90 step backward in the phase incrementation of the pulse that gives sign discrimination. This has the effect of shifting the spectrum by 1/4 of the sweep width relative to the carrier frequency, so the reference point should be placed at (npts/4)+1 rather than (npts/2)+1.
The reversed indirect dimension: some pulse programs have the phase incrementation for the pulse that determines sign discrimination such that the dimension is reversed when you process. Fix this by reprocessing taking the complex conjugate of the data in the dim (e.g. REVERSE flag in Topspin; best solution) or reversing the data post FT.
Which 1H is 1J to the 13C?: Analysis tries to guess which is the appropriate way to map the dimensions to the experiment prototype that it uses to know what crosspeaks mean. For experiments with two dims with the same nucleus, it doesn't always guess right - check carefully when you load the experiment and be prepared to switch the mapping.
Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
College of Medical, Veterinary & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089
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The University of Glasgow, charity number SC004401
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From: CcpNmr software mailing list [[log in to unmask]] on behalf of Wayne Boucher [[log in to unmask]]
Sent: 20 June 2018 08:55
To: [log in to unmask]
Subject: Re: Transpose axes in HCcH TOCSY
Hello,
That sounds like a referencing problem (assuming I am understanding what you are saying). (Assuming that the diagonal peaks indeed have the two 1H values equal.)
Wayne
> On 20 Jun 2018, at 07:36, Karjalainen, Mikael <[log in to unmask]> wrote:
>
> Hi!
>
> Thank you! That worked for me.
>
> I wonder why in Analysis example project the diagonal line in HCcH TOCSY spectrum is aligned with diagonal-peaks in spectrum, but in my spectrum they are not aligned. I can read my HCcH TOCSY, but just wondering why it is displayed in a different way.
>
> Regards,
> Mikael
>
>
> -----Original Message-----
> From: CcpNmr software mailing list <[log in to unmask]> On Behalf Of Wayne Boucher
> Sent: tiistai 19. kesäkuuta 2018 16:23
> To: [log in to unmask]
> Subject: Re: Transpose axes in HCcH TOCSY
>
> In the Window —> Windows dialog in the Spectrum & Peak List Mappings, you can transpose the 1H in the last column of the top table (double click to edit).
>
> Wayne
>
>> On 19 Jun 2018, at 14:18, Mikael Karjalainen <[log in to unmask]> wrote:
>>
>> Hi!
>>
>> I know how to make window for HCcH TOCSY spectrum that shows 1H at the x-axis, second 1H at the y-axis and 13C at the z-axis. However, I don't get similar view like here ->http://www.protein-nmr.org.uk/solution-nmr/spectrum-descriptions/hcch-tocsy/. I think I should transpose x- and y-axes.
>>
>> Can this be done?
>>
>> Regards,
>> Mikael
>>
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