Hi Carolin,
You can probably do this without format conversion. Using Peak:Peak Lists
- Synthetic Lists [Make transpose list]. This will give a separate peak
list (still associated with the same spectrum) with the peak dimensions
effectively swapped. This can be merged with the original peak list using
Peak:Peak Lists - [Copy Peaks]. You may end up with unassigned duplicate
peaks, but these are easily deleted.
Regards,
Tim
> I have a 2D spectrum, all peaks assigned but only on one side of the
> diagonal. Now I want to assign the other side of the diagonal, swapping
> dimension = > F1 should become F2 and vice versa. I cannot to it in >
> Peaks : Peaklist : = no option to change F1 and F2, is there? So, I
> exported the peaklist (I chose xeasy format), swaped x and y in the
> .peaks-file and then imported it again following the "strategy" Rasmus
> proposed to Matthias below. The peaks are imported correctly, but there
> is NO assignment displayed! If I import all 3 (.peaks, .prot, .assign),
> nothing changes. what to I do wrong?
>
> Carolin
>
>
>
>
>
> On Jul 15, 2011, at 5:10 PM, Rasmus Fogh wrote:
>
>> Dear Matthias,
>>
>> First the solution, then some comments.
>>
>> To import assigned peaks from CYANA, with your test files:
>>
>> - Open FormatConverter
>> - Go to M:Import:combined files:shifts and peaks:XEASY
>> - Set CYANA format on
>> - select peak file
>> - Select shift file
>> - Do *NOT* select a peak assignment file
>> - In advanced options:
>> - set 'Use existing Data Source' to the approriate spectrum
>> - leave 'Match existing Resonances' on
>> - Set 'Minimal Interactions
>>
>> - Press the button to import
>> - You will be asked how to map peak list dimensions to experiment
>> dimensions. Leave as is. If that gives the wrong result try again and swap
>> the dimensions.
>> - When the program asks you if you want to run 'linkResonaces' say *no*.
>>
>> You will now have an extra imported peak list, with assignments.
>> There will be no extra shift lists.
>>
>> To use structures to check unassigned NOEs:
>>
>> - Go to M:Experiment{Experiments}
>> - Double click the 'Mol Systems' column, and set the structure you want to
>> On.
>> - Now you will get a structure set when you go into the assignment dialogue
>> - Note that you only get distances showing when one of the peak dimensions
>> is assigned.
>>
>> Normally I think this is set automatically. I do not know why you need to
>> do it manually in this case.
>>
>> ========================================
>>
>> Some comments:
>>
>> Reading the .assign file gives you an error, something about 'invalid
>> literal for int() 'Corresponding'. Basically the .assign files you have are
>> totally wrong for the XEASY .assign file reader in FormatConverter. Anyway
>> CYANA keeps the assignments in the peaks file, so you do not need them.
>>
>> Apparently, linkResonances ot its equivalent is done automatically when
>> reading CYANA peak files.
>>
>> As you see, you can get the right result once you know the sequence of
>> steps to use. Finding the right steps can sometimes be difficult, as in
>> this case. FormatConverter was written to cover a *lot* of formats with a
>> generic approach and a minimum of special-case coding for each, and it does
>> its job. We are working on a replacement for FormatConverter,
>> FormatExchange, that will use the tested file parsers of FormatConverter,
>> but add an interface that is smoother, does more for you, and is easier to
>> get to grips with. It is a lot of work to write, though, so it will be
>> quite some time before it covers all the formats tha FOrmatConverter does.
>>
>> Yours,
>>
>> Rasmus
>>
>> ---------------------------------------------------------------------------
>> Dr. Rasmus H. Fogh Email: [log in to unmask]
>> Dept. of Biochemistry, University of Cambridge,
>> 80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002
>
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