Hi Tim,
Thanks. I solved that problem. You are right, that's the way to go.
But now I have another problem and again I need to import a peaklist :
There is a peaklist missing in my current project. But this list is
present in an old one.
I don't want to reassign the peaks as I did it.
So how to I get this peak list from the old project to the new one
including all assignments?
It doesn't seem to be straight forward. Is it?
Carolin
On Jul 25, 2011, at 12:54 PM, Tim Stevens wrote:
> 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
>>
>
>
> -------------------------------------------------------------------------------
> Dr Tim Stevens Email: [log in to unmask]
> Department of Biochemistry [log in to unmask]
> University of Cambridge Phone: +44 1223 766018 (office)
> 80 Tennis Court Road +44 7816 338275 (mobile)
> Old Addenbrooke's Site +44 1223 364613 (home)
> Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
> United Kingdom http://www.ccpn.ac.uk
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