Hello Wim,
thanks for the clarifying message;
I'm still not sure of one thing: let us say we forget nmrview cross peak
lists; I just want the sequence numbering to start from 320. How do
I go about it? Last time i built the sequence by reading in a sequence
text file w/ 3 letter code for a.a. residues.
cheers,
-chandraShekar
On Wed, 2 May 2007, Wim Vranken wrote:
> Hi chandraShekar,
>
> Sorry for the delay in getting back to you. Anyway here we go:
>
>> i am trying to import nmrview peak lists; it so happens that my
>> sequence numbering starts from 320; but the peaklists do not have
>> complete assignments; the most n-terminal assignment is for residue 327.
>>
>> now, there were quite a few error messages including "jump" in sequence.
>> so i tried the python commands in the window in which 'analysis' was fired
>> up and the commands executed w/o any complaints. but i still got the
>> error messages such as "jump" in sequence numbering; more importantly,
>> the linked resonances all had internal renumberings from ccpn;
>
> The 'jump' messages are normal - the FC is just telling you that the sequence
> numbering it imported from your assignments of your peak lists has gaps in
> it, and that it assumes the information in those gaps is missing (essentially
> that your sequence numbering is sequential). This is necessary because it
> also happens that people number their sequence from 1-100, then suddenly jump
> to 300 for the next residue. Anything can happen, basically, so that's why
> the linking of the CCPN sequence numbers to the 'format-imported' sequence
> number has to be rather complicated (it has to be generic enough).
>
>> lastly, i also have what we call as "pseudo" residues; i.e. for those
>> peaks, let us say in trhncacb3d, for which we know exists a peak in trosy,
>> trhnco and/or thrncocacb3d, the nmrview peak assignment boxes have
>> been filled w/ let's say 8.hn - 7.cb - 8.ca (but the real sequence
>> starts only from 320); is it better for me to drop these pseudo
>> resonances?
>
> So do you mean that you 'invent' the 7 and 8 sequence codes because you know
> these are sequentially linked, but you don't know where they are in the
> actual sequence yet? This information is not easily transferred, I'm afraid -
> there is currently no 'spinSystem' I/O support for NmrView at all. If you
> link your residues from 320 on to the CCPN sequence, you will still have the
> resonances for the 8.hn, 7.cb and 8.ca, but they will not be linked together
> in any way - probably easiest to do that by hand in Analysis later on. I'm
> not planning to add any spinSystem-level support for NmrView for the moment -
> it gets very complicated because it is more or less a free format for its
> atom and sequence numbering. I will have a think about adding in some support
> for this on the linkResonances level though... could be possible without too
> much hassle.
>
> Bye,
>
> Wim
>
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