> 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.
Hi,
Although Wim may be better able to advise on this, it might be easier to
load/enter the entire sequence in first and then link to this when
importing the peak list assignments.
> so i tried the python commands in the window in which 'analysis' was fired
> up and the commands executed w/o any complaints.
The python code Wayne posted is not to be used lightly, even putting aside
any potential issues that I mailed about eariler.
Even if you have gaps in the assignments for some residues it is generally
much better to aim to have the whole of the sequence (for your sample) in
the CCPN project.
> but i still got the error messages such as "jump" in sequence numbering;
> more importantly, the linked resonances all had internal renumberings
> from ccpn;
There is no choice about the internal serial number of resonances objects.
The way that resonances are annotated in Analysis is by an atomic
assignment, spin system, atom type and resonance name. The resonance names
could be set to display you original numbering system, but it might be
easier in the long-run to move across to the CCPN spin system/resonance
numbers for anything anonymous.
> 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?
The CCPN way is to have the 'pseudo residues' represented by
resonanceGoups; these are called spin systems within Analysis. Wim can
perhaps enlighen about FC's spin system import. I think it is in there.
> or is it best to drop all peaklists and start from scratch in ccpn?
We can usually get things sorted...
T.
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Dr Tim Stevens Email: [log in to unmask]
Department of Biochemistry [log in to unmask]
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