Dear Tomas,
Welcome to CCPN. Hope you will like it here.
It is hard to tell what is wrong without having the project to look at.
One thing you should always try is to go to:
M:Assignment:Quality Reports {Resonances} and see if there are any alerts.
There may not be much chance so early in the process, but if the data are
inconsistent it is anyones guess what may happen.
I do not think we have the 'pick and set to -1 spin system' functionality.
Actually it should work so that you get the peaks assigned correctly if
you use the 'Protein Sequence Assignment popup'.
What you can do is to set 'Assign non-Root dim?' in M:Assignment:Pick &
Assign From Roots {Windows and Spectra}(I would do it only on HNCO and
HNcoCACB to avoid duplicate resonances), use the ['Asign Non-root
Resonances'] button in M:Assignment:Pick &
Assign From Roots {Link Peaks}. If the automatic process does not get
you your assignments, you can later set relative spin systems using Right
Mouse:Assign:Set sequential spin systems.
It is possible that you will get better type assignments if you set the
sequential assignment first, adn go along the stretch.
Sorry to not be clearer, but if this does not help (and nobody else comes
up with anything), maybe we will have to look at your actual project.
Let us know how it goes,
Rasmus
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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
On Wed, 11 Sep 2013, Tomas Hosek wrote:
> Dear Madam/Sir,
> I would like to ask you for help. I am using CCPNMR version 2.3.1.
> I am beginner in the CCPNMR, I am learning by myself from your tutorial's, which are online.
>
> I just started the sequence specific assignment of my protein. I pick
> peaks in all 3D spectra (HNCACB, HNcoCACB, HNCO, HNcaCO) using "Pick &
> Assign From Roots" following my HSQC Root Resonances. Hence all peaks
> are assigned to some spin system in H and N dimension. The C dimension
> is not assign to any. The HNCACB strip corresponding one spin system
> clearly indicates that spin system is Ser or Thr and preceding residue
> is Gly (in my protein's primary sequence, the there is only one GS
> sequence and no GT). Peaks: Ca = 56.43 ppm (positive) Cb = 62.96 ppm
> (negative) Ca-1 = 44.78 ppm (positive) But ccpnmr is not offering me
> that this spin system correspond to Ser / The, but to Glen (yellow with
> score 11.2) ….and at the bottom of the list Ser (red with score 5.0). In
> "sequence location" box doesn't show option GS at all.
>
> Also I would like to ask whether is there an option how to set during peak picking that peak corresponds to Ca(i), Ca(i-1), Cb(i-1),… like it is e.g. in program CARA.
>
> Thank you very much for help
> Tomas Hosek
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