Thank you for the quick answer. I just wanted to know if there is a
way to set the peaks types in CCPN, from a standard HNCACB spectrum for
instance with intra-residual peaks picked, just using the sign of the peaks grouped in spin system.
By "mistakes" I wanted to say "unexpected behaviour for this task" :
some resonances belonging to different spin systems have been merged in my case by the algorithm even with Peak-Peak Match
Tolerances set to 0 and some picked peaks have not been identified.
Cheers,
Matthieu BENOIT
> Message du 19/07/11 11:45
> De : "Tim Stevens"
> A : [log in to unmask]
> Copie à :
> Objet : Re: Automated recognition of peaks types in picked HNC experiments
>
> There may be something that needs to be fixed with regards to the
> automated interpretation of iHNCACB for Gly, - this system was not
> intially built for iHNCACB, only the more traditional HNCACB, so it has
> had to be retro-fitted and has not had much testing. I will look into
> this. The other statement about "many mistakes" is a bit vague to take
> action on (I can only assume this is not the Gly issue). Please either
> send the project so I can test or give more details.
>
> Anyhow, the spin system labelling of i/i-1 and setting of CA/CB atom types
> is commonly done when the sequential assignment is made with the Protein
> Sequence Assignment system. In other words you don't have to pre-label i-1
> using this system until a link is made, and there is a button for setting
> HA/CA/CB etc. On the other hand you would have to use an automated setup
> for the automated assignment routines (MARS or Nexus).
>
> I'm not sure what the underlying aim is. Yes, there is an automated
> method, which is the one tried, even if it is not fully configured for the
> iHNCACB. (And this would always have a slot for a tolerance because often
> this would be needed to resolve overlap; designing a separate system just
> for pure intra experiments doesn't make sense). If the Protein Sequence
> Assignment system is to be used, then things may work out OK anyhow,
> otherwise I will aim to fix the Gly iHNCACB issue, and other issues with
> the automation if I get more info.
>
> Regards,
>
> Tim
>
> > I'm working on a set of 3 spectra to assign the backbone of a protein
> > : N-HSQC, HNcoCACB and HNCACB. I picked the 3D spectra manually
> > with the "Pick and Assign from root" menu and then used "Assign roots
> > resonances" in this menu to propagate the spin systems names to my 3D
> > peaks. So, for each spin system, I have no more than 2 peaks picked in
> > the HNCACB spectra (intra residual) and 2 picked in the HNcoCACB
> > spectra (from the previous residue). The resonances have not been
> > assigned so I only have N and H shifts in "Resonance : Resonances".
> >
> > Since my CA peaks are positive and my CB negative, the identification
> > of peaks type (CA vs CB) is straightforward, as well as their "nature"
> > (intra vs previous). Is there any automated way in ccpNmr to set the
> > peaks types and "nature" from this state ?
> >
> > I've tried the "Assignment : Automated Seq. Assignment : Spin Systems
> > : Find Resonances From Peaks" procedure. The result is close to what
> > I'm looking for but on the one hand this procedure ask for Peak-Peak
> > Match Tolerances that are not necessary in my umambiguous case and on
> > the other hand I saw many mistakes in my case, for instance most of my
> > positive intra residual CA glycine peaks are identified as CB.
> >
> > Any help would be very appreciated,
> >
> > Cheers,
> >
> > Matthieu BENOIT
> >
> >
>
>
> -------------------------------------------------------------------------------
> 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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