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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