Tim - can you please tell me how I can sign off this mailing list??!
Best,
Ella
________________________________
From: CcpNmr software mailing list on behalf of Tim Stevens
Sent: Thu 16/02/2006 19:21
To: [log in to unmask]
Subject: Re: Bug report: Propagation of assignment
> > Analysis has no innate way of knowing which HNCA spin system you meant
> > to connect an HNcoCA peak to. You have to make a choice on the basis
> > of matching peak positions and make the resonance connection yourself,
> > in the same way that you'd do any other assignment.
>
> It has the necessary information from the spin system number which is
> consistent and was connected (i and i-1) with the procedure described
> above. I have already made the resonance connection myself.
> Say for example, if spin system {5} is assigned to 4Tyr (anonymous
> assignment is converted to non-anonymous) and if spin system {6} is
> the preceding spin system (i-1) based on sequential connectivity
> established as described above, why can't spin system {6}
> automatically get 3Ser as its assignment. I thought it was
> sufficient. Isn't it?!
It is sufficient. This is how Analysis works, it is just that your project
has lots of spin systems that aren't connected sequentially. The
assignment propagation obviously doesn't work across these unconnected
spin systems.
To take examples from your project, considering residues 9 and 10:
You have HNCA peaks:
# F1 F2 F3
63 9LysH 9LysN 9LysCa
64 9LysH 9LysN {164}CA[408]
104 10SerH 10SerN 10SerCa
105 10SerH 10SerN {185}CA[511]
You have HNcoCA peaks:
# F1 F2 F3
33 9LysH 9LysN {164}CA[408]
58 10SerH 10SerN {185}CA[511]
And the corresponding spin systems are:
# Res Seq. Seg Resonances
4 9Lys 0:007 H N Cb Ca C HB[710] Ha Ha
78 10Ser 0:008 H N Ca Cb C
164 54:000 CB[405] CA[408] C[409] HB*[706] HA[707]
185 71:000 CB[510] CA[511] C[514] HA[789] HB2|HB3[790]
The inter residue 10Ser CA peaks (nums 105 & 53) in both the HNCA and
HNcoCA peaks are connected to the same resonance [511], fine, but this
resonance has been put in a completely different spin system {185} to the
backbone/assigned spin systems for 9Lys {4}. Also, this connecting
resonance [511] is not the same resonance that you have assigned to the
9Lys intra residue HNCA peak (9LysCa).
Only the assigned spin systems ({4} & {78}) are sequentially connected -
positions 7 & 8 of segment 0 respectively. The spin systems to which your
inter residue CA peaks have been linked ({185} & {164})have no sequential
connectivity. I have double checked this with the Seq. Segments. As {185}
& {164} have no sequential connectivity no assignment propagation can be
expected.
I will not comment further on this thread.
T.
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Dr Tim Stevens Email: [log in to unmask]
Department of Biochemistry [log in to unmask]
University of Cambridge Phone: +44 1223 766022 (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.pantonia.co.uk
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