Dear Murali,
For practical reasons I am answering your original report, rather than
your latest message. There are two problems with this report.
First, the situation you describe is not the right place to look for
sequential assignment in HNCA triple resonance backbone experiments. To
connect spin systems {27} and {33} (e.g.), you would look at the following
peaks the:
HNCA:
{27}N[45] {27}H[67] {92}CA[12] - HNCA i-1 peak
{27}N[45] {27}H[67] {27}CA[81] - HNCA i peak
HNcoCA:
{33}N[87] {33}H[111] {27}CA[81] - HNcoCA i-1 peak
You are looking at the HNCA and HNcoCA peaks of your spin system {5}, but
not at any of the peaks on the NH of your spin system {6}
Second, in order to prove that there is a problem with Analysis you need
to establish that
1) spin systems {x} and {y} are registered as i->i+1 connected
2) you are assigning spin system {x} to a specific residue
3) spin system {y} does not change.
In your example you are saying that resonance {6}CA[203] is the CA(-1)
peak relative to spin system {5}, seen in both the HNCA and the HNcoCA,
but you are saying nothing about the existence of an i->i+1 link between
{5} and {6}. The place to look is the EditSpinSystem popup.
I can understand that you are confused, but we can only spend so much
time on helping people with their confusion - we have to concentrate on
fixing known bugs. If you could work through the logic of the problem in
explicit detail it would be easier for us (or yourself) to solve.
Yours,
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, 15 Feb 2006, Murali Vadivelu wrote:
> Description of the problem:
> I have a set of triple resonance experiments and a 15N-HSQC. I initially
> picked the peaks from all the spectra anonymously. Given the set of typical
> triple resonance spectra, I was able to connect the peaks from the same
> residue and its preceding residue to their corresponding amide peak (NH) in
> the 15N-HSQC, i.e., establish i and i-1 connectivity of the anonymously
> numbered spin systems.
> Eg., HNCA: {5}N[10],{5}N[11],{5}CA[200] (added to the spin system using 'R:'
> menu); {5}N[10],{5}N[11],{6}CA[203] (added to the sequential spin system
> using 'R:' menu)
> HNcoCA: {5}N[10],{5}N[11],{6}CA[203]
> Please see below, 'steps to reproduce.'
>
> Version-Release number of selected component:
> 1.0.9 (may have been present in 1.0.8)
>
> How reproducible:
> Always
>
> Steps to Reproduce:
> 1. Assign a set of spectra as described above in the 'description of the
> problem.'
> 2. Now assign residue specific information and convert the annonymous spin
> system created in the previous step, eg., {5}N and {5}H to a (named and
> numbered) residue in the sequence of your molecule, say, MS1.
>
> Actual Results: T
> In the example above, spin system {5} and its corresponding intra-residual
> CA, {5}CA, gets the residue specific assignment (name and number) from MS1,
> eg., {5}CA becomes 4TyrCA (an atom of, say, residue i). However, despite the
> presence of inter-residual connectivity (say, i-1) information from the
> above steps, anonymous spin system {6}CA remains anonymous.
>
> Expected Results:
> You expect the inter-residual peak to get the corresponding assignment
> automatically. However, it does not. Exceptions are spectra like HNCA which
> have both i and i-1 information, where it seems to work fine. It remains
> anonymous in spectra that give only i-1 information like HNcoCA, HNCO.
>
> Additional info:
> NA
>
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