Hi Rasmus,
Thanks, I will try these at will let you know.
Once again, thanks,
Regards,
lalit
Dear Lalit,
We sdtill have the problem with specifying labelling separately for
different chains. But at least I can give you the refExperiments:
> a) 3D 15N-edited and 13C-edited NOESYs
> gnoesyChsqc_CNfilt: F1 13C, 15N-filtered, F2 13C-edited NOESY-HSQC.
That would be F1 H bound to unlabelled heavy atoms, F2, 13C, F3 H bound to
13C,
The 3D RefExperiment would be:
H[{c(0),n(0)}]_H[C].NOESY
The equivalent 15N 3D experiment would be
H[{c(0),n(0)}]_H[N].NOESY
2D experiments
F1 H bound to unlabelled heavy atoms,
F2 H bound to anything
H{[n(0)]+[c(0)]}_H.NOESY
H{[n(0)]+[c(0)]}_H.TOCSY
As you see there are a lot of variations. If these are not exactly
the experiments you are looking at, let me know what the differences are
and I shall give it another try
Yours,
Rasmus
PS. As it happens it looks like the reference names are in a bit of a
mess.
It is a matter of the square and curly braces not systematically being in
the same place. At some point I shall fix the names in a new release (and
do backwards compatibility code to make sure old data can be read), but
meanwhile you can use that data as they are.
Rasmus
---------------------------------------------------------------------------
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 Tue, 26 Jan 2010, Lalit Deshmukh wrote:
> hey Rasmus,
>
> Yes, that is correct.
>
> Regards,
> lalit
>
>
> Dear Lalti,
>
> Apologies, but I am out of active NMR for a few years now, and the
> difference between 'filtered' and 'edited' was never blindinhgly obvious.
> Can you confirm that:
> 'Filtered' means that you see protons on *unlabelled* heavy atoms?
> 'Edited' means that you see protons on *labelled* heavy atoms?
>
> This aside, we do not have a way to mark one chain as labeled, anothr as
> unlabeled. It is on the todo list, but not yet. But we can at least get
> the Experiment descriptions right.
>
> Yours,
>
> Rasmus
>
> ---------------------------------------------------------------------------
> 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 Mon, 25 Jan 2010, Lalit Deshmukh wrote:
>
>> Hey Rasmus,
>>
>> Following Filtered NOESY experiments (source: Varian Biopack) are done on
>> uniform 13C, 15N labeled protein+ non labeled peptide:
>>
>> a)gnoesyChsqc_CNfilt: F1 13C, 15N-filtered, F2 13C-edited NOESY-HSQC.
>> Isotope filtering is done according to the scheme by Stuart et al, JACS,
>> 121, 22, 5346-47, 1999.
>>
>> b)gnoesyNhsqc_CNfilt: F1 13C, 15N-filtered, F2 15N-edited NOESY-HSQC.
>> Isotope filtering is done the same way.
>>
>> c, d) 2D-CNfiltocsy and 2D-CNfilnoesy: 2D-tocsy and 2D noesy (F1
> 13C,15N
>> filtered, F2 13C,15N filtered) of bound peptide with suppression of signals
>> from 15N,13C labeled protein. Based upon original pulse sequence
>> noesyf1cnf2cn_h2o_pfg.c.
>>
>> Thanks in advance,
>>
>> Regards,
>> Lalit
>>
>>
>>
>>
>>> Dear Lalit,
>>>
>>> There are two issues here: How to describe the experiment types, and how
>>> to describe the molecule labelling state. On the topic of the first, could
>>> you describe exactly what each experiment does? What is on each axis,
>>> what is covalently bound to what, and what the pulse sequence does (HSQC,
>>> double-half finlter, ...)? I could make a good guess, but it is too easy
>>> to make misunderstandings here.
>>>
>>> We shall be coming back about how to specify the labelling state.
>>>
>>> Yours,
>>>
>>> Rasmus
>>>
>>> ---------------------------------------------------------------------------
>>> 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 Thu, 21 Jan 2010, Lalit Deshmukh wrote:
>>>
>>>> Hi,
>>>>
>>>> I am working with protein-peptide complex in Analysis. For the structure
>>>> calculations of the complex, I have three sets of spectra collected on
>>>> 13C,
>>>> 15N labeled protein+ non-labeled peptide sample:
>>>>
>>>> a) 3D 15N-edited and 13C-edited NOESYs
>>>> b) 2D and 3D 13C, 15N filtered-NOESYs
>>>>
>>>> When I define my Analysis project, I say Protein is chain A and Peptide
>>>> is
>>>> chain B. How to set up the Analysis project to distinguish between inter
>>>> and
>>>> intramolecular NOEs for these edited and filtered NOESY spectra?
>>>>
>>>> Thanks in advance,
>>>>
>>>> Regards,
>>>> Lalit
>>>>
>>>
>>
>
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