Hi Rasmus
At present the side chain amides are picked and assigned to spin
systems, but analysis doesn't know that they are side chain amides
because when I set the experiments up I didn't expect there to be any
side chain amides since the experiments were all TROSY experiments.
Simon
Rasmus Fogh wrote:
> Dear Simon,
>
> What is the status of your side chain amide peaks, exactly? Are they
> picked? Assigned, and if so to what?
>
> There is always the option of doing the picking and assigning
> manually, step by step. For a limited number of peaks in something
> already partially assigned that might actually be the simplest.
>
> 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, 29 Mar 2010, Wayne Boucher wrote:
>
>> Hello,
>>
>> I guess you mean the same spin system. (So the two amide H will have
>> the same N resonance but that will be different than the other
>> resonances for the spin system.) So there are several options here.
>> If you don't know anything else about the spin system (such as which
>> residue it is) then you could use the Resonance --> Spin Systems
>> dialog and use the Merge button at the bottom. But if you do assign
>> them to the same residue then the spin systems should automatically
>> be merged.
>>
>> But Initialise Root Resonances should also work assuming the peaks
>> are not already assigned (so if they are already assigned even with
>> just anonymous resonances then it won't work). So when you say
>> nothing happened do you mean that there were no Amide Side Chain
>> Peaks listed or ...?
>>
>> Wayne
>>
>> On Mon, 29 Mar 2010, S.P. Skinner wrote:
>>
>>> how do you make sure that they have the same n resonances as the
>>> backbone. I tried to intialise root resonances after starting
>>> assignment, but nothing happened. any ideas?
>>>
>>> Wayne Boucher wrote:
>>>> Hello,
>>>>
>>>> We're not quite sure we understand the question. So you can assign
>>>> these peaks in the normal way, only obviously make sure that they
>>>> have the same N resonance, and that the spin system is the same as
>>>> for the backbone. But possibly that's not what you are asking!
>>>>
>>>> Wayne
>>>>
>>>> On Mon, 29 Mar 2010, S.P. Skinner wrote:
>>>>
>>>>> Hey Guys
>>>>>
>>>>> Is there a way to include side chain amide peaks onto an HSQC once
>>>>> assignment has begun and approx 70% of the protein is assigned?
>>>>>
>>>>> Regards
>>>>>
>>>>> Simon
>>>>>
>>>>> --
>>>>> Simon P Skinner
>>>>> Protein Chemistry Group
>>>>> Leiden Institute of Chemistry, Universiteit Leiden
>>>>> Phone: +31 71 527 6089 / Fax: +31 71 527 4349
>>>>> E-mail : [log in to unmask]
>>>
>>> --
>>> Simon P Skinner
>>> Protein Chemistry Group
>>> Leiden Institute of Chemistry, Universiteit Leiden
>>> Phone: +31 71 527 6089 / Fax: +31 71 527 4349
>>> E-mail : [log in to unmask]
>>
--
Simon P Skinner
Protein Chemistry Group
Leiden Institute of Chemistry, Universiteit Leiden
Phone: +31 71 527 6089 / Fax: +31 71 527 4349
E-mail : [log in to unmask]
|