Dear Simon,
That makes sense. But could you tell me more about what happened when you
tried using a MolSystem with three different chains?
The correct way to handle this would be a separate facility fo assigning a
given resonance to different frequencies in different states of the
molecule. That is not yet implemented, though it is in the data model and
somewhere on the TODO list. Meanwhile using separate chains is the best
workaround we have. We would hope that that worked, and would try to fix
any problems.
Just as a matter of science rather than software: You are getting three
separate sets of signals from the Proline. How many other signals are
duplicated? And where would the third set come from? I remember Proline
cis/trans isomerism, but can not imagine how a single proline coudl have
three different conformations. Just curious.
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, 25 Nov 2010, S.P. Skinner wrote:
> Dear Rasmus
>
> We have one peptide wherein the proline adopts three conformations, thereby
> giving three resonances of differing intensities. We wish to use the FUDA
> program to perform linewidth analysis and therefore require a sparky
> formatted peak list. We wanted to assign each proline resonance
> corresponding to each conformation in order that three separate peak lists
> could be exported for this analysis. But using three different chains did
> not prove effective.
>
> Regards
>
> Simon
>
> On 11/24/2010 03:19 PM, Rasmus Fogh wrote:
>> Dear Simon,
>>
>> Not sure I understand this. You have three different peptides in your
>> sample? Do you also have three different chains in your MolSystem (you
>> should)? Are you assigning the different peaks to different chains? Do all
>> the peptides have a Pro-4? Why are you trying to assign a new resonance to
>> something that is already assigned elsewhere, instead of assigning the peak
>> to the same pre-existing resonance?
>>
>> Some more details might help,
>>
>> 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, 23 Nov 2010, S.P. Skinner wrote:
>>
>>> Hi All
>>>
>>> I am using a 1H-13C HSQC spectrum of three separate molecules all in one.
>>> I am attempting to assign more than one peak to a C-H resonance. When I
>>> attempt to assign a resonance in a sister list of a spectrum, that has
>>> already been assigned previously in another list, the message: Redundant
>>> resonance: There are more resonances (3) than atoms set for 4Pro HD3/HD2.
>>> The reason for multiple assignment is that the three different peptides
>>> have different intensities and therefore require their own assignment.
>>>
>>> Any suggestions on how to circumvent this problem?
>>>
>>> Kind Regards
>>>
>>> Simon Skinner
>>>
>>> --
>>> 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]
>
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