Dear Rasmus,
separate chains did not work because we could not export a peak list for
each chain, only a complete peaklist into sparky, we could export the
shifts, but not the assignments with them. This was the problem. Using
3 separate molecules gave a redundant resonances error. Regarding the
science question that is at this point unknown and I cannot elaborate
any further on that I am afraid.
I will go with Dan's suggestion of peak separator for the moment and see
if that works. That may circumvent the exportation issue.
Simon
On 11/25/2010 12:23 PM, Rasmus Fogh wrote:
> 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]
>>
--
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]
|