Dear Simon,
If I understand it correctly you need to export three separate peak lists,
one for each conformation. Is that correct? If it is, I would recommend:
1) make three different chains of the same peptide within a single
MolSystem.
2) Assign the peaks for each conformation, using a separate chain in a
spearate peak list for each.
3) Export the peak lists one by one.
If most of the peaks are the same in the three states, you could pick the
comon peaks first and then use the [Copy Peaks] button in M:Peak->Peak
Lists {Peak Lists}. If there are still problems a small script might fix
them.
This is for the record. Hopefully Dans program will do the whole thing in
a simper way.
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,
>
> 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]
>
|