Hi,
For CPMG, R2eff values will be calculated from:
R2eff = ( 1/delayT ) * ln ( Icpmg / Iref )
There is an error on Icpmg and Iref values ; this can be obtained from
duplicate measurements.
For other relaxation dispersion experiments (e.g. R1rho), R2eff values
could be extracted from curve fitting of exponential decays. Errors
could also be obtained from duplicate measurements.
For R2eff direct reading, what relax should do is simply store the
values with their respective CPMG frequency (for CPMG data) and
spectrometer frequency. Then, relax should pass these informations to
the code so curve fitting can proceed.
What's proposed at:
https://mail.gna.org/public/relax-devel/2009-02/msg00009.html
(Message-id:
<[email protected]>)
seems fine as long as there are no differences between analyses
proceeding from intensities (both Icpmg and Iref) or directly from
R2eff, i.e. as long as data can be shared easily within relax.
I am not sure, however, about how this should be handled... but the way
it is done for intensities seems quite versatile and could allow the
flexibility needed.
Regards,
Séb
P.S. Sorry if this is not clear. I'm quite confused with all this...
Edward d'Auvergne wrote:
> Hi,
>
> How would you design this data around the idea proposed at
> https://mail.gna.org/public/relax-devel/2009-02/msg00009.html
> (Message-id: <[email protected]>)?
> What about R2eff error values? And what about the source of the
> R2eff values and errors?
>
> Regards,
>
> Edward
>
>
>
> On Thu, Jan 29, 2009 at 2:59 PM, Sébastien Morin
> <[email protected]> wrote:
>
>> Hi,
>>
>> A list of R2eff to input directly to relax would contain R2eff for every
>> residue as a function of the cpmg frequency (cpmg_frq).
>>
>> We could have the data input as for intensities, i.e. a list (i.e. a
>> file) for every cpmg frequency, such as :
>>
>> =========== cpmg_frq ============
>> spin R2eff dR2eff
>> spin R2eff dR2eff
>> ...
>>
>> This wouldn't need too much effort as it is similar to what is done for
>> intensities.
>>
>> Is that what you had in mind ?
>>
>> Regards,
>>
>>
>> Séb :)
>>
>>
>>
>>
>> Edward d'Auvergne wrote:
>>
>>> Do you have an example of what this R2eff data will look like for a
>>> single spin system?
>>>
>>> Regards,
>>>
>>> Edward
>>>
>>>
>>> On Wed, Jan 28, 2009 at 11:39 PM, Sébastien Morin
>>> <[email protected]> wrote:
>>>
>>>
>>>> Hi,
>>>>
>>>> relax_data.read() could be modified to allow the reading of r2eff data.
>>>>
>>>> I will try to work this out.
>>>>
>>>> Do you see any special problem that might arise ?
>>>>
>>>> Thanks for the advice !
>>>>
>>>>
>>>> Séb :)
>>>>
>>>>
>>>>
>>>> Edward d'Auvergne wrote:
>>>>
>>>>
>>>>> Hi,
>>>>>
>>>>> This user function should be very, very similar to the
>>>>> relax_data.read() user function. Actually, do you think that
>>>>> relax_data.read() could be modified and used instead?
>>>>>
>>>>> Regards,
>>>>>
>>>>> Edward
>>>>>
>>>>>
>>>>> On Thu, Jan 15, 2009 at 3:04 PM, <[email protected]> wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Author: semor
>>>>>> Date: Thu Jan 15 15:04:33 2009
>>>>>> New Revision: 8472
>>>>>>
>>>>>> URL: http://svn.gna.org/viewcvs/relax?rev=8472&view=rev
>>>>>> Log:
>>>>>> Started to implement a function for reading 'R2eff' values directly.
>>>>>>
>>>>>> This is as proposed in a post at:
>>>>>> https://mail.gna.org/public/relax-devel/2009-01/msg00020.html
>>>>>> (Message-id:
>>>>>> <[email protected]>)
>>>>>>
>>>>>> The function does not contain code yet.
>>>>>>
>>>>>>
>>>>>> Modified:
>>>>>> branches/relax_disp/prompt/relax_disp.py
>>>>>> branches/relax_disp/specific_fns/relax_disp.py
>>>>>>
>>>>>> Modified: branches/relax_disp/prompt/relax_disp.py
>>>>>> URL:
>>>>>> http://svn.gna.org/viewcvs/relax/branches/relax_disp/prompt/relax_disp.py?rev=8472&r1=8471&r2=8472&view=diff
>>>>>> ==============================================================================
>>>>>> --- branches/relax_disp/prompt/relax_disp.py (original)
>>>>>> +++ branches/relax_disp/prompt/relax_disp.py Thu Jan 15 15:04:33 2009
>>>>>> @@ -182,6 +182,22 @@
>>>>>> relax_disp_obj.exp_type(exp=exp)
>>>>>>
>>>>>>
>>>>>> + def r2eff_read(self):
>>>>>> + """Function for reading 'R2eff' values directly, instead of
>>>>>> calculating them within relax
>>>>>> + starting from the intensities.
>>>>>> +
>>>>>> + THIS FUNCTION IS NOT WRITTEN YET.
>>>>>> +
>>>>>> + Keyword Arguments
>>>>>> + ~~~~~~~~~~~~~~~~~
>>>>>> +
>>>>>> +
>>>>>> + Examples
>>>>>> + ~~~~~~~~
>>>>>> +
>>>>>> + """
>>>>>> +
>>>>>> +
>>>>>> def select_model(self, model='fast'):
>>>>>> """Function for the selection of the relaxation dispersion curve
>>>>>> type.
>>>>>>
>>>>>>
>>>>>> Modified: branches/relax_disp/specific_fns/relax_disp.py
>>>>>> URL:
>>>>>> http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/relax_disp.py?rev=8472&r1=8471&r2=8472&view=diff
>>>>>> ==============================================================================
>>>>>> --- branches/relax_disp/specific_fns/relax_disp.py (original)
>>>>>> +++ branches/relax_disp/specific_fns/relax_disp.py Thu Jan 15 15:04:33
>>>>>> 2009
>>>>>> @@ -1084,6 +1084,14 @@
>>>>>> continue
>>>>>>
>>>>>>
>>>>>> + def r2eff_read(self):
>>>>>> + """Function for reading 'R2eff' values directly, instead of
>>>>>> calculating them within relax
>>>>>> + starting from the intensities.
>>>>>> +
>>>>>> + THIS FUNCTION IS NOT WRITTEN YET.
>>>>>> + """
>>>>>> +
>>>>>> +
>>>>>> def return_data(self, spin):
>>>>>> """Function for returning the peak intensity data structure.
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> relax (http://nmr-relax.com)
>>>>>>
>>>>>> This is the relax-commits mailing list
>>>>>> [email protected]
>>>>>>
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>>>>>> reminder, or change your subscription options,
>>>>>> visit the list information page at
>>>>>> https://mail.gna.org/listinfo/relax-commits
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> relax (http://nmr-relax.com)
>>>>>
>>>>> This is the relax-devel mailing list
>>>>> [email protected]
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>>>>>
>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> relax (http://nmr-relax.com)
>>>>
>>>> This is the relax-devel mailing list
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>>>>
>>>
>>>
>>
>
>
--
Sébastien Morin
PhD Student
S. Gagné NMR Laboratory
Université Laval & PROTEO
Québec, Canada
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