Thanks everyone. I asked BMRB about the error field and this was the response:
"We do not actually have a set way of defining error. Typically, authors
fill in this tag with what them deem as fairly accurate standard margins
of error. For most authors, these values seem to be about 0.05 for H,
0.1-0.2 for C, and 0.2-0.5 for N. I hope this helps a little."
Cat
On Wed, Mar 2, 2011 at 6:59 AM, Rasmus Fogh <[log in to unmask]> wrote:
> Dear All,
>
> Just an additional comment: If the BMRB knows how that error ought to be
> calculated, could the BMRB tell us? Otherwise they will be getting all
> kinds of funny numbers.
>
> 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 Wed, 2 Mar 2011, Wayne Boucher wrote:
>
>> Hello,
>>
>> The standard deviation in Analysis is calculated using the actual peak shift
>> values, and so 0.0 usually means there is only one peak (or no peaks) for the
>> associated resonance. (If by complete luck all the resonance peaks happen to
>> have exactly the same shift value then you could still get 0.0 even with more
>> than one peak.) (The shift averaging can also be weighted by spectrum, so
>> you can say that some spectra are more, or less, accurate than others, for
>> example.)
>>
>> I guess the question now is how best to put in the information that the BMRB
>> wants, so where in the code. As Aleks says, the desired value is probably
>> the max of the standard deviation and the digital resolution (or maybe it
>> should be the sqrt of the sum of the squares, I don't know). Should this be
>> in the BMRB export code or somewhere "higher" up inside Analysis somewhere?
>>
>> Wayne
>>
>> On Wed, 2 Mar 2011, Aleksandras Gutmanas wrote:
>>
>>> Hi Catherine,
>>>
>>> Usually there is some precision with which you determine the chemical shift
>>> values based on digital resolution of your spectrum and linewidth of you
>>> peaks - basically a function of your spectrometer(s). In addition, CCPN
>>> Analysis would provide a non-zero error if your assignment is connected to
>>> more than one peak (right, Tim, Wayne?). The larger of the two values for
>>> each nucleus is what BMRB would need.
>>> In my experience, typical final values are in the range of 0.03-0.05ppm for
>>> 1H and 0.3-0.5ppm for 13C and 15N.
>>>
>>> Best,
>>> Aleks
>>>> Date: Tue, 1 Mar 2011 13:09:54 -0800
>>>> From: Catherine Foo<[log in to unmask]>
>>>> Subject: chemical shift error / BMRB deposition
>>>>
>>>> I tried searching in the archives but could not find the answer
>>>> successfully (because "error" is not a very useful search term! :).
>>>>
>>>> I have submitted chemical shifts to BMRB and some of my error values
>>>> are 0.000, and BMRB wants me to provide the correct error information.
>>>> I'm not sure what sort of error BMRB is looking for, and I'm hoping
>>>> someone here with more experience could help me out.
>>>>
>>>> Am I correct in my assumption that analysis calculates error simply as
>>>> the standard deviation of all the corresponding peaks?
>>>> Is that the type of error that BMRB wants?
>>>> If I only have one peak picked for that resonance in my project, then
>>>> the SD is by definition zero?
>>>>
>>>> I am using analysis 2.0.7 and I exported the chemical shift list via
>>>> Format Converter.
>>>>
>>>> Cat
>>>>
>>>
>>
>
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