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.
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:
> 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
> 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?
> 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.
>>> 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.