Hi Wayne,
thank you as well for the details... I am happy with the "unify peaks" option.
still I have 2 more questions.
On Jun 5, 2012, at 3:58 PM, Wayne Boucher wrote:
> More from Tim:
>
> "RMM" is just Right Mouse Menu. ;-)
>
> The average chemical shifts can be found from any peak table (e.g. of selected peaks) by clicking the peak's row and then [Resonances]. - The peak position can be typed into the table to be the average. (Though it would be possible to add a function to Analysis to set a peak position to its resonance average). The moved peak could then be the reference to unite the resonance positions.
>
> Also, it may be worth noting that playing with peak positions so that overlapped/distorted regions don't influence the chemical shift average can often be avoided by decreasing the influence of individual spectra on the averaging calculation: Menu:Experiment:Spectra:Tolerances - Shift Weighting column. For example a precise well-separated spectrum, as an authoritative source of shift values, may have a shift weighting of more than 1.0, but a severely overlapped or ambiguous one may have almost none.
Currently I have around 20 spectra in the project, if I want to align the peaks in 1 of them, I would set this to 1 and all others to 0.1.
Or is there a difference between a 10 : 1 ratio and a 1 : 0.1 ratio?
>
> There is no means to align resonances from a table; we generally felt that this operation was not so scientific and so the user should at least be looking at the spectrum. We could create a macro script if this really causes a problem.
I was rather wondering if there is an option in the resonance table that can "activate the peaks". For example, currently in e.g. the peaklist one can click on a peak and say "Mark selected", so two lines appear and cross at the peak position. I think for the "unify resonance option" it would be great to have an option that (1) you select a bunch of peaks of 1 atom in the same amino acid (e.g. 6 ProCa), then (2) you can say "activate the peaks" (they all get a square around the cross and are RMM active) in the spectrum, (3) you go back to the spectrum and say RMM:Assign:Unify peaks. Since this is much easier than going through the spectrum and selecting all the peaks of interest by hand. Is there already a way to do that?
>
> Another functionality that may help is the synthetic peak list creation: Menu:Peak:Peak Lists - Synthetic Lists. This will use shift list averages to create whole peak lists for most types of experiment. Although, naturally you need to have an authoritative set of chemical shifts first.
That works well actually. But also... in solid-state spectra there are tiny shifts between spectra as you cannot 100% control the temperature. So one needs to center them or go through and check. Anyhow, I really like this option, too. In the combination with unify resonances its even better!
>
> Wayne
Thank you
Carolin
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