> > > - can I use the "Follow shift changes" dialog for ligand titrations?
> >
> > Yes. This is the place. It will group series of peaks, assign them and
> > extract the shift changes.
> >
> but how exactly do you do it? Is there an online help page available for
> this function (clicking in our installation on the "help" button in the
> FollowShiftChanges dialogue just opens up an empty help window...).

In-line with other mailing list threads, the documentation is a bit out of
date and is just missing for the FollowShiftChanges popup because it is a
newer one.


> What are peak groups, and how do you use them?

By peak groups I mean peaks assigned to or derived from to the same
resonances, so that you can follow chemical shift changes and intensity
changes.


> We are in the situation where we have 25 HSQCs loaded in (pH titration),
> with 25 peak lists, but when we open FollowShiftChanges it complains
> that "there is only one shift list, do you want to create the rest?".

When following a resonance in a titration the idea is to record different
chemical shifts for the resonance under different conditions. Each shift
list contains all the shifts for a given set of conditions.


> Sure enough, after clicking "yes", "Measurement lists" shows 25 shift
> lists and only one of them has peaks in it, but peaks from 3 HSQCs
> (that's how many we have assigned at the moment).

So the peaks are associated with a given shift list by virtue of their
experiment being associated with the conditions that the given shift list
represents.

If all the experiments in the series were linked initially to only one
shift list then that list would have chemical shifts for all of the
assigned peak lists that contribute to the experiments.

If the experiments are now put into separate shift lists the shifts would
still be recorded in the initial list even if there are now no peaks to
represent them.

When chemical shifts are curated they have values calculated from a
weighted average of peak positions for a specific shift list. If you
unlink an experiment from a shift list the values are recalculated using
the remaining experiments.

Shifts representing no peaks can be removed with "Delete Orphans" in the
BrowseResonances popup.


> What exactly is the difference between shift lists and peak lists, and
> how do you get the program to put new peaks in the correct list?
>
> If you delete the peaks from the second and third HSQC in shiftlist1,
> and use "copy assignments" the peaks still end up in
> peaklist2(shiftlist1) instead of shiftlist2...

Hopefully I've covered most of the shift list explanation above. Peaks
only go with a list because of their experiments. So if you want the peaks
from an experiment to contribute to a different shift list then the
experiment has to be linked to that shift list.

The shift values are weighted averages from positions, this is separate
from real picked peaks and resonances allow assignments to be recorded
for the same atoms under different conditions.


If you have three HSQC peak lists that cannot use separate shift lists
then I think all of the spectra for those peak lists might be linked to
only one experiment. (This is just a guess from what you describe, so let
me know if this is wrong.)

In the CCPN data model experiments (what you did) are separate from
spectra (a resultant bit of data) so you can record FIDs, projections etc
under the same experiment.

Although it is not enforced by the underlying data model, if you load a
spectrum and call its experiment "HSQC", when you already have one with
that name, Analysis thinks you mean to associate multiple spectra with
that one experiment. Hence all "HSQC" spectra and peaks work with only one
shift list.

The solution in this instance would be to reload two of the HSQC spectra
into experiments with different names, copy peaks from their equivalent in
the original multi-spectrum experiment, then delete the extra spectra in
this original spectrum.

Hope this helps,

T.

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 Dr Tim Stevens			Email: [log in to unmask]
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