The way I read the code right now the peaks should not be picked outside
of the allowed region. However, it is worth pointing out that we
discovered yesterday (courtesy of Magnus) that there is a bug in
calculating the allowed region. The subject of the email I sent out was
"minAliasedFreq, maxAliasedFreq bug fix" and you can find it on the CCPNMR
archives at http://www.jiscmail.ac.uk/lists/ccpnmr.html if you have
deleted it already from your inbox. This bug could cause the region to be
bigger than it should be.
Wayne
On Fri, 21 Oct 2005, Magnus Helgstrand wrote:
> Hello,
>
> I have noticed that Ctrl-Shift-Click picks a peak in all visible
> spectra. Since they (usually) are perfectly overlapped, only one of
> them is shown.
>
> Could this be the reason you got a peak outside the "allowed" region?
>
> By the way, I think Tim agreed to change the behavior of the Ctrl-
> Shift-Click to just pick one peak in one spectrum. (Am I right, Tim?)
> The problem is then which spectrum the peak should be added to. Could
> there be added some kind of "list" to the graphics window from which
> the active spectrum for peak picking could be selected?
>
> Magnus
>
> 21 okt 2005 kl. 09.37 skrev Rasmus Fogh:
>
> > Dear Justin,
> >
> > Ideally min ppm and max ppm would be set when you first enter the
> > spectrum
> > and never changed. This requires knowing if you can actually have
> > aliased
> > peaks and in what region, so the user would have to enter it
> > explicitly.
> > But to make it easier, Analysis calculates a default settiing for you.
> > Then, if you pick a peak (or alias one) outside the allowed region,
> > Analysis automatically expands the allowed region. The user is always
> > right, if the user says there is a peak there it has to be allowed. In
> > your case you maybe picked a peak outside the allowed area, or somehow
> > unaliased or moved one there. Maybe you picked a peak in the TOCSY-
> > HSQC
> > when you thought is was the 2D TOCSY. That would have the effect
> > you saw.
> > Or, of course, it could be that picking peaks in the 2D TOCSY or some
> > other innocuous activity had this as an undesirable side effect.
> > Tim would
> > be the only one to have an opinion there. These things can go wrong
> > - what
> > we are trying to do is to get the right settings for you instead of
> > forcing the users to enter them by hand for every spectrum, and
> > that is
> > simply not easy.
> >
> > Yours,
> >
> > 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 Thu, 20 Oct 2005, Justin T Douglas wrote:
> >
> >
> >>
> >>
> >>> Are you sure you are seeing a mirror image and not a
> >>> displaced image?
> >>>
> >>
> >> You are correct. I misspoke. I observe displaced
> >> images, NOT mirror images.
> >>
> >>
> >>> Then go to 'Edit Spectra', click 'Referencing', and
> >>> look under
> >>> 'Minimum aliased Frequency' and 'Maximum aliased
> >>> frequency'. for the HNHN> dimension of your
> >>>
> >> HSHSQCOTOCSYIf you have no peaks
> >>
> >>> outside the acquired
> >>> region, reset the frequency limits so that they
> >>> correspond to the limits
> >>> of what you have asascuiredYour ghost peaks should
> >>> then disappear.
> >>>
> >>
> >> Once again you are correct. Resetting min. ppm fixed
> >> the problem.
> >>
> >> I do have one question. Why did Analysis miscalculate
> >> min ppm for me? Referencing, number of points and
> >> sweep width were all set correctly.
> >>
> >>
> >>
> >>
> >>
> >>
> >> __________________________________
> >> Yahoo! Mail - PC Magazine Editors' Choice 2005
> >> http://mail.yahoo.com
> >>
> >
>
|