Whoops, we didn't realise that had made it into the last release, it
wasn't supposed to have, that part of the tutorial is still being worked
on, and in particular the data sets to which that specifically applies
have not yet been included in the tutorial data download (but when they do
get included the 0, -1, 0 will apply specifically for that data). That
part of the tutorial has also not been well tested. Caveat emptor!
Wayne
On Tue, 13 Dec 2005, Murali Vadivelu wrote:
> That's interesting to note because the extended tutorial seem to make
> the same assumption as I did, it says 0, -1, 0 for sequential
> assignment with a preceding C.
>
> On 13 Dec 2005, at 03:57 pm, Wayne Boucher wrote:
>
> > F1 F2 F3 are the dimensions of the spectrum (and hence the peak),
> > in the
> > order of the data on disk, I think (in theory that might not be
> > true but
> > in practise I think it is). It is also the order that things are
> > listed
> > in the Edit Assignment popup. This is independent of window
> > dimensions
> > and in particular is not in general the same as the x, y, z of the
> > windows. So if you have an (H, N, C) spectrum then F1=H, F2=N,
> > F3=C but
> > this spectrum can get mapped onto a window with x=C, y=H and z=N
> > (or any
> > of the six permutations). Hope that helps.
> >
> > Wayne
> >
> > On Tue, 13 Dec 2005, Murali Vadivelu wrote:
> >
> >> Eureka!
> >>
> >> x, y, z != F1 F2 F3 or I have understood it wrong, the way it works
> >> in analysis.
> >>
> >> When, I used F1 0 F2 0 F3 -1, it worked! I have x=1H, y=13C, z=15N,
> >> which I thought should be F1, F2, F3, respectively (as mentioned
> >> yesterday in the first few e-mails I sent). I discovered this as the
> >> N=z changed as I applied the sequential spin system as 0, -1, 0 --
> >> after applying the upgrade.
> >>
> >> On 13 Dec 2005, at 03:05 pm, Murali Vadivelu wrote:
> >>
> >>> I have upgraded the file. Then restarted analyis, propagated NH
> >>> assignment from a 15N-HSQC to an HNCO experiment. I set the atom
> >>> type of the CO to C using the 'edit assignment' popup. Then set the
> >>> sequential spin system 0, -1, 0. It didn't do anything. I repeated
> >>> it many times and no output on the command line either. Nothing
> >>> happened. I tried R:Assign:Add to spin system and analysis adds the
> >>> CO to the NH spin system and not to a new spin system or an already
> >>> existing spin system which corresponds to the C which I created
> >>> manually for the CA and CB in CBCACONH spectra.
> >>>
> >>> To double check, I started anew from a completely different NH in
> >>> the 15N-HSQC. I still have the same problem. Sequential spin system
> >>> does not seem to work as described. I am pretty sure, by now, I
> >>> understand you clearly!
> >>>
> >>> Could you suggest anything to try out to debug this? I would be
> >>> very happy to try out.
> >>>
> >>>
> >>> On 13 Dec 2005, at 11:49 am, Tim Stevens wrote:
> >>>
> >>>>>>>> Ca, then the same i-1 spin system will be picked up again.
> >>>>>> Are there any error messages appearing on the command line where
> >>>>>> Analysis
> >>>>>> was started?
> >>>>>
> >>>>> Nope. Not at all... Could it be that analysis is sensitive to
> >>>>> which
> >>>>> kind of atom is in which axis (C vs N in F3)? Unlikely?
> >>>>
> >>>> I have just found an error message. It was appearing on the
> >>>> command line
> >>>> when seq spin system was set for the second time. The bug seems to
> >>>> explain
> >>>> the issue entirely. A patch has been posted on the update server.
> >>>>
> >>>> Although I suspect that any error message in your case may be long
> >>>> gone,
> >>>> i.e. it may not have been triggered after restarting Analysis,
> >>>> always look
> >>>> out for these as they can save a lot of e-mailing.
> >>>>
> >>>> Tim
> >>>>
> >>>> -------------------------------------------------------------------
> >>>> --
> >>>> ----------
> >>>> Dr Tim Stevens Email: [log in to unmask]
> >>>> Department of Biochemistry [log in to unmask]
> >>>> University of Cambridge Phone: +44 1223 766022 (office)
> >>>> 80 Tennis Court Road +44 7816 338275 (mobile)
> >>>> Old Addenbrooke's Site +44 1223 364613 (home)
> >>>> Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
> >>>> United Kingdom http://www.pantonia.co.uk
> >>>> -------------------------------------------------------------------
> >>>> --
> >>>> ----------
> >>>> ------ +NH3CH(CH(CH3)OH)C(O)NHCH(CH(CH3)CH2CH3)C(O)NHCH(CH2CH2SCH3)
> >>>> CO2- -------
> >>>> -------------------------------------------------------------------
> >>>> --
> >>>> ----------
> >>
>
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