OK, after a bit of a struggle I have put some extra code in which will
work for this kind of dim ordering issue now. I have a feeling it might
not work in a fairly unusual situation (multiple peakLists with different
dim orderings) but fixing that would require unbelievably major changes to
the code so is best left undone for now.
Patch on the update server.
Wayne
On Wed, 29 May 2013, Xue Liu wrote:
> Hi Wayne,
> Thanks a lot! I would be very appreciated if you can update me once the question is solved.
>
> Xuehui
>
> ___________________________________________________________________________________________
> From: Wayne Boucher <[log in to unmask]>
> To: [log in to unmask]
> Sent: Thursday, May 30, 2013 2:10 AM
> Subject: Re: Problem with the Assignment: Protein Sequence Assignment
>
> Hello,
>
> I know what the problem is now (it is assuming that the spectrum
> dimensions for the x and z axes are in the same order as the window, and
> that is not the case here). But this is definitely a non-trivial thing to
> fix so will take a bit of time.
>
> Wayne
>
> On Tue, 28 May 2013, Xue Liu wrote:
>
> >
> > Hi Wayne,
> > I am using linux(remote logged in from windows). And please see the project folder in the
> > attachment.
> > Thank you very much for your help!
> >
> > Best regards,
> >
> > Xuehui
> >
> >__________________________________________________________________________________________
> _
> > From: Wayne Boucher <[log in to unmask]>
> > To: Xue Liu <[log in to unmask]>
> > Sent: Wednesday, May 29, 2013 7:01 AM
> > Subject: Re: Problem with the Assignment: Protein Sequence Assignment
> >
> > Hello,
> >
> > I spoke with Tim today (he's working in another location these days, so I
> > don't see him that often) and he suggested that you send us the project
> > (not the spectra) zipped or tar gzipped, so I mean the directory
> > containing the project.
> >
> > Regards, Wayne
> >
> > On Tue, 28 May 2013, Wayne Boucher wrote:
> >
> > > Hello,
> > >
> > > That is odd. If you click on the same row in the top table a second time
> > > does it then sort itself? By the way, are you using Windows (so rather than
> > > Linux)? It's possible there is some odd Windows-specific issue here (for
> > > reasons I can't guess!).
> > >
> > > Wayne
> > >
> > > On Mon, 27 May 2013, Xue Liu wrote:
> > >
> > >> Hi Wayne,
> > >> Thank you for the suggestion. But I think that maybe not the problem, cause
> > >> I have only one set of resonance.
> > >> This is what I did, is there anything wrong?
> > >> 1. Open the spectra (I opened Nhsqc, cbcaconh, hncacb)
> > >> 2. Manually peak picked the Nhsqc.
> > >> 3. Assignment->Initialise Root Resonace (selected the sidechains and
> > >> confirm)
> > >> 4. Assignment->Pick & Assign form Root (adjust the tolerence 0.2ppm for N15
> > >> and 0.02ppm for proton)->Pick all
> > >> & Assign Root Resonance
> > >> 5. Molecule->Add seqence (To build the protein molecule)
> > >> 6. Window->Clone (To clone a triple resonance window, say the former one is
> > >> window3, the new one is window4)
> > >> 7. Assignment->Protein sequence Assignment (query window use window3 and
> > >> cbcaconh, match window use window4
> > >> and hncacb. leave {options}untouched)
> > >> 8. in the {spin systems tab}, when I click on one spin system, I could see
> > >> the query window works ok, but the
> > >> match window doesn't show any match strips. It seemed that the match window
> > >> had found something, since when I
> > >> click on differenct spin systems, different numbers of strips were opened.
> > >> But nothing is in the strip
> > >> because every strip in the match window is showing the middle of proton
> > >> chemical shift, lowest N15 chemical
> > >> shift and the right C13 chemical shift.
> > >>
> > >> I've attached a screenshot, hope I could do that in a maillist and you can
> > >> see it.
> > >>
> > >> Thank you very much!
> > >>
> > >> Best Regards,
> > >>
> > >> Xuehui
> > >>
> > >>
> >>>________________________________________________________________________________________
> __
> > ___________________
> > >> From: Wayne Boucher <[log in to unmask]>
> > >> To: [log in to unmask]
> > >> Sent: Friday, May 24, 2013 5:13 PM
> > >> Subject: Re: Problem with the Assignment: Protein Sequence Assignment
> > >>
> > >> Hello,
> > >>
> > >> Tim suggests to check that the triple resonance peaks in both spectra are
> > >> assigned to amide root resonances and that both spectra are assigned to
> > >> the same set of resonances.
> > >>
> > >> Wayne
> > >>
> > >> On Wed, 22 May 2013, Xue Liu wrote:
> > >>
> > >> > Hi
> > >> > I am a new user of the CCPNMR and am trying a backbone assign job with it
> > >> now. I think i've followed
> > >> > every step of the tutorial
> > >> （http://www.ccpn.ac.uk/software/tutorials/analysis-beginners）, but I got
> > >> > this problem with the Protein Sequence Assignment. When I click on the
> > >> spin systems, I should get the
> > >> > matching strips on the Match Window according to the turtorial, but I get
> > >> nothing but hollow strips
> > >> > showing the middle of proton chemical shift range and N15 set to the
> > >> lowest frequency with the C13
> > >> > showing the Ca and Cb ruler positions.
> > >> > I 've tried several times and I even tried the windows version. I also
> > >> checked the mailing list posts
> > >> > for answers but I did not find anything.
> > >> > By the way, I am using CBCACONH in the query window and HNCACB in the
> > >> match window.
> > >> > Can anyone give some suggestion on this, thanks a lot.
> > >> >
> > >> >
> > >> > Best Regards,
> > >> >
> > >> > Xuehui
> > >> >
> > >> >
> > >>
> > >>
> > >
> >
> >
> >
>
>
>
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