Dear Carl,
The reason you are not seeing anything is that the standard display region
for 15N is set to 80-155ppm. To change that go to menu
Other->Axes and Panels and change teh 15N 'Region' column.
Modifying or making a new NmrExpPrototype is done in the menu
Experiment->Experiment Prototypes.
For simplicity I have made an NmrExpPrototype that corresponds to your
experiment. I shall either make it available or mail it to you as soon as
I check with the others what is the best way to do it.
In gereral we recommend people editing their own prototypes. A few
hints:
- You will likely have to go to the
Project->Save as
menu and set the ccp.nmr.NmrExpPrototype to isModifiable=True.
- You need to edit both the main prototype popup, the ExpGraphs popup and
the RefExperiments popup.
- The easiest way to do it is to make a copy of a similar prototpye and
modify it (keeps the number of clicks down). I started from HC_CH.TOCSY
in this case. When making the RefExperiments the easiest way is to make
the full version first (5D in this case) and the make the others by
copying and editing the copy.
- There is documentation in the normal place. Warning: NmrExpPrototypes
are only changeable when freshly made. The way around this, in case you
need it, is in the documentation (we do not want people modifying the
reference experiments willy-nilly).
More soon,
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 Mon, 3 Mar 2008, Carl Diehl wrote:
> Hello.
> I've been running an experiment that is basically a hCC-NcH-TOCSY. In
> the experiment the 13C-shifts of the sidechain is correlated with the
> sidechain 15N-shifts of lysines (~33 ppm) and arginines (~79 ppm) and
> the neighbouring 1H-shifts (Hdelta and Hepsilon).
> I process my spectra in nmrPipe and import them as UCSF-format.
>
> As reference experiment I choose hC_cNH.TOCSY, which is the closest
> match to the actual experiment, I believe.
>
> The problems starts when I try to view the spectra in CCPNMR. In the
> 1H-15N window (with 13C as z-axis) I cannot go below 80 ppm and since my
> reference ppm is 58.3, I can't see anything.
> Is there a way to shift the 1H-15N spectra to show spectra that are not
> located in the normal amide backbone range?
>
> In the 1H-13C window (with 15N as z-axis), I dont' see anything even at
> basically zero contour level, even if get the dotted square indicating
> my spectral window. If I activate sidetraces it is possible to view the
> intensities as 1D-slices and they seem OK. Have I chosen the wrong type
> of reference experiment? How do you create your own custom experiment?
>
> Regards
>
> --
> Carl Diehl
> Department of Biophysical Chemistry
> Lund University
> 046-2220384
>
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