Dear Johnny,
tFrst congatulations for trying to make your own experiments. That was
always hte idea, but you are the first one to do it outside our lab.
We do have an experiment that should be at lest close to what you seek. It
is called H{CA|Cca}CONH and is a 5D. The trivial name is HBCB/HACACONNH,
and it is no. 59 in my files. One of the RefExperiments in it is
h{CA|Cca}coNH (no 5 in my files) which is a 3D with CA-or-CB, N and H on
the axes. The magnetisation starts on HA/HB, goes on to H and ends there.
If you also start on H that should probably do you. If you actually *do*
start on C, you will need a new experiment. You should make one that was
pretty much identical to the one I mentioned, except that the first H and
everything that references it should be removed. You will need to remove
some of the refExperiments, and also to add a couple of new ones - I did
not add all possible RefExperiments, though maybe I should have.
It might actually be the simplest if I made it for you. But if you do not
mind trying, that would give a user test of the experiment editor, which
would be much appreciated. One trick you should note: When you create a new
experiment (and similarly a new RefExperiment) they are freely editable.
When you store them and reload them they are no longer editable. It
actually says in the documentation how to make them editable. I put that
information in a discreet spot, because people who modify thye reference
experiments should preferably know what they are doing. If you do make it,
could you please send me the XML back, so I can incorporate it into our
reference data?
Oh, the otehr error: The Storage that keeps track of NmrExpPrototypes is
set as isModifiable = False. This is reference data, and we wet it to
unmodifiable as defalut, just to be safe. To set it to modifiable, you
first get hold of teh storage object. From memory either of these should
work, according to your erro message: myStorage =
project.findFirstStorage(serial=30) myStorage =
project.findFirstStorage(packageName='NmrExpPrototype') (You do know that
the project can be got on the command line as top.project, no?) You then do
myStorage.isModifiable=True Maybe you hsould check that the actual files in
the file system are set to writble, just in case.
Please let me know how it goes.
Yours,
Rasmus
PS. Nomenclature.
H[N[co[CA[CB]]] would be a 4D out-and-back experiment where all the
magnetisation goes all the way out to CB and then back. If you have CA and
CB on the same axis, you would call it H[N[co[{CA|caC}]]], which in this
version (i.e. wihtout measuring the CO) would be an out-and-back 3D with
some magnetisation going to CB and some staying on CA.
Rasmus
On Mar 28 2007, Johnny Croy wrote:
> We have an experiment that is not listed in the experiment type. The
> experiment is a CBCA(CO)NH, which gives you a 3D spectra consisting of
> the I amide/proton and the CA and CB residues of the I-1 residue. The
> closest experiment type that is given in the standard set of experiments
> is what appears to be a 4D/5D called HNCOCACB. This experiment appears to
> be an "out and back" type experiment that is defined as H[N[CO[C[C]]],
> which appears to have four/five dimensions (depending on how you look at
> it) N, H, CA/CB and CO.
>
> Our experiment is a bit different. We instead start on the CB of the I-1
> residue and transfer through to the amide of the I residue. Evolutions
> are allowed for the CA/CB and N dimensions and H is evolved during
> acquisition.
> This would suggest that we should define our experiment as follows:
>
> H[N[co[CA[CB]]]. Would this be correct? Not quite sure about the
> nomenclature that analysis uses, but I think that this is right.
>
> Anyway, when we tried to define a new experiment prototype using the
> Experiment --> Experiment Prototypes --> Create New, we got the following
> error in our X11 window:
>
> >>> Exception in Tkinter callback
> Traceback (most recent call last):
> File "/sw/lib/python2.5/lib-tk/Tkinter.py", line 1403, in __call__
> return self.func(*args)
> File
> "/Applications/ccpnmr2/ccpnmr1.0/python/ccp/gui/NmrExpPrototypeEditor.py",
> line 466, in newNmrExpPrototype
> obj = self.project.newNmrExpPrototype(name='dummy', category='other')
> File
> "/Applications/ccpnmr2/ccpnmr1.0/python/memops/api/Implementation.py",
> line 17529, in newNmrExpPrototype
> return NmrExpPrototype(self, **attrlinks)
> File
> "/Applications/ccpnmr2/ccpnmr1.0/python/ccp/api/nmr/NmrExpPrototype.py",
> line 8724, in __init__
> "%s" % (storage,)
> ApiError: ccp.nmr.NmrExpPrototype.NmrExpPrototype.__init__:Storage not
> modifiable:<memops.Implementation.NormalStorage [30]>
>
> Any ideas?
>
> -J
>
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