Rasmus,

We tried to use the experiment that you mentioned.  However, when we  
were linking our spin systems we found that it would always give us  
the I+1 linkage, rather than the I-1 linkage that we would expect  
from this experiment.  The CBCACONH experiment that we use is not an  
"out and back" type experiment, but rather occurs following this  
pathway:

1.  All protons are excited and transfer to CA/CB occurs
2.  CA/CB evolution
3.  Magnetization transfer via CO to N
4.  N evolution
5.  Magnetization transfer to H
6.  Direct acquire (H evolution)

  I followed your suggestions about enabling the access to the  
refExperiment storage file and was able to create a new experiment.   
However, I got stuck making a new experiment prototype so I do have a  
few questions regarding the creation of a new experiment.

1.  Setting a proper name
	-  The name setting appears to have the magnetization pathway  
shown.  For my non-out and back or straight through CBCACONH I would  
assume that the name would look something like this:  CB/CAcoNH.  Is  
this is right?

2.  Max Dim
	-  I guess one could see that this could be construed as a 4D  
experiment (CB, CA, N and H).  From the documentation it appears that  
this value is set by the refExperiments.

3.  Synonym, Keyword and isEditable
	-  These are self-explanatory:  Synonym was set to CBCACONH,  
Keywords was set to ('protein') and isEditable was set to Yes

I then clicked on the newly creased experiment and then set the  
AtomSites as follows:

	-  Created new types of atoms that were involved in the experiment  
(both observed and those only used for mag transfer): CB, CA, CO, N,  
and H.  These were set to #1,2,3, 4, and 5 respectively and I used  
the default values for the min and max shifts for CA and changed the  
min and max shift for CB from 0-47 to 40-90 (I assume that these are  
measuring min and max shifts in ppm?).  The min number and number  
steps were kept at the default 1 values.

ExpMeasurements

	-  The # value cooresponds to the value found in the # value in the  
AtomSites table.
	-  The type for each atom was set to shift.  I am not sure that this  
is completely right since I am not observing the CO shift
	-  atomSites were set to each specific atom.  I.e. 1(CB), 2(CA), 3 
(CO), 4(N), 5(H)

RefExperiments

1.  Pretty much stuck on this one.  I don't think that I can create a  
set of reference experiments without having the nomenclature correct.

Any suggestions you have would be great.  Or better yet (if you have  
time) you could write up how this experiment would look and then I  
can retrace how you did it.  I think that I have a pretty good idea  
of what to do, but seeing it done would be a big help!  Let me know  
what works for you.  Thanks again for all of your help!

-J


On Mar 29, 2007, at 7:46 AM, [log in to unmask] wrote:

> 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