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CCPNMR  April 2007

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Subject:

Re: Error When Trying To Create Experiment Prototype

From:

Johnny Eugene Croy <[log in to unmask]>

Reply-To:

CcpNmr software mailing list <[log in to unmask]>

Date:

Thu, 12 Apr 2007 08:56:05 -0600

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (241 lines)

Rasmus,

Thanks for the primer on creating experiments.  I will take a more  
detailed look into your comments and suggestions and get back to you  
with any questions.  In the meantime, I think that we indeed use the  
experiment that you suggested (which worked beautifully!).  Thanks  
again for all of your help!

- Johnny

On Apr 12, 2007, at 7:15 AM, [log in to unmask] wrote:

> Dear Johnny,
>
> Sorry for the delay - I have been on holiday.
>
> From what you write, I really, really think that the experiment you  
> want is H{CA|Cca}CONH, trivial name HBCB/HACACONNH, no. 59 in my  
> files. Did you have a look at this, and if so can you tell me where  
> this experiment differs from yours?
>
> Maybe I should explain the name: MAgneetisation starts on H (any  
> H). It then splits in two different pathways (that is what the  
> curly braces with '|' in them mean): one part goes to CA  
> (measured), the other part goes to C (any C, measured), and then on  
> to CA (not measured). From there the paths join - both go to CO,  
> then to N, and then to H where you acquire.
>
> Just to maek sure we are talking about the same thing: The way the  
> actual experiment works, as I remember, magnetisation is  
> transferred from H to the directly bound C. It is then left for 4/J  
> seconds (I think) anyway long enough for the magnetisation to  
> evolve from C1x into 0.7C1x + 0.7C1yC2z. A 90 deg crbon pulse will  
> then transfer the C1yC2z to -C1zC2y. At this point you transfer  
> from CA to CO and onwards. The net effect is that you keep 70% of  
> the signal thata started no HA, and get a new signal of 70% of what  
> started on HB (minus losses from other couplings).
>
> Answers to your specific questions interspersed below.
>
> Yours,
>
> Rasmus
>
> On Mar 29 2007, Johnny Eugene Croy wrote:
>
>> 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?
> No, because we do not use 'CB/CA' or any similar constructino. If  
> you have two alternative pathways, you must use curly braces and  
> separator, as in '{CA|Cca}
>
>
>> 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.
> I would construe this as a 5D prototype: H, C, CO, N and HN. What  
> you are acquiring in practice (the RefExperiment) would be a 3D -  
> C, N and HN. CA and CB are no the same axis. The way it works is  
> that you define teh NmrExpPrototype as the highest dimensionality  
> experiment you could record with a given pulse sequence, which is  
> 5D ni this case. You then define RefExperiments for the subset of  
> dimensions that you actually acquire. That way you only describe  
> the magentisation transfer once, and you can make various 2D/3D/4D  
> RefExperiments taht use teh same transfer pathway.
>
>> 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.
>
> Yes, these are shifts in ppm.
>
>> 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)
>
> Yes, except taht you would need the first H as well. See the  
> experiment I proposed, though, for how we do it.
>
>
>> 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
>>

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