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
>>
|