Setting my experiment

Analysis Version 3
1

I’d like to set my experiment as an CONCACX(through-space), but that’s not listed as an option. Is it possible to be added?

I would greatly appreciate any assistance or guidance.

2

Hi Ida,

yes, it looks like we haven’t ever supported that experiment type. Is there a particular reason why you need to set this experiment type? In Version 3 we don’t use Experiment Types very often, so I would have thought you could get away without it.

We probably can create it for you, but it is likely to take a while, as we haven’t done this kind of thing for a while. Also, our Conference is coming up in 2 weeks which is always a hectic time for us and I can’t really see us having time to get this done until the conference is over. So it would be good to know why you particularly need this - perhaps we could organise something quicker and easier.

Vicky

3

Hi Vicky,

Thanks for your response. I need both experiments for my project. I would be appreciative if you could do me a favor and define this path (CONCACX(through-space).

Thank you

4

Hi Ida,

I’ll look into this as soon as I get time. A couple of questions in the meantime:

  • What do you mean when you say “both experiments”? So far, you have only mentioned the through-space CONCACX. Is there another experiment type you need which is missing?
  • What are you unable to do without the Experiment Type? You should be able to open the spectrum, pick-pick it, assign it etc. without specifying the Experiment Type.

Vicky

5

Hi Vicky,
I hope you are doing well. Thanks for your support.
I made a mistake I shouldn’t have mentioned 2 experiments so forget about it. I just need CONCACX.

Ida

6

Hi Vicky,
Is there a way to simulate spectrum (say NCOCX) to get to CANCOCX?
I mean, I want to load the assignment of NCOCX on the CANCOCX, How it could be possible?
Thanks

7

I can probably add the CANCOCX (with intra-residue CX links only) for PeakList simulation. You will then be able to create the CANCOCX peaks from a ChemicalShiftList (which you will have, if your NCOCX is assigned). Am I right in thinking that you will want this as a CANcoCX style 3D?

Vicky

8

Hi Vicky,
Honestly, I am a novice in NMR, so I am not sure what short “co” means in CANcoCX.

I just need :

  1. 4D of CANCOCX to be defined.

  2. Then, simulate the data of NCOCX to CANCOCX.

Are these possible?

I really appreciate your support and sorry for any confusion If I made.

best,
Ida

9

Sorry I have to edit my email:

I just need :

  1. 4D of through-space CONCACX to be defined.

  2. Then, simulate the data of NCOCX to CANCOCX ( it is defined in CCPN already).

Are these possible?

I really appreciate your support and sorry for any confusion If I made.

best,
Ida

10

Hi Ida,

the latest updates which went live on Friday now include a reference experiment for the CONCACX (through-space) (including lower dimension versions of it).
Note that CONCACX means that the magnetisation transfers go from the CO nuclei to the N nuclei, then the CAs and then finally any other carbon atom which is close in space (that is the CX through-space part). It is obviously possible to collect a 4D version of this where each nucleus is on a different axis. But you can also collect a 3D version, e.g. where the CA and CX are on the same axis. In this case you would refer to this as a CONcaCX experiment because the CA is not evolved onto it its own axis/dimension.

If you have already assigned your NCOCX, then the chemical shifts from this spectrum will be collected in your ChemicalShiftList. Open up the ChemicalShiftLists in the sidebar and you can then drag it into the DropArea /Open as module to have a look at it. You should be able to see assignments for your N, C, CA and perhaps also other carbon atoms. (If not, you won’t be able to create a CANCOCX peak list).

To create a PeakList from for a new experiment, simply right-click on your ChemicalShiftList in the sidebar and select Create Synthetic PeakList. Then give it a name and select the Experiment Type and click Create.
I’ve added a 3D CANcoCX (relayed) to the list. Note that the relayed means that the final magnetisation transfer is only within the residue (intra-residue) rather than being inter-residue. I should be able to implement a 4D version of this as well - but not quite sure how much time I’ll have for it this week as it’s our conference.

I’m afraid at the moment we are not able to create synthetic peakLists for through-space experiments. We won’t start work on that until later in the year.

Note that the synthetic peak list will go into a dummy spectrum. You can then copy it from there to a real spectrum if you have one.

Vicky