Problem in adding BEST_HNCA spectrum

Hello,
I wish to add a BEST_HNCO spectrum to synchroscope with a 2D HSQC spectrum but I am unable to see any spectrum at all in the strip with HNCO. Moreover,whenever i am loading my spectrum,the original spectrum doesn't show the CO dimension.
Please help me solve this.

Thankyou,

Renuka

Hi Renuka,
thanks for your inquiry regarding CARA.

From what I understand, you were able to load both the 2D HSQC15N and the 3D BEST-HNCO into your project using the appropriate SpectrumTypes (2D HSQC15N and 3D HNCO) respectively. However, after opening the HSQC15N with SynchroScope and then selecting the HNCO in the strips context-menu, you are unable to see any contours in the strip. Is that right?

The second part I did not understand "Moreover,whenever i am loading my spectrum,the original spectrum doesn't show the CO dimension.". By this do you mean that you loaded the 3D HNCO into the project using the 3D HNCO SpectrumType and then opened the HNCO with a different Scope? Which one? MonoScope?

Are you able to open the 3D HNCO using the Tools-Open Spectrum menu of CARA, and do you see contours there?

What format is the spectrum and can you see the contours in any other program?

Fred

damberger
Hi Fred,
The first part you got me correct.Yes I am having problem with Synchroscope not showing any contours for the 3D HNCO.

The second part is that whenever I add my 3D HNCO spectrum a window appears which shows a Mapped Dimension vertically and Original Dimensions Horizontally, where in the original dimension there is no option for CO or C dimension as mentioned in Mapped dimension i.e.in place of any CO dimension or C, NH appears as Z axis dimesion instead of CO.

I am able to open a Monoscope for 3D HNCO after mapping my spectrum to these dimensions and contours are visible. But still unable to open Synchroscope.

My spectrum is in Bruker format.

Thankyou,

Renuka

Hi Renuka
I suspect that you are misassigning the CO and N dimensions of the HNCO. Try the opposite mapping for Y and Z dimensions.

Some background:

CARA tries to guess the correct mapping of input spectrum dimension to SpectrumType based on chemical shift ranges in ppm:

< 10 ppm = 1H
10-100 ppm = 13C
> 100 ppm = 15N

This is why it identifies both the Y and Z dimension of the loaded HNCO to be 15N dimensions (CO shifts are all > 100 ppm). In this situation you need to use your knowledge of the identity of the dimensions of the experiment being loaded to manually set the correct mapping.

After loading the spectrum:

- go the SpectraExplorer, and expand the node of the newly loaded spectrum, check the shift ranges versus the nucleus type of the SpectrumType dimension (the nucleus type that is NOT in parentheses)

- if this is not correct you will need to fix the Map to Type either by right-clicking on the spectrum listed in the SpectraExplorer and selecting Map To Type, or by reloading the spectrum into the project and changing the mapping to reflect correctly the relation between input dimensions nuclei and the SpectrumType nuclei.

I am including some screenshots demonstrating the effects of the different mappings on the HNCO appearance in SynchroScope.


Finally, I suggest you use PolyScope instead of SynchroScope. It is more advanced than SynchroScope and can do all the things SynchroScope does. Just follow the instructions for SynchroScope replacing it with PolyScope.

Map to Type of HNCO with no change

Mapt to Type of HNCO with Y and Z dim swapped

Here is the Map to Type with revsered Y and Z dimensions.

... and here is what one sees in SynchroScope for the HNCO loaded with the two different permutations of Y and Z dimension mapping. In my example, the Y dimension is CO and so the mapping X->X, Y->Y, Z->Z gives the correct orientation of the HNCO.

With the reverse mapping, no signal is seen in the strip because you are looking in a ppm location outside the spectrum. You can see this if you click in the strip. The message "Out of Spectrum" appears at the bottom of the SynchroScope on the status line.

Depending on the order that the dimensions were measured in, the input HNCO could have either orientation. So it is necessary to determine which combination is correct for YOUR experiment (might be the opposite pairing to my example).

Hope this clears things up!