Inconsistent CSP bar plot in the 'chemical shift mapping' module

Hi all,

I am using the chemical shift mapping module to analize titrations. I get a different bar plot when using a spectrum group containing all the titration spectra vs when I use a spectrum group with just 2 of the spectra: the reference spectrum and the last titration point spectrum.
Additionally, the paterns I get when doing the chemical shift perturbation manually in excel (using a different equation) are different to the paterns on the bar plot of this module.
Could someone please help me to figure out what is going on? Thanks in advance!

Hi Carolina,

happy to look into this for you. If you send us your project to support@ccpn.ac.uk (spectra not needed), then we can have a look at what is going on.

Vicky

Thank you very much again Vicky!

See my reply at

for an answer to this issue.
Vicky

Dear Vicky,

thank you very much for this reply. I am now getting the same results with the Alpha module.
There is just one issue I am getting with the barplot in the x-axis with the numeration, the side chains are plot in disorder and at the end of the barplot (not plot directly after their corresponding N,H residue) and one of the normal N,H residues is also plot at the end (completely random out of sequence).
The side chains have all the same assign system, in my case: N.HE21, N.HE22, N.HD21, N.HD22
I figure it plots according to their order in the collection, but I cannot reorder the collection (e.g. by dragging the residue). Is there somethig I can do to reorder how the residue numbers are plot?

Thanks again and best wishes,
Carolina

Dear Carolina,

in my case, I am plotting the nmrResidueCode along the x-axis (see the Appearance tab in the Settings) and then the side-chains are in amongst the NHs:

The NmrAtoms I am using are of the form A.66.GLN.NE2/HE21/HE22 and A.160.ASN.ND2/HD21/HD22. Are you doing something different?

Best wishes,
Vicky

Hello Vicky,

My NmrAtoms are exactly as yours, the problem is when the collection is created the numbering is not in order. I have tried couple of times (sorting my reference peak list in the correct order) but the collection is still created not in order: as I said before, just for one N,H residue and for all the side chains. I can sort the table by nmrResidueCode but this does not update the bar plot.
Adittionally, is there a way to include the unassigned residues in the plot? with the previous module they appeared and one could give them a color and a ‘Disappeared value’.
Thank you very much for your help.

P.S. Watching the video again, the side chain of Q66 also appears at the end in the collection, not in order as you showed me in the above screenshot

Best wishes,
Carolina

Hi Carolina,

this is probably where the “alpha version” bit comes in. I think for the moment, if you want a bespoke order for your graph (e.g. for publication), then you will have to export the data and do that in the different program. You can export the data either from the table in the Chemical Shift Mapping module, or you can drag the Results DataTable into the DropArea and then export that.

We’ve got plans for all of this, but not had time to implement it all. Part of the problem is that different people will want different things. You may like to see your side-chains alongside the backbone NH, but there is obviously also a case for having a graph of only the backbone NHs and leaving gaps where they are etc. Our plan is that you will be able to switch different groups (e.g. side chain/backbone/methyl etc. on/off, or whether to show disappearing peaks etc. but it isn’t going to be entirely straight forward to code all the different options that people might be interested in.

Best wishes,
Vicky

Hi Vicky,

I see, thanks for all your work.

Best wishes,
Carolina

Thought it might be helpful to add the following information to this thread:

We’ve now got the new Chemical Shift Perturbation Tutorial on our Tutorials page. This uses our new Alpha Chemical Shift Mapping module which is actually more reliable than the old one. It is also more flexible in being able to deal with unassigned residues. In our next release this will be available from the main menu. There are still a few things to iron out with regard to plotting the BarChart (how to handle gaps or a mixture of backbone/side-chain etc.). But that should all improve over the next few months. Some of it may have to wait till the 3.2 release - but probably that won’t be so far off, either.

The pdf is at https://ccpn.ac.uk/wp-content/uploads/2023/04/CSPAlphaTutorial.pdf
The data is part of the Solution NMR data bundle at https://ccpn.le.ac.uk/download/ccpnmr/v3TutorialData/3.1/CcpnTutorialDataSolutionNmrApril2023.zip
Or you can download just the Chemical Shift Perturbation data from https://ccpn.le.ac.uk/download/ccpnmr/v3TutorialData/3.1/CcpnCSPTutorial.zip

Vicky

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