Chemical Shift Mapping

Analysis Version 3
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#1

Hey,

for some reason, when I do the chemical shift mapping, it doesnt adjust the color code to the graph. It plots everything in the disappeared peaks color. This happened in my HN spectra but not with my NCAs, and also not in the tutorial data. All the settings for th CSM (e.g threshold) are the same. What could be the problem?

Thanks in advance.

#2

Hi,
I noticed the same. I got the colors back after removing all but H, N, and side chain NH-group atoms from the NmrChains, NC:A - mimicking the atom list in the Tstar tutorial. Not very practical, though, and in your case, would not allow for plotting other type of data anymore.
BR. Helena

#3

Hi, it could be related to the Axis codes in different spectra, non compatible nmrAtoms or most probably including spectra which don`t have all the same assigned peaks. Are you able to share the projects? Even as NEF files. Thanks

#4

Hello All
I see the last discussion on this is two years ago and so my problem might be something that propped up recently with newer version.
I am just trying to work with the tutorials file for Chemical Shift Perturbation analysis and followed all the steps given in the tutorial documentation. But I don’t see the bar graph that shows the CSP for different residues for the model Protein : Tstar.
I thought the issue could be with my running version of Assign on my Fedora platform. So, I brought up the same project in NMRBox’s Assign GUI. There too, I see an empty window at the stage of Chemical Shift Mapping. The Binding Curve module also looks empty.
By the way, I opened the TStarCompleted project file as well and it too has the same result.
I will much appreciate if someone can give me a hand here.

Thank you very much.

#5

Hi, Thank you for reporting this. We did some changes recently, now the CSM works only using spectrumGroups. Make sure you create one from sidebar, include the desired spectra and add the series values (last tab in the spectrumGroup editor popup).
Once you have the groupm you should be able to select it from the CSM module settings panel. Update the module and it should display the graphs.

#6

Hi Luca
Thank you so much for guiding me. Those steps work perfectly well, even on my Assign program running on the Fedora platform. One quick question. In the NMRAtoms settings dialog, the default for H realtive contrib. is set to be 7.0 but the documentation suggests 6.5. Which one is the preferred value ?

Thank you…

#7

Hi,
7 is probably the more usual number - or indeed often the values are actually set at 1 for 1H and 0.14 (=1/7) for 15N. There is no hard and fast rule, but these are commonly used in the literature. See Mike Williamson’s paper in Progress in NMR Spectroscopy paper for a brief discussion on this (Redirecting).
Vicky