Hello,
I noticed when I was using the chemical shift mapping to compare peak heights between two 15N HSQC spectra, the software was strangely inconsistent with how it calculated the Ddelta. If i had Spectra X and Spectra Y, for some peaks it would do X/Y for the height values and for other peaks it would do Y/X. Changing between delta or raw in the ‘display data’ option did not change anything. Any ideas what could be causing this?
Thanks!
Hi,
We’ve now moved to a new Chemical Shift Mapping module: in Version 3.1.1 you can access it from the Macros menu: Macros → Run CCPN Macros … → Chemical Shift Mapping Module (alpha) . In version 3.2 it is available directly from the main menu: View → Chemical Shift Mapping (beta) (shortcut CM).
This is on the whole much better and more reliable than the old Chemical Shift Mapping module - and it’s the only one where we are now fixing any bugs etc.
For comparing peak heights, however, I would recommend you use the Heteronuclear NOE part of the new (related) Relaxation Analysis module. Also in Macros → Run CCPN Macros … in 3.1.1. or View → Relaxation Analysis (beta) (shortcut RA) in 3.2.
Details on how to use these are provided in the Chemical Shift Perturbation Analysis and Dynamics Tutorials at Tutorials - CCPN - Collaborative Computing Project for NMR.
So have a go with that, and if you are still encountering strange/inconsistent data, please let us know.
Thanks,
Vicky
Hello,
Thank you! I went ahead and ran the macros for both the chemical shift mapping and the Relaxation analysis and have been playing around with them for a bit.
I followed the tutorials for both and for the Chemical shift mapping I was able to generate a CS perturbation plot for my residues, but the fitting graph is blank for each residue.
For the peak heights I tried the relaxation analysis module, but all my values just come out at 1 and the fitting graphs are also blank.
I noticed for both modules the fitting graph X axis is labeled as ‘nan’
I’m just inputting a series of 15N HSQCs that I have in a SpectrumGroup and im trying to track the chemical shift changes and the peak intensity changes.
I’ll keep playing around with it, but if you have any advice that would be appreciated.
Thank you!
Hi,
it could be that the Series values have either not been entered or weren’t saved properly - we haven’t got any proper error checking put in place for that yet.
So double-click on your Spectrum Group in the sidebar and see whether there are any values in the Series tab or not (and obviously also make sure you are fully up-to-date with all the Updates - there are a few bugs in there which we recently updated).
Vicky
Hello,
Yup i think it might have been something with the spectrum groups. I updated the software and deleted and remade all the spectrum groups which seems to have fixed it!
Thank you!