AA prediction does not appears

I may be doing something wrong, but while I do my sequence assignment and I link one aa after the other, the software doesn`t predict which aa may it be. Neither the lines connecting the atoms in the `Sequence graph` don`t appear colored. May you know why this may be due to?
I am using v3.0.3. Thank you very much.


Hi Martí,

If you go to the Sequence Graph Settings (click on the gear icon top left), then make sure that Show Predictions and Show peak assignments are ticked - this is what should enable the two functions you describe.
It is also worth pointing out that our recent updates include a number of improvements to the Sequence Graph (including that it is significantly faster than it used to be).

Best wishes,

Both are selected, but I don`t see the aa prediction:

(attached image)

It looks as though you have several Chemical Shift lists. Do you have the correct one selected? What happens if you select the other one?

It was the right Chemical Shift List selected. I tried changing to other ones, though, and found that with `default` one it finds me something (but only 5% Ala in all the aa)

I don`t understand why, but apparently it works with the `default` ChemicalShiftList and not with the one I was working with, I`ll try to push forward. Many thanks!

Looks to me like there is a bug lurking here in the way in which the program is using multiple chemical shift lists. We`ll investigate!
Thanks for raising this,

Hi Martí,

thanks for sending your project. In the end, it turned out that it wasn`t the Chemical Shift Lists that were causing the problems in the Sequence Graph (although you do have to select the correct one). The real issue is that the program will only recognise the NEF atom names, i.e. H and N for the backbone amide, not Hn and Nh. I suspect the Hn and Nh names may have come from the V2 project. Anyway, if you run the following macro, then the Hn and Nh NmrAtoms are all renamed (or merged with H and N atoms where these are also already present) and then the peak connections and AA type predictions all appear as they should.
To run the macro, just go to Macros / New, copy/paste the code below and then press the green Play button. It will take a while to run, as there are lots of NmrAtoms in your project, but you can watch the progress in the terminal or in the bottom left hand corner.

  1. for nc in project.nmrChains:
  2. for nr in nc.nmrResidues:
  3. nan = None
  4. nah = None
  5. for na in nr.nmrAtoms:
  6. if na.name == `N`:
  7. nan = na
  8. elif na.name == `H`:
  9. nah = na
  10. for na in nr.nmrAtoms:
  11. if na.name == `Nh`:
  12. if nan is not None:
  13. nan.mergeNmrAtoms(na)
  14. else:
  15. na.rename(`N`)
  16. elif na.name == `Hn`:
  17. if nah is not None:
  18. nah.mergeNmrAtoms(na)
  19. else:
  20. na.rename(`H`)

Best wishes,