I am attempting to calculate distance restraints from my proton proton NOESY. I have fully assigned my NOESY. What I have been trying is to Run CCPN Macros and do the calculate distance restraints. When I do this I pick the spectrum that I am working on and and click calculate. I get a new table under structure data that is completely emtpy. How can I calculate distance restraints from My 1H-1H NOESY so that I can run a structure calculation on ARIA and have my structure and nef file with the restraints to submit to the PDB?
Thanks
Hi,
This macro is not suited for 2D NMR data (this code that was transported a while ago into V3 from V2 as a temporary measure).
If you export NEF file with your assigned peaks (and chain together with your chemical shifts list) you can use it in AriaWeb (ariaweb.pasteur.fr), once calculation is done you will have all files needed for wwPDB.
You can also import results of the calculations (NEF file) back into your V3 project to inspect your spectra (you can have a look at our tutorials: https://ccpn.ac.uk/wp-content/uploads/2023/03/StructureTutorialMarch2023.pdf).
If you have any more questions please let us know.
Kind regards,
Eliza
Hello,
Thank you for the advice. I have been using aria but seem to run into a problem where in CCPN I am unable to calculate peak heights/volumes. I try to click on it under spectrum but I do not get anything out of it. Any advice?
Hi,
When you calculate structure in Aria (and AriaWeb) you can select to use either heights or volume of the peak.
You can recalculate peak heights:
and volumes (peaks need to be fitted first): Go to: Spectrum > Estimate PeakList Volumes…
Are you using local Aria installation or Aria Web?
Best wishaes,
Eliza
Hello.
I and using the aria web. When I try to calculate heights it seems like it does not do it. I get this message at the bottom g “ get(‘PL:WT_MAAC_NOESY_975UM_800.1’).estimateVolumes(peaks=None, volumelntegralLimit=2.0, noWarning=True)” it seems like somehow it doesn’t recognize that I have peaks.
Would you be able to send us your project, or at least NEF file with your peak list?
Eliza
Yes,
I just sent it to the support team .
Thanks