Discussion group for the ARIA software

[Poanna Tran <poanna.tran AT gmail.com>]

Hi Mariana,

Thank you so much for your quick and helpful response! I had found your paper but didn't have the github files! I am trying to follow the instructions in your paper but I've run into an issue - the "install" and "run patches" commands don't work for me because I don't seem to have permission to use them on the virtual machine I'm using (NMRBox). Do you know if there's a workaround?

Poanna Tran

On Sun, Jun 30, 2024 at 8:32 PM Mariana Quezado <aria-discuss AT services.cnrs.fr> wrote:

Dear Poanna Tran,

We had the same problem and we manage to solve the problem8
Please check Dr. bruno Santos github page and our manuscript at biorxiv.

https://github.com/bposantos/CCPNMR-ARIA2-PTM-Toolkit

https://www.biorxiv.org/content/10.1101/2020.12.08.414565v2.full.pdf+html

On Sun, 30 Jun 2024, 12:04 "Poanna Tran", <aria-discuss AT services.cnrs.fr> wrote:

Hello,

I'm having trouble finding information on determining a peptide structure with
a C-terminal amide. I used CCPNMR3.1.1 for the chemical shift assignments but
didn't know how to add the amide there. I just added new atoms to the C-
terminal amino acid and used them to assign the N and H peaks, but I couldn't
find the nomenclature anywhere so I made up my own... Apparently you can't
indicate that you want a C-terminal amide when inputting the sequence in this
version.

Does anyone know how it should have been done in CCPNMR so that ARIA could use
the assignments too, or (preferably) how the peaks/prot files can be edited
manually to include a C-terminal amide so that it will work in ARIA without
needing CCPNMR?

Thanks!