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Systems not showing on spectra

Author docz3d

#1 | Posted: 27 Jun 2018 16:52 
Good afternoon,

I started using Cara yesterday, I did read the documentation which did help a lot but I got two major problems, the last one still being unsolved.

The preliminary spectra HSQC15N, and 15N-NOESY/TOCSY are used here for my 98 residue protein. I created the project based on the last repository for protein in liquid NMR spectroscopy I downloaded here.

1: Using SynchroScope, I can't pick systems nor spins, they are disappearing as soon as I labeled them. I managed to avoid this error by using PolyScope instead. I labeled all the spins in more than 60 systems.
The problem is, I did try to run a script to rename all the systems (ReplaceDegeneratedSpinsByGroup) and now I cannot see any of my systems when I open any spectrum. I can still show the list filled with my systems (the script obviously didn't work because the first system is number 6). The "Goto" doesn't work as well...

I have no idea how to fix this, as I read again all of the documentation & FAQ, i didn't find anything that worked for me. Did I run the wrong script?

Thank you very much,
Have a nice day,

Author docz3d

#2 | Posted: 28 Jun 2018 09:18 | Edited by: docz3d 
I found a way to show the systems:
"Plane > Show peaks with unknown label"
I still don't know how to replace the degenerated numbers of systems though..

EDIT: It didn't work exactly as planned, I'll have to do it manually again...

Author damberger

#3 | Posted: 19 Mar 2019 00:38 
Hi docz3d,

I'm sorry to hear you had to do your work again. I am not sure what happened.

As described in the header at the top of the script (or on the LUA scripts page) this script is intended to remove degenerate spins which are present if you load assignments from a BMRB file. It should only delete redundant information (e.g. all protons of a Ala methyl group (HB1, HB2 & HB3) have the same shift in solution NMR so in the CARA templates it is represented by HB. The script would delete HB2 and HB3 and rename HB1 to HB. I don't understand how your SpinSystems dissapeared from the scopes, but remained visible in the SpinSystem explorer. This would happen if they were named something that's not in your residue library.

Generally I advise to back up repositories before running scripts which make extensive modifications since there is no undo.

If you have this issue in the future, we can interact to trace the cause.

Best regards,

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