Transfer information from a former ccpnmr2.5.2 project to v3

Analysis Version 3
1

Dear all,
I have a former project made in 2.5.2 that contains all my assignments. Now I am working (and are happy) with v3 (recently upgraded to 3.3.2.2 on a M2 Mac). I managed to export a .str file from the v2 project (opened with the old v2 version), but I am neither able to import this:
error message
INFO : application.loadData(‘/Users/bersch/Documents/ColN/ColN-R/bmrb/ColN-R_new.str’)
WARNING: Loading “/Users/bersch/Documents/ColN/ColN-R/bmrb/ColN-R_new.str” failed:

‘submission_date’ (ContextManagers.catchExceptions:224)
WARNING: No objects were loaded from “/Users/bersch/Documents/ColN/ColN-R/bmrb/ColN-R_new.str” (GuiBase._loadDataIgnoreExtension:508)

nor to import this completed project directly into v3:
I am asked whether I want to continue loading (YES, please), but then I get a window that states:
There was a problem loading project /Users/bersch/Documents/ColN/ccpnmr/ColN_Rdomain_bb3

Please check the log for more information.

  • where is the log ?

  • error message in the terminal:
    INFO : application.loadProject(‘/Users/bersch/Documents/ColN/ccpnmr/ColN_Rdomain_bb3’)
    Error loading file for: <ccp.nmr.Nmr.NmrProject [‘ColN_Rdomain_bb’]>
    Reading: <_io.TextIOWrapper name=‘/Users/bersch/Documents/ColN/ccpnmr/ColN_Rdomain_bb3/ccp/nmr/Nmr/ColN_Rdomain_bb+ColN_Rdomain_bb_bersch_2022-05-13-13-21-54-716_00002.xml’ mode=‘r’ encoding=‘UTF-8’>
    Last xml tag read: NMR.Experiment.refExperiment
    Parser state was: reading
    Current object was: <ccp.nmr.Nmr.Experiment [‘ColN_Rdomain_bb’, 5]>
    WARNING: Error loading “/Users/bersch/Documents/ColN/ccpnmr/ColN_Rdomain_bb3”: No valid NMR project data could be loaded from “/Users/bersch/Documents/ColN/ccpnmr/ColN_Rdomain_bb3” (Framework._loadV2Project:1407)

Can anybody help me to resolve this issue ?
Thank you very much !
Beate

2

Hi Beate,

Sorry you are having trouble - we would hope that these things should just work of course.

Are you exporting the whole project as NmrStar or just the chemical shifts?

Have you checked your NmrStar file’s contents with a text editor? If it looks OK, does the NmrStar visualizer read it OK https://bmrb.io/dictionary/starviewer/

If the NmrStar file looks OK, it might be worth trying to convert it to nef to then import to AnalysisAssign using GT’s nef-pipelines. You should have an “install_nef_pipelines” script in your V3 bin (or bat on windows) directory (if this doesn’t work straight away and complains about setuptools setup.py you may need to add: “${CONDA_PYTHON3}” -m pip install backports.tarfile before the other similar lines in the script. Once you have nef-pipelines installed try

<path_to>/ccpnmr/bin/nef nmrstar import project <nmrstar_file.str> > <nef_file.nef>

to see if the conversion works - if it does it’s very likely the nef file will import OK.

The direct V2 project import can get tripped up by many things. In this case the mention of NMR.Experiment.refExperiment makes me wonder if you have added any additional experiment types that aren’t in the default list?

If you don’t spot anything obvious send us the project (tar & gzip without spectra) and/or star file to support@ccpn.ac.uk and/or to me via the transfer.gla.ac.uk service.

Brian

3

Hi Beate,

Have you tried just dropping your v2 project on new (sperate) AnalysisAssign v3 window? If it opens ok, you could then export whatever you need as NEF file and import it into your existing project. That would be the first thing I try.

BW,
Eliza

4

Thank you Eliza, yes, this is what I tried

5

Dear Brian
Thank you for your reply.

  • Are you exporting the whole project as NmrStar or just the chemical shifts?

I had a BMRB-deposit-ready project file in v2.5.2 - I copied it to a new project and removed as much information as I could. At the end, I exported chemical shifts, molecule and one peak file as a .str.
I had some issues that I could correct in the .str file (excellent idea to try the NMRStar visualizer - I did not know - or had forgotten - this way to test).
The protein sequence was written on multiple lines and v3 was expecting a deposition date (but I finally unticked the entry information) and kept just chemical shifts and molecular chain.
Now I managed to import the .str file with my chemical shifts and was able to create a synthetic H/N peaklist !

Many thanks

  • The direct V2 project import can get tripped up by many things. In this case the mention of NMR.Experiment.refExperiment makes me wonder if you have added any additional experiment types that aren’t in the default list?

YES, that was one issue, but I had many others and finally, I was able to improve the loading progress but it did not go through

Last error message:
File “/Applications/ccpnmr/src/python/ccpn/core/_implementation/AbstractWrapperObject.py”, line 424, in _uniqueApiName
names = [sib._wrappedData.name.lower() for sib in getattr(project, cls._pluralLinkName)]
File “/Applications/ccpnmr/src/python/ccpn/core/_implementation/AbstractWrapperObject.py”, line 424, in
names = [sib._wrappedData.name.lower() for sib in getattr(project, cls._pluralLinkName)]
AttributeError: ‘NoneType’ object has no attribute ‘lower’

However, I am happy with my chemical shifts in a V3 project and can always switch back to the v2 project if I need to check some assignments.

Thank you very much for your prompt help !

All the best, Beate

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