It might be a silly question, but I’m experiencing something at my processed files.
It doesn’t generate a violations_fold.nef file after I process my run.
found 20 ensembles of size 1
found 20 ensembles of size 1
found 20 ensembles of size 0
Floating point exception (core dumped)
Traceback (most recent call last):
File “/home/renanpfreire/ccpnmr/src/python/ccpn/AnalysisStructure/gui/ProcessXplorStructureCalculationPopup.py”, line 317, in _processXplorCalculation
myRun._runViolationAnalysis()
File “/home/renanpfreire/ccpnmr/src/python/ccpn/AnalysisStructure/lib/runManagers/XplorNihRunManager.py”, line 534, in _runViolationAnalysis
analyseXplorViolations(path=self._foldDirectory / self.LOWEST_ENERGY,
File “/home/renanpfreire/ccpnmr/src/python/ccpn/AnalysisStructure/lib/runManagers/analyseXplorViolations.py”, line 47, in analyseXplorViolations
resultDict = parseViolations(paths, matcher)
File “/home/renanpfreire/ccpnmr/src/python/ccpn/AnalysisStructure/lib/runManagers/analyseXplorViolations.py”, line 393, in parseViolations
result = data_as_nef(overall_result)
File “/home/renanpfreire/ccpnmr/src/python/ccpn/AnalysisStructure/lib/runManagers/analyseXplorViolations.py”, line 320, in data_as_nef
frame.add_tag(“nef_spectrum”, f"nef_nmr_spectrum{list(table_data.values())[0][‘restraint-list’]}")
IndexError: list index out of range
There are 20 structures on the ensemble archive. One of them (3/20) its close to what I expected, but the others are different at all. It has 20 conformational states, and I’m not sure what is the problem.
Does anyone had the same experience as mine? I can give more details that should be revelant to work through this.
Can i just check which version of ccpn are you using? Have you updated recently?
I have not seen this error before (thank you for providing a traceback!). Do you have both fold_##.sa.stats and refine_##.sa.stats files in your run folder before processing? Did you get any traceback in the terminal where you run Xplor NIH? Did you try not ticking the generate violations part?
I am very happy to do trail run if you can send me you input.nef (support@ccpn.ac.uk) or you can send me out.nef and i can run fold and refine part.
Sorry for my late response. I’m running the last version, 3.3.4 and my system is Ubuntu 24.04.3 LTS
I’m going to answer all of your questions separately:
Do you have both fold_##.sa.stats and refine_##.sa.stats files in your run folder before processing?
Yes, both of the archives are present.
Did you get any traceback in the terminal where you run Xplor NIH?
The run didn’t see to have any crashes or bugs. I’m sorry that I can’t provide the complete traceback
Did you try not ticking the generate violations part?
I did this morning. Seems the same.
An important comment is that my assignments from cnoesy a nnoesy is not complete. Although I assigned a lot of protons, it is my first time doing the assignments and work with the ccpnmr, so I need to check those spectras again. Maybe if I sent to you by email and you can check for me what is going on, I will be very happy with it.
Thanks for all answers and sorry you have encountered troubles!
When using Xplor NIH you do not need to worry about peak assignments as it does not use them anyway. If your result (ensemble) was sensible you could still do a lot of analysis with just out.nef.
Yes please if you could send us those files it would be great. I will do thorough testing.