mcellteam / cellblender

Create, Simulate, Visualize, and Analyze Realistic 3D Cell Models
http://mcell.org/tutorials/index.html
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Issue when trying to import BNGL model into CellBlender 2.93 #121

Closed FAnderl closed 1 year ago

FAnderl commented 1 year ago

I am tring to import a BNG model (specifically the example model [_organelletransport.bngl] from (https://github.com/RuleWorld/BNGTutorial/blob/master/CBNGL/organelle_transport.bngl ) into CellBlender 2.93.

I am using the import option File->Import->BioNetGen/SBML model (.bngl,.xml) and I receive the error:

Python: Traceback (most recent call last): File "/Applications/Blender-2.93-CellBlender/Blender.app/Contents/Resources/2.93/scripts/addons/cellblender/bng/init.py", line 43, in execute external_operators.filePath=findCellBlenderDirectory()+'bng{0}'.format(os.sep) + self.filepath.split(os.sep)[-1] File "/Applications/Blender-2.93-CellBlender/Blender.app/Contents/Resources/2.93/scripts/addons/cellblender/bng/init.py", line 14, in findCellBlenderDirectory cellblenderDir = [x for x in os.listdir(directory) if 'cellblender' in x] FileNotFoundError: [Errno 2] No such file or directory: '/Applications/Blender-2.93-CellBlender/Blender.app/Contents/Resources/2.93/python/lib/python39.zip'

location: :-1

However, the import via the option File->Import->Compartmental BioNetGen model (.bngl) works just fine.

tmbartol commented 1 year ago

Thanks for reporting this issue, Florian. I will add a comment to organelle_transport.bngl that states that this file is a compartmental BNGL file and is intended to be imported into CellBlender using: File->Import->Compartmental BioNetGen model (.bngl)

FAnderl commented 1 year ago

Thank you.

However, I think there is an actual issue here. I receive the same error message when I am trying to import an non-compartmental model like e.g., LG.bngl also from the BNGL tutorial site.