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NGLview won't display solvated system #633
[sdoerr@loro Wed12:38 Downloads] python -c 'import nglview; print(nglview.__version__)' 0.6.5 [sdoerr@loro Wed12:40 Downloads] python -c 'import ipywidgets; print(ipywidgets.__version__)' 5.2.2
Hi, I'm trying to visualize a solvated system but it doesn't show anything. No protein, no ligand, no water. I tried deleting all configurations in
I attach the two files.
import nglview nglview.show_structure_file('mol.pdb') nglview.show_structure_file('smol.pdb')
referenced this issue
Jul 21, 2017
@stefdoerr which notebook version you are using?
I think the v5 version restricts how much data will be sent from Python to frontend (JS).
[I 23:30:42.996 NotebookApp] Adapting to protocol v5.1 for kernel a100ee13-f7eb-4e2a-9bbe-e400bdcfd828 [W 23:31:10.938 NotebookApp] IOPub data rate exceeded. The notebook server will temporarily stop sending output to the client in order to avoid crashing it. To change this limit, set the config variable `--NotebookApp.iopub_data_rate_limit`.
I think your solvated system (4 MB) is pretty big for notebook v5. I am not sure what we can do. uhm.