id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7624 KeyError in read_json_pae_matrix chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.4.dev202204200426 (2022-04-20 04:26:30 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.4.dev202204200426 (2022-04-20) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show AlphaFold > alphafold predict > MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRRGGMQIFVKTPTRKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLYLMRLRGL,RDYKRKYEFFRRKLKKQNDIPNKFEMKLRRATVLEDSYRRIMGVKRADFLKARLWIEFDGEKGLDYGGVAREWFFLISKEMFNPYYGLFEYSATDNYTLQINPNSGLCNEDHLSYFKFIGRVAGMAVYHGKLLDGFFIRPFYKMMLHKPITLHDMESVDSEYYNSLRWILENDPTELDLRFIIDEELFGQTHQHELKNGGSEIVVTNKNKKEYIYLVIQWRFVNRIQKQMAAFKEGFFELIPQDLIKIFDENELELLMCGLGDVDVNDWREHTKYKNGYSANHQVIQWFWKAVLMMDSEKRIRLLQFVTGTSRVPMNGFAELYGSNGPQSFTVEQWGTPEKLPRAHTCFNRLDLPPYESFEELWDKLQMAIENTQGFDGVD Running AlphaFold prediction > open ""/Users/default/Desktop/ChimeraX/AlphaFold/prediction_1_HECT Ub3variant > +UB/HECT:Ub:Ub-Ub-UbV1.pdb"" Chain information for HECT:Ub:Ub-Ub-UbV1.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > hide #1 models AlphaFold prediction finished Results in /Users/default/Downloads/ChimeraX/AlphaFold/prediction_1 Chain information for best_model.pdb #2 --- Chain | Description A | No description available B | No description available Must choose path to predicted aligned file [Repeated 1 time(s)] > alphafold pae #2 file /Users/default/Downloads/ChimeraX/AlphaFold/HECT+Ub- > UbV1/best_model_pae.json Traceback (most recent call last): File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 145, in _choose_pae_file self._open_pae() File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 158, in _open_pae self._open_pae_from_file(s) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 182, in _open_pae_from_file run(self.session, cmd) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 708, in alphafold_pae pae = AlphaFoldPAE(file, structure) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 477, in __init__ self._pae_matrix = read_pae_matrix(pae_path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 547, in read_pae_matrix return read_json_pae_matrix(path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] KeyError: 0 KeyError: 0 File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] See log for complete Python traceback. > alphafold pae #2 file /Users/default/Downloads/ChimeraX/AlphaFold/HECT+Ub- > UbV1/best_model_pae.json Traceback (most recent call last): File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 158, in _open_pae self._open_pae_from_file(s) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 182, in _open_pae_from_file run(self.session, cmd) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 708, in alphafold_pae pae = AlphaFoldPAE(file, structure) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 477, in __init__ self._pae_matrix = read_pae_matrix(pae_path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 547, in read_pae_matrix return read_json_pae_matrix(path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] KeyError: 0 KeyError: 0 File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] See log for complete Python traceback. Populating font family aliases took 240 ms. Replace uses of missing font family "".AppleSystemUIFont"" with one that exists to avoid this cost. > alphafold pae #2 file /Users/default/Downloads/ChimeraX/AlphaFold/HECT+Ub- > UbV1/best_model_pae.json Traceback (most recent call last): File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 158, in _open_pae self._open_pae_from_file(s) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 182, in _open_pae_from_file run(self.session, cmd) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 708, in alphafold_pae pae = AlphaFoldPAE(file, structure) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 477, in __init__ self._pae_matrix = read_pae_matrix(pae_path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 547, in read_pae_matrix return read_json_pae_matrix(path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] KeyError: 0 KeyError: 0 File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] See log for complete Python traceback. > select add #2 8768 atoms, 8868 bonds, 531 residues, 1 model selected > alphafold pae #2 file /Users/default/Downloads/ChimeraX/AlphaFold/HECT+Ub- > UbV1/best_model_pae.json Traceback (most recent call last): File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 158, in _open_pae self._open_pae_from_file(s) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 182, in _open_pae_from_file run(self.session, cmd) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 708, in alphafold_pae pae = AlphaFoldPAE(file, structure) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 477, in __init__ self._pae_matrix = read_pae_matrix(pae_path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 547, in read_pae_matrix return read_json_pae_matrix(path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] KeyError: 0 KeyError: 0 File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] See log for complete Python traceback. > hide #2 models > show #2 models > alphafold pae #2 file /Users/default/Downloads/ChimeraX/AlphaFold/HECT+Ub- > UbV1/af531_unrelaxed_rank_5_model_2_scores.json Traceback (most recent call last): File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 145, in _choose_pae_file self._open_pae() File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 158, in _open_pae self._open_pae_from_file(s) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 182, in _open_pae_from_file run(self.session, cmd) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 708, in alphafold_pae pae = AlphaFoldPAE(file, structure) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 477, in __init__ self._pae_matrix = read_pae_matrix(pae_path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 547, in read_pae_matrix return read_json_pae_matrix(path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] KeyError: 0 KeyError: 0 File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] See log for complete Python traceback. > alphafold pae #2 file /Users/default/Downloads/ChimeraX/AlphaFold/HECT+Ub- > UbV1/af531_unrelaxed_rank_5_model_2_scores.json Traceback (most recent call last): File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 158, in _open_pae self._open_pae_from_file(s) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 182, in _open_pae_from_file run(self.session, cmd) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 708, in alphafold_pae pae = AlphaFoldPAE(file, structure) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 477, in __init__ self._pae_matrix = read_pae_matrix(pae_path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 547, in read_pae_matrix return read_json_pae_matrix(path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] KeyError: 0 KeyError: 0 File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] See log for complete Python traceback. > alphafold pae #2 file /Users/default/Downloads/ChimeraX/AlphaFold/HECT+Ub- > UbV1/af531_unrelaxed_rank_5_model_2_scores.json Traceback (most recent call last): File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 158, in _open_pae self._open_pae_from_file(s) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 182, in _open_pae_from_file run(self.session, cmd) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 708, in alphafold_pae pae = AlphaFoldPAE(file, structure) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 477, in __init__ self._pae_matrix = read_pae_matrix(pae_path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 547, in read_pae_matrix return read_json_pae_matrix(path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] KeyError: 0 KeyError: 0 File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] See log for complete Python traceback. > alphafold pae #2 file /Users/default/Downloads/ChimeraX/AlphaFold/HECT+Ub- > UbV1/best_model_pae.json Traceback (most recent call last): File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 145, in _choose_pae_file self._open_pae() File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 158, in _open_pae self._open_pae_from_file(s) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 182, in _open_pae_from_file run(self.session, cmd) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 708, in alphafold_pae pae = AlphaFoldPAE(file, structure) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 477, in __init__ self._pae_matrix = read_pae_matrix(pae_path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 547, in read_pae_matrix return read_json_pae_matrix(path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] KeyError: 0 KeyError: 0 File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] See log for complete Python traceback. > alphafold pae #2 file /Users/default/Downloads/ChimeraX/AlphaFold/HECT+Ub- > UbV1/af531_unrelaxed_rank_1_model_4_scores.json Traceback (most recent call last): File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 145, in _choose_pae_file self._open_pae() File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 158, in _open_pae self._open_pae_from_file(s) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 182, in _open_pae_from_file run(self.session, cmd) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 708, in alphafold_pae pae = AlphaFoldPAE(file, structure) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 477, in __init__ self._pae_matrix = read_pae_matrix(pae_path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 547, in read_pae_matrix return read_json_pae_matrix(path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] KeyError: 0 KeyError: 0 File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] See log for complete Python traceback. > alphafold pae #2 file /Users/default/Downloads/ChimeraX/AlphaFold/HECT+Ub- > UbV1/config.json Traceback (most recent call last): File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 145, in _choose_pae_file self._open_pae() File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 158, in _open_pae self._open_pae_from_file(s) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 182, in _open_pae_from_file run(self.session, cmd) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 708, in alphafold_pae pae = AlphaFoldPAE(file, structure) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 477, in __init__ self._pae_matrix = read_pae_matrix(pae_path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 547, in read_pae_matrix return read_json_pae_matrix(path) File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] KeyError: 0 KeyError: 0 File ""/Users/default/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/alphafold/pae.py"", line 562, in read_json_pae_matrix d = j[0] See log for complete Python traceback. OpenGL version: 4.1 ATI-3.10.23 OpenGL renderer: AMD Radeon Pro 5700 OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.2.3, Qt 6.2.3 Qt runtime version: 6.2.4 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac20,2 Processor Name: 10-Core Intel Core i9 Processor Speed: 3.6 GHz Number of Processors: 1 Total Number of Cores: 10 L2 Cache (per Core): 256 KB L3 Cache: 20 MB Hyper-Threading Technology: Enabled Memory: 32 GB Boot ROM Version: 1731.140.2.0.0 (iBridge: 19.16.16066.0.0,0) Software: System Software Overview: System Version: macOS 10.15.7 (19H1824) Kernel Version: Darwin 19.6.0 Time since boot: 27 days 5:52 Graphics/Displays: AMD Radeon Pro 5700: Chipset Model: AMD Radeon Pro 5700 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x731b Revision ID: 0x0040 ROM Revision: 113-D1820Q-231 VBIOS Version: 113-D182A2XG-012 Option ROM Version: 113-D182A2XG-012 EFI Driver Version: 01.01.231 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: iMac: Display Type: LCD Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.37.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.3 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4.dev202204200426 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.16.5 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.32.0 funcparserlib: 1.0.0a1 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.8 PyQt6-commercial: 6.2.3 PyQt6-Qt6: 6.2.4 PyQt6-sip: 13.2.1 PyQt6-WebEngine-commercial: 6.2.1 PyQt6-WebEngine-Qt6: 6.2.4 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 22.3.0 qtconsole: 5.3.0 QtPy: 2.0.1 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Structure Prediction fixed all ChimeraX