id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9574 Restoring new session in old ChimeraX anushka.ghosh@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/anushkaghosh/Downloads/version_3.cxs format session Log from Tue Jul 18 14:54:53 2023UCSF ChimeraX version: 1.7.dev202307100059 (2023-07-10) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/adminjh/Documents/ChimeraX/DTHP/Missense3D/cxs/version_2.cxs > format session Log from Tue Jul 18 14:37:06 2023UCSF ChimeraX version: 1.7.dev202307100059 (2023-07-10) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/adminjh/Documents/ChimeraX/DTHP/Missense3D/cxs/version_1.cxs > format session Log from Thu Jul 13 14:25:21 2023 Startup Errors --- error | Bundle 'ChimeraX-Dicom' custom initialization failed warning | Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 490, in get_module m = importlib.import_module(self.package_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py"", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File """", line 1206, in _gcd_import File """", line 1178, in _find_and_load File """", line 1149, in _find_and_load_unlocked File """", line 690, in _load_unlocked File """", line 940, in exec_module File """", line 241, in _call_with_frames_removed File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dicom/__init__.py"", line 17, in from .dicom import ( File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dicom/dicom/__init__.py"", line 3, in from .ui import DICOMBrowserTool, DICOMDatabases File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dicom/dicom/ui/__init__.py"", line 16, in from .dicom_databases import * File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dicom/dicom/ui/dicom_databases.py"", line 29, in from ..databases import TCIADatabase File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dicom/dicom/databases/__init__.py"", line 1, in from .tcia import TCIADatabase File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dicom/dicom/databases/tcia.py"", line 24, in from tcia_utils import nbia File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tcia_utils/__init__.py"", line 2, in from . import datacite File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tcia_utils/datacite.py"", line 1, in import pandas as pd ModuleNotFoundError: No module named 'pandas' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 364, in initialize api = self._get_api(session.logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 509, in _get_api m = self.get_module() ^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 492, in get_module raise ToolshedError(""Error importing bundle %s's module: %s"" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-Dicom's module: No module named 'pandas' notes | 2023-07-13 07:30:06,187:INFO:OpenGL_accelerate module loaded 2023-07-13 07:30:06,202:INFO:Using accelerated ArrayDatatype UCSF ChimeraX version: 1.7.dev202307100059 (2023-07-10) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/adminjh/Desktop/Missense3D/PDB-7ppt-coot-0-A-53ASP.sc.pdb format > pdb No such file/path: /Users/adminjh/Desktop/Missense3D/PDB-7ppt- coot-0-A-53ASP.sc.pdb > open /Users/adminjh/Desktop/Missense3D/PDB-7ppt-coot-0-A-53ASP.sc.pdb format > pdb No such file/path: /Users/adminjh/Desktop/Missense3D/PDB-7ppt- coot-0-A-53ASP.sc.pdb > open /Users/adminjh/Documents/ChimeraX/DTHP/Missense3D/model_maps/PDB- > hthp_bessy090621_p622-B-25HIS.sc.pdb Chain information for PDB-hthp_bessy090621_p622-B-25HIS.sc.pdb #1 --- Chain | Description B | No description available > show :25 > open > /Users/adminjh/Documents/ChimeraX/DTHP/Missense3D/model_maps/HTHP_bessy090621_P622.pdb Chain information for HTHP_bessy090621_P622.pdb #2 --- Chain | Description B | No description available > toolshed show Downloading bundle ChimeraX_PICKLUSTER-0.1-py3-none-any.whl Errors may have occurred when running pip: pip standard error: \--- [notice] A new release of pip is available: 23.0 -> 23.1.2 [notice] To update, run: /Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/adminjh/Downloads/ChimeraX_PICKLUSTER-0.1-py3-none-any.whl Requirement already satisfied: ChimeraX-Core~=1.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-PICKLUSTER==0.1) (1.7.dev202307100059) Requirement already satisfied: ChimeraX-UI~=1.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-PICKLUSTER==0.1) (1.30.1) Requirement already satisfied: Jinja2>=3.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-PICKLUSTER==0.1) (3.1.2) Requirement already satisfied: ChimeraX-Graphics~=1.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-UI~=1.0->ChimeraX-PICKLUSTER==0.1) (1.1.1) Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-UI~=1.0->ChimeraX-PICKLUSTER==0.1) (1.2) Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-UI~=1.0->ChimeraX-PICKLUSTER==0.1) (1.0) Requirement already satisfied: MarkupSafe>=2.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from Jinja2>=3.0->ChimeraX-PICKLUSTER==0.1) (2.1.3) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX- PICKLUSTER==0.1) (1.1) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX- PICKLUSTER==0.1) (1.3) Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX- PICKLUSTER==0.1) (1.0.1) Installing collected packages: ChimeraX-PICKLUSTER Successfully installed ChimeraX-PICKLUSTER-0.1 \--- Successfully installed ChimeraX-PICKLUSTER-0.1 Installed ChimeraX-Dicom (1.2) Installed ChimeraX-PICKLUSTER (0.1) Replacing data format 'DICOM medical imaging' as defined by ChimeraX-Dicom with definition from ChimeraX-Dicom Replacing fetcher for 'tcia' and format DICOM medical imaging from Dicom bundle with that from Dicom bundle Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 490, in get_module m = importlib.import_module(self.package_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py"", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File """", line 1206, in _gcd_import File """", line 1178, in _find_and_load File """", line 1149, in _find_and_load_unlocked File """", line 690, in _load_unlocked File """", line 940, in exec_module File """", line 241, in _call_with_frames_removed File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dicom/__init__.py"", line 17, in from .dicom import ( File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dicom/dicom/__init__.py"", line 3, in from .ui import DICOMBrowserTool, DICOMDatabases File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dicom/dicom/ui/__init__.py"", line 16, in from .dicom_databases import * File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dicom/dicom/ui/dicom_databases.py"", line 29, in from ..databases import TCIADatabase File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dicom/dicom/databases/__init__.py"", line 1, in from .tcia import TCIADatabase File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dicom/dicom/databases/tcia.py"", line 24, in from tcia_utils import nbia File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tcia_utils/__init__.py"", line 2, in from . import datacite File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tcia_utils/datacite.py"", line 1, in import pandas as pd ModuleNotFoundError: No module named 'pandas' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 364, in initialize api = self._get_api(session.logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 509, in _get_api m = self.get_module() ^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 492, in get_module raise ToolshedError(""Error importing bundle %s's module: %s"" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-Dicom's module: No module named 'pandas' ChimeraX-Dicom (installed) [version: 1.2] [api package: chimerax.dicom] [category: Medical Imaging] [tool: DICOM Browser [categories: Medical Imaging] [synopsis: View the metadata of a patient's DICOM files]] [tool: Download DICOM [categories: Medical Imaging] [synopsis: View the contents of public DICOM datasets from within ChimeraX]] [tool: Segmentations [categories: Medical Imaging] [synopsis: Interactively segment medical images]] [command: dicom view [categories: Medical Imaging] [synopsis: See medical images in a 4-panel viewer]] [command: dicom segmentations [categories: Medical Imaging] [synopsis: Create or destory segmentations]]: custom initialization failed Downloading bundle SEQCROW-1.7.1-py3-none-any.whl Errors may have occurred when running pip: pip standard error: \--- [notice] A new release of pip is available: 23.0 -> 23.1.2 [notice] To update, run: /Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/adminjh/Downloads/SEQCROW-1.7.1-py3-none-any.whl Requirement already satisfied: ChimeraX-Core<=1.7,>=1.3 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from SEQCROW==1.7.1) (1.7.dev202307100059) Requirement already satisfied: scipy in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from SEQCROW==1.7.1) (1.9.3) Collecting Send2Trash Using cached Send2Trash-1.8.2-py3-none-any.whl (18 kB) Requirement already satisfied: psutil in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from SEQCROW==1.7.1) (5.9.4) Requirement already satisfied: jinja2 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from SEQCROW==1.7.1) (3.1.2) Requirement already satisfied: MarkupSafe>=2.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from jinja2->SEQCROW==1.7.1) (2.1.3) Requirement already satisfied: numpy<1.26.0,>=1.18.5 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from scipy->SEQCROW==1.7.1) (1.23.5) Installing collected packages: Send2Trash, SEQCROW Successfully installed SEQCROW-1.7.1 Send2Trash-1.8.2 \--- Successfully installed SEQCROW-1.7.1 Send2Trash-1.8.2 Installed SEQCROW (1.7.1) Downloading bundle ChimeraX_Cytoscape-0.1-py3-none-any.whl Errors may have occurred when running pip: pip standard error: \--- [notice] A new release of pip is available: 23.0 -> 23.1.2 [notice] To update, run: /Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/adminjh/Downloads/ChimeraX_Cytoscape-0.1-py3-none-any.whl Requirement already satisfied: ChimeraX-Core>=0.1 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Cytoscape==0.1) (1.7.dev202307100059) Installing collected packages: ChimeraX-Cytoscape Successfully installed ChimeraX-Cytoscape-0.1 \--- Successfully installed ChimeraX-Cytoscape-0.1 Installed ChimeraX-Cytoscape (0.1) > open /Users/adminjh/Documents/ChimeraX/DTHP/Missense3D/model_maps/PDB-pdb- > hthp_bessy090621_p622-b-29his-B-38GLU.sc.pdb Chain information for PDB-pdb-hthp_bessy090621_p622-b-29his-B-38GLU.sc.pdb #3 --- Chain | Description B | No description available > hide #!2 models > hide #1 models > show :29,38 > show #!2 models > save /Users/adminjh/Documents/ChimeraX/DTHP/Missense3D/cxs/version_1.cxs ——— End of log from Thu Jul 13 14:25:21 2023 ——— opened ChimeraX session > open /Users/adminjh/Documents/ChimeraX/DTHP/Missense3D/model_maps/PDB-pdb- > hthp_bessy090621_p622-b-45his-B-42ALA.sc.pdb Chain information for PDB-pdb-hthp_bessy090621_p622-b-45his-B-42ALA.sc.pdb #4 --- Chain | Description B | No description available > show #4/B:42,45 > select #2/A:1@C2A 1 atom, 1 residue, 1 model selected > select up 73 atoms, 76 bonds, 1 residue, 1 model selected > hide #2 > display sel > select clear > select #4/B:42@CB 1 atom, 1 residue, 1 model selected > select add #4/B:45@CE1 2 atoms, 2 residues, 1 model selected > select up 15 atoms, 14 bonds, 2 residues, 1 model selected > size sel stickRadius 1 Changed 14 bond radii > select clear > select #2/B:52 19 atoms, 18 bonds, 1 residue, 1 model selected > select clear > show #2 > hide H atoms > hide solvent > save /Users/adminjh/Documents/ChimeraX/DTHP/Missense3D/cxs/version_2.cxs ——— End of log from Tue Jul 18 14:37:06 2023 ——— opened ChimeraX session > select #2/A:1@CHA 1 atom, 1 residue, 1 model selected > select up 73 atoms, 76 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,0.048051,0,1,0,0.0235,0,0,1,-0.071456 > hide sel > open /Users/adminjh/Documents/ChimeraX/DTHP/Missense3D/model_maps/HEME.txt Unrecognized file suffix '.txt' > open /Users/adminjh/Documents/ChimeraX/DTHP/Missense3D/model_maps/HEME.pdb Summary of feedback from opening /Users/adminjh/Documents/ChimeraX/DTHP/Missense3D/model_maps/HEME.pdb --- warning | Ignored bad PDB record found on line 74 > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 73 atoms, 76 bonds, 1 residue, 1 model selected > view matrix models #5,1,0,0,-0.19722,0,1,0,-0.038585,0,0,1,-0.049304 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.99796,0.045769,-0.044563,1.7985,-0.037563,0.9847,0.17016,-4.9457,0.05167,-0.16814,0.98441,-2.4843 > select #5/A:1@FE 1 atom, 1 residue, 1 model selected > select add #4/B:45@NE2 2 atoms, 2 residues, 2 models selected > distance sel Distance between HEME.pdb #5/A HEM 1 FE and PDB-pdb- hthp_bessy090621_p622-b-45his-B-42ALA.sc.pdb #4/B HIS 45 NE2: 3.780Å > view matrix models > #4,0.99788,-0.018619,0.062312,-1.447,0.018543,0.99983,0.0017931,-0.31895,-0.062334,-0.00063384,0.99806,0.97532,#5,0.99976,0.016862,0.013703,0.28499,-0.018959,0.98508,0.17107,-5.2349,-0.010614,-0.17129,0.98516,-1.6131 > view matrix models > #4,0.99999,0.0011936,-0.0040042,0.095043,-0.0011939,1,-7.5573e-05,0.019583,0.0040041,8.0354e-05,0.99999,-0.059476,#5,0.9977,0.047618,-0.048302,1.8976,-0.038758,0.98466,0.17014,-4.9281,0.055662,-0.16787,0.98424,-2.537 > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 73 atoms, 76 bonds, 1 residue, 1 model selected > view matrix models > #5,0.99582,0.085941,-0.030795,1.8792,-0.082319,0.99116,0.10409,-2.1777,0.039468,-0.10112,0.99409,-1.7456 > view matrix models > #5,0.98029,-0.010865,0.19728,-6.1853,-0.012059,0.99334,0.11463,-3.488,-0.19721,-0.11475,0.97362,2.1227 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.98029,-0.010865,0.19728,-6.0654,-0.012059,0.99334,0.11463,-3.7877,-0.19721,-0.11475,0.97362,3.1359 > view matrix models > #5,0.98029,-0.010865,0.19728,-6.139,-0.012059,0.99334,0.11463,-3.7546,-0.19721,-0.11475,0.97362,3.0362 > view matrix models > #5,0.98029,-0.010865,0.19728,-6.2424,-0.012059,0.99334,0.11463,-3.8445,-0.19721,-0.11475,0.97362,3.2419 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.97718,0.026718,0.21071,-6.1268,-0.06897,0.97821,0.19582,-5.7247,-0.20089,-0.20588,0.95774,2.6084 > ui mousemode right select > surface #2 > hide surfaces #2 Expected ',' or a keyword > ~tsbond surface #2 Missing or invalid ""selection"" argument: invalid objects specifier > hdie surface Unknown command: hdie surface > hide surfaces > show surfaces #4 Expected ',' or a keyword > surface #4 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.96775,0.082035,0.23817,-6.1241,-0.11013,0.98812,0.10716,-2.2671,-0.22655,-0.12993,0.96529,3.726 > view matrix models > #5,0.97121,0.092625,0.2195,-5.4607,-0.13932,0.96818,0.20791,-5.213,-0.19325,-0.2325,0.9532,2.2944 > view matrix models > #5,0.98063,0.11029,0.1619,-3.5909,-0.14155,0.97024,0.19644,-4.8003,-0.13541,-0.21555,0.96706,1.2517 > view matrix models > #5,0.98027,0.11311,0.16211,-3.5558,-0.14578,0.96754,0.20643,-5.0824,-0.1335,-0.22598,0.96494,1.1547 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.98027,0.11311,0.16211,-3.6354,-0.14578,0.96754,0.20643,-5.0502,-0.1335,-0.22598,0.96494,1.3027 > save /Users/adminjh/Documents/ChimeraX/DTHP/Missense3D/cxs/version_3.cxs ——— End of log from Tue Jul 18 14:54:53 2023 ——— opened ChimeraX session > open /Users/anushkaghosh/Documents/chimaera/HTHPvsDTHP.cxs format session Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 335, in interceptRequest self._callback(info) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 93, in _intercept return interceptor(request_info, *args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 368, in intercept chimerax_intercept(*args, view=view, session=session) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 470, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 399, in thread_safe func(*args, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 461, in defer cxcmd(session, topic) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 479, in cxcmd run(session, cmd) File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 458, in collated_open return remember_data_format() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 1001, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 739, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' AttributeError: 'list' object has no attribute 'values' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): See log for complete Python traceback. Populating font family aliases took 185 ms. Replace uses of missing font family "".AppleSystemUIFont"" with one that exists to avoid this cost. > open /Users/anushkaghosh/Documents/chimaera/HTHPvsDTHP.cxs format session Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 335, in interceptRequest self._callback(info) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 93, in _intercept return interceptor(request_info, *args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 368, in intercept chimerax_intercept(*args, view=view, session=session) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 470, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 399, in thread_safe func(*args, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 461, in defer cxcmd(session, topic) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 479, in cxcmd run(session, cmd) File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 458, in collated_open return remember_data_format() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 1001, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 739, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' AttributeError: 'list' object has no attribute 'values' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): See log for complete Python traceback. > open /Users/anushkaghosh/Documents/chimaera/HTHPvsDTHP.cxs format session Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 335, in interceptRequest self._callback(info) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 93, in _intercept return interceptor(request_info, *args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 368, in intercept chimerax_intercept(*args, view=view, session=session) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 470, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 399, in thread_safe func(*args, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 461, in defer cxcmd(session, topic) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 479, in cxcmd run(session, cmd) File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 458, in collated_open return remember_data_format() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 1001, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 739, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' AttributeError: 'list' object has no attribute 'values' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): See log for complete Python traceback. > open ""/Users/anushkaghosh/Documents/chimaera/co mutations.cxs"" format > session Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 335, in interceptRequest self._callback(info) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 93, in _intercept return interceptor(request_info, *args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 368, in intercept chimerax_intercept(*args, view=view, session=session) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 470, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 399, in thread_safe func(*args, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 461, in defer cxcmd(session, topic) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 479, in cxcmd run(session, cmd) File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 458, in collated_open return remember_data_format() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 1001, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 739, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' AttributeError: 'list' object has no attribute 'values' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): See log for complete Python traceback. > open ""/Users/anushkaghosh/Documents/chimaera/co mutations.cxs"" format > session Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 335, in interceptRequest self._callback(info) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 93, in _intercept return interceptor(request_info, *args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 368, in intercept chimerax_intercept(*args, view=view, session=session) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 470, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 399, in thread_safe func(*args, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 461, in defer cxcmd(session, topic) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 479, in cxcmd run(session, cmd) File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 458, in collated_open return remember_data_format() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 1001, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 739, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' AttributeError: 'list' object has no attribute 'values' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): See log for complete Python traceback. > open ""/Users/anushkaghosh/Desktop/HTHP dodecamer.cxs"" format session Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 335, in interceptRequest self._callback(info) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 93, in _intercept return interceptor(request_info, *args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 368, in intercept chimerax_intercept(*args, view=view, session=session) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 470, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 399, in thread_safe func(*args, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 461, in defer cxcmd(session, topic) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 479, in cxcmd run(session, cmd) File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 458, in collated_open return remember_data_format() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 1001, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 739, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' AttributeError: 'list' object has no attribute 'values' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): See log for complete Python traceback. > open ""/Users/anushkaghosh/Desktop/HTHP dodecamer.cxs"" format session Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 335, in interceptRequest self._callback(info) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 93, in _intercept return interceptor(request_info, *args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 368, in intercept chimerax_intercept(*args, view=view, session=session) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 470, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 399, in thread_safe func(*args, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 461, in defer cxcmd(session, topic) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 479, in cxcmd run(session, cmd) File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 458, in collated_open return remember_data_format() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 1001, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 739, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' AttributeError: 'list' object has no attribute 'values' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): See log for complete Python traceback. > open /Users/anushkaghosh/Desktop/test.pdb format pdb Chain information for test.pdb #1 --- Chain | Description A | No description available > open /Users/anushkaghosh/Desktop/Monomerwithfe.pdb format pdb Chain information for Monomerwithfe.pdb #2 --- Chain | Description A | No description available > hide #!1 models > hide #!2 models > open ""/Users/anushkaghosh/Documents/chimaera/co mutations.cxs"" format > session Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 335, in interceptRequest self._callback(info) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 93, in _intercept return interceptor(request_info, *args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 368, in intercept chimerax_intercept(*args, view=view, session=session) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 470, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 399, in thread_safe func(*args, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 461, in defer cxcmd(session, topic) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 479, in cxcmd run(session, cmd) File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 458, in collated_open return remember_data_format() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 1001, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 739, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' AttributeError: 'list' object has no attribute 'values' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): See log for complete Python traceback. > open ""/Users/anushkaghosh/Desktop/HTHP dodecamer.cxs"" format session Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 335, in interceptRequest self._callback(info) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 93, in _intercept return interceptor(request_info, *args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 368, in intercept chimerax_intercept(*args, view=view, session=session) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 470, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 399, in thread_safe func(*args, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 461, in defer cxcmd(session, topic) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 479, in cxcmd run(session, cmd) File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 458, in collated_open return remember_data_format() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 1001, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 739, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' AttributeError: 'list' object has no attribute 'values' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): See log for complete Python traceback. > open /Users/anushkaghosh/Documents/chimaera/HTHPvsDTHP.cxs Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 697, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/dialog.py"", line 162, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.4.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 ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 458, in collated_open return remember_data_format() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 1001, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 739, in restore self.reset() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 541, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' AttributeError: 'list' object has no attribute 'values' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): See log for complete Python traceback. OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac mini Model Identifier: Macmini9,1 Model Number: Z12N0006DD/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8419.41.10 OS Loader Version: 8419.41.10 Software: System Software Overview: System Version: macOS 13.0.1 (22A400) Kernel Version: Darwin 22.1.0 Time since boot: 4 days, 2 hours, 42 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL U2720Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 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: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 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: 2.7 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: 2.2.4 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 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: 1.2 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: 1.1.1 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: 1.5.1 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: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 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: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 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: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 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 Sessions limitation all ChimeraX